Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T06958 | Target Info | |||
| Target Name | DNA polymerase beta (POLB) | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | POLB | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Adenosine triphosphate | Ligand Info | |||||
| Structure Description | DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF ATP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) | PDB:8ICN | ||||
| Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | No | [1] |
| PDB Sequence |
ETLNGGITDM
18 LTELANFEKN28 VSQAIHKYNA38 YRKAASVIAK48 YPHKIKSGAE58 AKKLPGVGTK 68 IAEKIDEFLA78 TGKLRKLEKI88 RQDDTSSSIN98 FLTRVSGIGP108 SAARKFVDEG 118 IKTLEDLRKN128 EDKLNHHQRI138 GLKYFGDFEK148 RIPREEMLQM158 QDIVLNEVKK 168 VDSEYIATVC178 GSFRRGAESS188 GDMDVLLTHP198 SFTSESTKQP208 KLLHQVVEQL 218 QKVHFITDTL228 SKGETKFMGV238 CQLPSKNDEK248 EYPHRRIDIR258 LIPKDQYYCG 268 VLYFTGSDIF278 NKNMRAHALE288 KGFTINEYTI298 RPLGVTGVAG308 EPLPVDSEKD 318 IFDYIQWKYR328 EPKDRSE
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| Ligand Name: Cisplatin | Ligand Info | |||||
| Structure Description | Human DNA polymerase beta inserting dCMPNPP opposite the 5'G of cisplatin crosslinked Gs (Pt-GG2) | PDB:4TUR | ||||
| Method | X-ray diffraction | Resolution | 2.17 Å | Mutation | No | [2] |
| PDB Sequence |
PQETLNGGIT
16 DMLTELANFE26 KNVSQAIHKY36 NAYRKAASVI46 AKYPHKIKSG56 AEAKKLPGVG 66 TKIAEKIDEF76 LATGKLRKLE86 KIRQDDTSSS96 INFLTRVSGI106 GPSAARKFVD 116 EGIKTLEDLR126 KNEDKLNHHQ136 RIGLKYFGDF146 EKRIPREEML156 QMQDIVLNEV 166 KKVDSEYIAT176 VCGSFRRGAE186 SSGDMDVLLT196 HPSFTSESQP208 KLLHQVVEQL 218 QKVHFITDTL228 SKGETKFMGV238 CQLPSKNDEK248 EYPHRRIDIR258 LIPKDQYYCG 268 VLYFTGSDIF278 NKNMRAHALE288 KGFTINEYTI298 RPLGVTGVAG308 EPLPVDSEKD 318 IFDYIQWKYR328 EPKDRSE
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2',3'-Dideoxycytidine-5'-Monophosphate | Ligand Info | |||||
| Structure Description | DNA Polymerase beta with a terminated gapped DNA substrate and ddCTP with sodium in the catalytic site | PDB:2FMP | ||||
| Method | X-ray diffraction | Resolution | 1.65 Å | Mutation | No | [3] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DOC or .DOC2 or .DOC3 or :3DOC;style chemicals stick;color identity;select .A:190 or .A:192 or .A:234 or .A:236 or .A:254 or .A:256 or .A:271 or .A:272; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: dATP | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with dATP | PDB:6CR4 | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DTP or .DTP2 or .DTP3 or :3DTP;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2',3'-Dideoxythymidine-5'-Monophosphate | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CHF analogue of dGTP | PDB:6NKV | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [5] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2DT or .2DT2 or .2DT3 or :32DT;style chemicals stick;color identity;select .A:190 or .A:192 or .A:234 or .A:236 or .A:254 or .A:256 or .A:271 or .A:272; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-Deoxycytidine-5'-Monophosphate | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF (R & S isomers), beta, gamma dCTP analogue | PDB:6CTR | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DC or .DC2 or .DC3 or :3DC;style chemicals stick;color identity;select .A:174 or .A:175 or .A:176 or .A:194 or .A:195 or .A:196 or .A:262 or .A:265 or .A:266; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Alpha,beta-methylene-dATP | Ligand Info | |||||
| Structure Description | Open ternary mismatch complex of R283K DNA polymerase beta with a dATP analog | PDB:4F5P | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | Yes | [6] |
| PDB Sequence |
PQETLNGGIT
16 DMLTELANFE26 KNVSQAIHKY36 NAYRKAASVI46 AKYPHKIKSG56 AEAKKLPGVG 66 TKIAEKIDEF76 LATGKLRKLE86 KIRQDDTSSS96 INFLTRVSGI106 GPSAARKFVD 116 EGIKTLEDLR126 KNEDKLNHHQ136 RIGLKYFGDF146 EKRIPREEML156 QMQDIVLNEV 166 KKVDSEYIAT176 VCGSFRRGAE186 SSGDMDVLLT196 HPSFTSESPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMKAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .F2A or .F2A2 or .F2A3 or :3F2A;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Alpha,beta-methylene-dCTP | Ligand Info | |||||
| Structure Description | Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dCTP analog | PDB:7S9P | ||||
| Method | X-ray diffraction | Resolution | 1.86 Å | Mutation | No | [7] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .XC5 or .XC52 or .XC53 or :3XC5;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: CTP | Ligand Info | |||||
| Structure Description | DNA Polymerase Beta with a dideoxy-terminated primer with an incoming ribonucleotide (rCTP) | PDB:3RH4 | ||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | No | [8] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CTP or .CTP2 or .CTP3 or :3CTP;style chemicals stick;color identity;select .A:149 or .A:174 or .A:175 or .A:176 or .A:179 or .A:180 or .A:182 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:194 or .A:195 or .A:196 or .A:256 or .A:262 or .A:265 or .A:266 or .A:270 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:316; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ARG149
3.977
ILE174
3.048
ALA175
4.281
THR176
3.020
GLY179
3.428
SER180
2.676
ARG182
3.821
ARG183
2.724
SER187
4.814
SER188
3.735
GLY189
2.867
ASP190
2.985
ASP192
2.975
LEU194
4.355
LEU195
4.842
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Guanosine-5'-Triphosphate | Ligand Info | |||||
| Structure Description | Y271G DNA polymerase beta substrate complex with a templating cytosine and incoming rGTP | PDB:6UOL | ||||
| Method | X-ray diffraction | Resolution | 1.94 Å | Mutation | Yes | [9] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LGFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GTP or .GTP2 or .GTP3 or :3GTP;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:270 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Alpha,beta-methylene-dGTP | Ligand Info | |||||
| Structure Description | DNA polymerase beta ternary complex with a templating 5ClC and incoming dGTP analog | PDB:5BOL | ||||
| Method | X-ray diffraction | Resolution | 1.98 Å | Mutation | No | [10] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTVAGEP310 LPVDSEKDIF 320 DYIQWKYREP330 KDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1GC or .1GC2 or .1GC3 or :31GC;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2',3'-ddATP | Ligand Info | |||||
| Structure Description | DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DDATP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) | PDB:8ICU | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | No | [1] |
| PDB Sequence |
ETLNGGITDM
18 LTELANFEKN28 VSQAIHKYNA38 YRKAASVIAK48 YPHKIKSGAE58 AKKLPGVGTK 68 IAEKIDEFLA78 TGKLRKLEKI88 RQDDTSSSIN98 FLTRVSGIGP108 SAARKFVDEG 118 IKTLEDLRKN128 EDKLNHHQRI138 GLKYFGDFEK148 RIPREEMLQM158 QDIVLNEVKK 168 VDSEYIATVC178 GSFRRGAESS188 GDMDVLLTHP198 SFTSESTKQP208 KLLHQVVEQL 218 QKVHFITDTL228 SKGETKFMGV238 CQLPSKNDEK248 EYPHRRIDIR258 LIPKDQYYCG 268 VLYFTGSDIF278 NKNMRAHALE288 KGFTINEYTI298 RPLGVTGVAG308 EPLPVDSEKD 318 IFDYIQWKYR328 EPKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DAD or .DAD2 or .DAD3 or :3DAD;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:272; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: dATPalphaS | Ligand Info | |||||
| Structure Description | DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYADENOSINE-5'-O-(1-THIOTRIPHOSPHATE), SOAKED IN THE PRESENCE OF DATP(ALPHA)S AND MNCL2 | PDB:9ICA | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | No | [11] |
| PDB Sequence |
ETLNGGITDM
18 LTELANFEKN28 VSQAIHKYNA38 YRKAASVIAK48 YPHKIKSGAE58 AKKLPGVGTK 68 IAEKIDEFLA78 TGKLRKLEKI88 RQDDTSSSIN98 FLTRVSGIGP108 SAARKFVDEG 118 IKTLEDLRKN128 EDKLNHHQRI138 GLKYFGDFEK148 RIPREEMLQM158 QDIVLNEVKK 168 VDSEYIATVC178 GSFRRGAESS188 GDMDVLLTHP198 SFTSESTKQP208 KLLHQVVEQL 218 QKVHFITDTL228 SKGETKFMGV238 CQLPSKNDEK248 EYPHRRIDIR258 LIPKDQYYCG 268 VLYFTGSDIF278 NKNMRAHALE288 KGFTINEYTI298 RPLGVTGVAG308 EPLPVDSEKD 318 IFDYIQWKYR328 EPKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .STP or .STP2 or .STP3 or :3STP;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:272; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5'-dAMP | Ligand Info | |||||
| Structure Description | Human DNA Polymerase Beta Complexed With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine and dAMP | PDB:1MQ2 | ||||
| Method | X-ray diffraction | Resolution | 3.10 Å | Mutation | No | [12] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DA or .DA2 or .DA3 or :3DA;style chemicals stick;color identity;select .A:271 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2'-deoxythymidine triphosphate | Ligand Info | |||||
| Structure Description | Human DNA polymerase beta 8-oxoG:dA extension with dTTP after 90 s | PDB:5VS3 | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [13] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TTP or .TTP2 or .TTP3 or :3TTP;style chemicals stick;color identity;select .A:40 or .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-Deoxy-5-Formyluridine 5'-(Tetrahydrogen Triphosphate) | Ligand Info | |||||
| Structure Description | DNA polymerase beta substrate complex with incoming 5-FodUTP | PDB:5WO0 | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [14] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .B7A or .B7A2 or .B7A3 or :3B7A;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2',3'-Dideoxycytidine 5'-triphosphate | Ligand Info | |||||
| Structure Description | DNA Polymerase beta with a terminated gapped DNA substrate and ddCTP with sodium in the catalytic site | PDB:2FMP | ||||
| Method | X-ray diffraction | Resolution | 1.65 Å | Mutation | No | [3] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DCT or .DCT2 or .DCT3 or :3DCT;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-Deoxy-5'-O-[(S)-{difluoro[(S)-Hydroxy(Phosphonooxy)phosphoryl]methyl}(Hydroxy)phosphoryl]cytidine | Ligand Info | |||||
| Structure Description | Open ternary complex of R283K DNA polymerase beta with a metal free dCTP analog | PDB:4F5N | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | Yes | [6] |
| PDB Sequence |
QETLNGGITD
17 MLTELANFEK27 NVSQAIHKYN37 AYRKAASVIA47 KYPHKIKSGA57 EAKKLPGVGT 67 KIAEKIDEFL77 ATGKLRKLEK87 IRQDDTSSSI97 NFLTRVSGIG107 PSAARKFVDE 117 GIKTLEDLRK127 NEDKLNHHQR137 IGLKYFGDFE147 KRIPREEMLQ157 MQDIVLNEVK 167 KVDSEYIATV177 CGSFRRGAES187 SGDMDVLLTH197 PSFTSESPKL210 LHQVVEQLQK 220 VHFITDTLSK230 GETKFMGVCQ240 LPSDEKEYPH252 RRIDIRLIPK262 DQYYCGVLYF 272 TGSDIFNKNM282 KAHALEKGFT292 INEYTIRPLG302 VTGVAGEPLP312 VDSEKDIFDY 322 IQWKYREPKD332 RSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6CF or .6CF2 or .6CF3 or :36CF;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2',3'-Dideoxyadenosine-5'-monophosphate | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF (R & S isomers), beta, gamma dCTP analogue | PDB:6CTR | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2DA or .2DA2 or .2DA3 or :32DA;style chemicals stick;color identity;select .A:190 or .A:192 or .A:234 or .A:236 or .A:254 or .A:256 or .A:271 or .A:272; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-deoxy-5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF (R & S isomers), beta, gamma dCTP analogue | PDB:6CTR | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .F3C or .F3C2 or .F3C3 or :3F3C;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-Deoxy-5'-O-[(R)-{[(R)-[(R)-Fluoro(Phosphono)methyl](Hydroxy)phosphoryl]oxy}(Hydroxy)phosphoryl]guanosine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CHF analogue of dGTP | PDB:6NKV | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [5] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GFH or .GFH2 or .GFH3 or :3GFH;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-deoxy-5'-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF (R & S isomers), beta, gamma dCTP analogue | PDB:6CTR | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FF4 or .FF42 or .FF43 or :3FF4;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5'-O-[(R)-{[(R)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with S-isomer of beta-gamma-CHCL-dCTP | PDB:6BEM | ||||
| Method | X-ray diffraction | Resolution | 1.88 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DJJ or .DJJ2 or .DJJ3 or :3DJJ;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 8-Oxo-dgtp | Ligand Info | |||||
| Structure Description | DNA polymerase beta reactant complex with a templating adenine and incoming 8-oxodGTP, 20 s | PDB:4UAZ | ||||
| Method | X-ray diffraction | Resolution | 1.88 Å | Mutation | No | [15] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGTGVAGEP310 LPVDSEKDIF 320 DYIQWKYREP330 KDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8DG or .8DG2 or .8DG3 or :38DG;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol | Ligand Info | |||||
| Structure Description | D276G DNA polymerase beta substrate complex with templating adenine and incoming Fapy-dGTP analog | PDB:6MR8 | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | Yes | [16] |
| PDB Sequence |
LNGGITDMLT
20 ELANFEKNVS30 QAIHKYNAYR40 KAASVIAKYP50 HKIKSGAEAK60 KLPGVGTKIA 70 EKIDEFLATG80 KLRKLEKIRQ90 DDTSSSINFL100 TRVSGIGPSA110 ARKFVDEGIK 120 TLEDLRKNED130 KLNHHQRIGL140 KYFGDFEKRI150 PREEMLQMQD160 IVLNEVKKVD 170 SEYIATVCGS180 FRRGAESSGD190 MDVLLTHPSF200 TSESPKLLHQ213 VVEQLQKVHF 223 ITDTLSKGET233 KFMGVCQLPS243 KEKEYPHRRI255 DIRLIPKDQY265 YCGVLYFTGS 275 GIFNKNMRAH285 ALEKGFTINE295 YTIRPLGVTG305 VAGEPLPVDS315 EKDIFDYIQW 325 KYREPKDRSE335
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GKS or .GKS2 or .GKS3 or :3GKS;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:258 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-Deoxyguanosine-5'-triphosphate | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with dGTP | PDB:6NKU | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [5] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DGT or .DGT2 or .DGT3 or :3DGT;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 4-amino-1-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL, beta, gamma dCTP analogue | PDB:6CTU | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .VC6 or .VC62 or .VC63 or :3VC6;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5'-O-[(R)-{[(S)-[(R)-bromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine | Ligand Info | |||||
| Structure Description | Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monoBromo methylene triphosphate | PDB:3JPQ | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [17] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GBR or .GBR2 or .GBR3 or :3GBR;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Imidodiphosphoric acid | Ligand Info | |||||
| Structure Description | DNA polymerase beta nick complex with imidodiphosphate | PDB:5UGO | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [18] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2PN or .2PN2 or .2PN3 or :32PN;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:273 or .A:275 or .A:276; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2',3'-Dideoxy-guanosine-5'-monophosphate | Ligand Info | |||||
| Structure Description | DNA Polymerase Beta with a dideoxy-terminated primer with an incoming ribonucleotide (rCTP) | PDB:3RH4 | ||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | No | [8] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DDG or .DDG2 or .DDG3 or :3DDG;style chemicals stick;color identity;select .A:190 or .A:192 or .A:234 or .A:236 or .A:254 or .A:256 or .A:271 or .A:272 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-Deoxy-5'-O-[(S)-Hydroxy{[(R)-Hydroxy(Phosphonomethyl)phosphoryl]amino}phosphoryl]-3,4-Dihydrothymidine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with (alpha, beta)-NH-(beta,gamma)-CH2-dTTP | PDB:4RT3 | ||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | No | [19] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .C6T or .C6T2 or .C6T3 or :3C6T;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2'-Deoxy-5'-O-[(S)-Hydroxy{[(S)-Hydroxy(Phosphonoamino)phosphoryl]methyl}phosphoryl]-3,4-Dihydrothymidine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with (alpha,beta)-CH2-(beta,gamma)-NH-dTTP | PDB:4RT2 | ||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | No | [19] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .N6T or .N6T2 or .N6T3 or :3N6T;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 5'-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL,beta-gamma dTTP analogue | PDB:6CTN | ||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .VT6 or .VT62 or .VT63 or :3VT6;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2'-Deoxy-5'-O-[(R)-Hydroxy{[(R)-Hydroxy(Phosphonooxy)phosphoryl]amino}phosphoryl]cytidine | Ligand Info | |||||
| Structure Description | Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable CTP | PDB:6CPQ | ||||
| Method | X-ray diffraction | Resolution | 1.93 Å | Mutation | No | [20] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0KX or .0KX2 or .0KX3 or :30KX;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dATP analogue | PDB:6CR3 | ||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .H84 or .H842 or .H843 or :3H84;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5'-O-[(R)-{[(S)-[(S)-Chloro(Phosphono)methyl](Hydroxy)phosphoryl]oxy}(Hydroxy)phosphoryl]-2'-Deoxyguanosine | Ligand Info | |||||
| Structure Description | Ternary complex of dna polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding of S-isomer | PDB:4DOC | ||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [21] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .G1C or .G1C2 or .G1C3 or :3G1C;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:181 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-Deoxy-5'-O-[(R)-Hydroxy{[(R)-Hydroxy(Phosphonoamino)phosphoryl]oxy}phosphoryl]cytidine | Ligand Info | |||||
| Structure Description | DNA polymerase beta complex with a 1nt gap and dCMPPNP | PDB:5UGP | ||||
| Method | X-ray diffraction | Resolution | 1.96 Å | Mutation | No | [18] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVAGEPLP312 VDSEKDIFDY 322 IQWKYREPKD332 RSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8CP or .8CP2 or .8CP3 or :38CP;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 5'-O-[(R)-Hydroxy{[(R)-Hydroxy(Phosphonooxy)phosphoryl]amino}phosphoryl]thymidine | Ligand Info | |||||
| Structure Description | Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable TTP | PDB:6E3V | ||||
| Method | X-ray diffraction | Resolution | 1.96 Å | Mutation | No | [22] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1FZ or .1FZ2 or .1FZ3 or :31FZ;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 8-hydroxy-dAMP | Ligand Info | |||||
| Structure Description | Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable TTP | PDB:6E3V | ||||
| Method | X-ray diffraction | Resolution | 1.96 Å | Mutation | No | [22] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .A38 or .A382 or .A383 or :3A38;style chemicals stick;color identity;select .A:37 or .A:276 or .A:279 or .A:280 or .A:283 or .A:284 or .A:287; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 9-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-D-threo-pentofuranosyl}-9H-purin-6-amine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL, beta, gamma dATP analogue | PDB:6CR9 | ||||
| Method | X-ray diffraction | Resolution | 1.96 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .VA5 or .VA52 or .VA53 or :3VA5;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:181 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2'-Deoxy-5'-O-[({[difluoro(Phosphono)methyl](Hydroxy)phosphoryl}oxy)(Hydroxy)phosphoryl]guanosine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of K289M variant of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CF2 analogue of dGTP | PDB:6NL0 | ||||
| Method | X-ray diffraction | Resolution | 1.97 Å | Mutation | Yes | [5] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEM289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GFF or .GFF2 or .GFF3 or :3GFF;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-Deoxy-5'-O-(hydroxy{[hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl)guanosine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with beta-gamma-methylene dGTP | PDB:6NKW | ||||
| Method | X-ray diffraction | Resolution | 1.98 Å | Mutation | No | [5] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GGH or .GGH2 or .GGH3 or :3GGH;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]adenosine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CH2-beta, gamma dATP analogue | PDB:6CR5 | ||||
| Method | X-ray diffraction | Resolution | 1.98 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FCJ or .FCJ2 or .FCJ3 or :3FCJ;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 4-amino-1-{2-deoxy-5-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CCL2, beta, gamma dCTP analogue | PDB:6CTW | ||||
| Method | X-ray diffraction | Resolution | 1.98 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .VC8 or .VC82 or .VC83 or :3VC8;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 5-Chloro-2'-deoxycytidine 5'-(dihydrogen phosphate) | Ligand Info | |||||
| Structure Description | DNA polymerase beta ternary complex with a templating 5ClC and incoming dGTP analog | PDB:5BOL | ||||
| Method | X-ray diffraction | Resolution | 1.98 Å | Mutation | No | [10] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTVAGEP310 LPVDSEKDIF 320 DYIQWKYREP330 KDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4U3 or .4U32 or .4U33 or :34U3;style chemicals stick;color identity;select .A:37 or .A:40 or .A:279 or .A:280 or .A:283 or .A:284 or .A:287; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-Deoxy-5'-O-[(S)-{(S)-Fluoro[(S)-Hydroxy(Phosphonooxy)phosphoryl]methyl}(Hydroxy)phosphoryl]adenosine | Ligand Info | |||||
| Structure Description | Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, b dAMP(CFH)PP in the active site: Stereoselective binding of (S) isomer | PDB:3TFS | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [23] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FHA or .FHA2 or .FHA3 or :3FHA;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2'-Deoxy-5'-O-[(S)-{difluoro[(S)-Hydroxy(Phosphonooxy)phosphoryl]methyl}(Hydroxy)phosphoryl]adenosine | Ligand Info | |||||
| Structure Description | Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, b dAMP(CF2)PP in the active site | PDB:3TFR | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [23] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .F3A or .F3A2 or .F3A3 or :3F3A;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2'-deoxy-5'-O-[(S)-{[(S)-[(1R)-1-fluoro-1-phosphonoethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine | Ligand Info | |||||
| Structure Description | Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-fluoro methyl methylene triphosphate | PDB:3JPS | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [17] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GFM or .GFM2 or .GFM3 or :3GFM;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (R & S isomers, beta, gamma dCTP analogue | PDB:6CTT | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FF7 or .FF72 or .FF73 or :3FF7;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL-R/S isomers, beta, gamma dTTP analogue | PDB:6CTL | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FDJ or .FDJ2 or .FDJ3 or :3FDJ;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CCL2, beta, gamma dTTP analogue | PDB:6CTI | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .VT8 or .VT82 or .VT83 or :3VT8;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: [[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methylphosphonic acid | Ligand Info | |||||
| Structure Description | Abortive ternary complex crystal structure of DNA polymerase Beta with 8OG-dC base pair at the primer terminus and flipped out dA | PDB:6W2M | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [24] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SFV or .SFV2 or .SFV3 or :3SFV;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2'-Deoxy-5'-O-[(R)-Hydroxy{[(R)-Hydroxy(Phosphonooxy)phosphoryl]amino}phosphoryl]guanosine | Ligand Info | |||||
| Structure Description | Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable GTP | PDB:6E3W | ||||
| Method | X-ray diffraction | Resolution | 2.02 Å | Mutation | No | [22] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .XG4 or .XG42 or .XG43 or :3XG4;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dCTP analogue | PDB:6CTX | ||||
| Method | X-ray diffraction | Resolution | 2.02 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .VC9 or .VC92 or .VC93 or :3VC9;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2'-deoxy-5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dCTP analogue | PDB:6CTV | ||||
| Method | X-ray diffraction | Resolution | 2.02 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FFJ or .FFJ2 or .FFJ3 or :3FFJ;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dTTP analogue | PDB:6CTO | ||||
| Method | X-ray diffraction | Resolution | 2.04 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .VT7 or .VT72 or .VT73 or :3VT7;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2'-Deoxy-5'-O-[(R)-Hydroxy{[(R)-Hydroxy(Phosphonooxy)phosphoryl]amino}phosphoryl]adenosine | Ligand Info | |||||
| Structure Description | Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable ATP and MANGANESE | PDB:6CUB | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [25] |
| PDB Sequence |
PQETLNGGIT
16 DMLTELANFE26 KNVSQAIHKY36 NAYRKAASVI46 AKYPHKIKSG56 AEAKKLPGVG 66 TKIAEKIDEF76 LATGKLRKLE86 KIRQDDTSSS96 INFLTRVSGI106 GPSAARKFVD 116 EGIKTLEDLR126 KNEDKLNHHQ136 RIGLKYFGDF146 EKRIPREEML156 QMQDIVLNEV 166 KKVDSEYIAT176 VCGSFRRGAE186 SSGDMDVLLT196 HPSFTSESQP208 KLLHQVVEQL 218 QKVHFITDTL228 SKGETKFMGV238 CQLPSKNDEK248 EYPHRRIDIR258 LIPKDQYYCG 268 VLYFTGSDIF278 NKNMRAHALE288 KGFTINEYTI298 RPLGVTGVAG308 EPLPVDSEKD 318 IFDYIQWKYR328 EPKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DZ4 or .DZ42 or .DZ43 or :3DZ4;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-Deoxy-5'-O-[(R)-{[(R)-[(S)-Fluoro(Phosphono)methyl](Hydroxy)phosphoryl]oxy}(Hydroxy)phosphoryl]guanosine | Ligand Info | |||||
| Structure Description | Ternary complex of dna polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monofluoromethylene triphosphate: non-interactive binding of s-isomer | PDB:4DOA | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [21] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FHG or .FHG2 or .FHG3 or :3FHG;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyadenosine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (R & S isomers), beta, gamma dATP analogue | PDB:6CR8 | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .VA4 or .VA42 or .VA43 or :3VA4;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 5'-O-[(R)-{[(R)-[(R)-Chloro(Phosphono)methyl](Hydroxy)phosphoryl]oxy}(Hydroxy)phosphoryl]-2'-Deoxyguanosine | Ligand Info | |||||
| Structure Description | Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate: Stereoselective binding of R-isomer | PDB:4DOB | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [21] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GRC or .GRC2 or .GRC3 or :3GRC;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-Oxo-guanosine-5'-triphosphate | Ligand Info | |||||
| Structure Description | Y271G DNA polymerase beta ternary complex with templating adenine and incoming r8-oxo-GTP | PDB:6UOM | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | Yes | [9] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LGFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8GT or .8GT2 or .8GT3 or :38GT;style chemicals stick;color identity;select .A:40 or .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:270 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG40
4.350
ARG149
3.639
GLY179
3.216
SER180
2.537
ARG183
2.638
SER187
4.504
SER188
3.654
GLY189
2.963
ASP190
2.947
ASP192
2.518
|
|||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2-Amino-9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-1,9-dihydro-6H-purin-6-one | Ligand Info | |||||
| Structure Description | Mutagenicity of 7-Benzyl guanine lesion and Replication by Human DNA Polymerase beta | PDB:5EOZ | ||||
| Method | X-ray diffraction | Resolution | 2.09 Å | Mutation | No | [26] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GFL or .GFL2 or .GFL3 or :3GFL;style chemicals stick;color identity;select .A:37 or .A:271 or .A:276 or .A:279 or .A:280 or .A:283 or .A:284 or .A:287 or .A:292; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (1S)-1,2,3,4-Tetrahydro-benzo[C]phenanthrene-2,3,4-triol | Ligand Info | |||||
| Structure Description | DNA Polymerase Beta with a Benzo[c]phenanthrene diol epoxide adducted guanine base | PDB:2I9G | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [27] |
| PDB Sequence |
ETLNGGITDM
18 LTELANFEKN28 VSQAIHKYNA38 YRKAASVIAK48 YPHKIKSGAE58 AKKLPGVGTK 68 IAEKIDEFLA78 TGKLRKLEKI88 RQDDTSSSIN98 FLTRVSGIGP108 SAARKFVDEG 118 IKTLEDLRKN128 EDKLNHHQRI138 GLKYFGDFEK148 RIPREEMLQM158 QDIVLNEVKK 168 VDSEYIATVC178 GSFRRGAESS188 GDMDVLLTHP198 SFTSESQPKL210 LHQVVEQLQK 220 VHFITDTLSK230 GETKFMGVCQ240 LPSKNDEKEY250 PHRRIDIRLI260 PKDQYYCGVL 270 YFTGSDIFNK280 NMRAHALEKG290 FTINEYTIRP300 LGVTGVAGEP310 LPVDSEKDIF 320 DYIQWKYREP330 KDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BPI or .BPI2 or .BPI3 or :3BPI;style chemicals stick;color identity;select .A:36 or .A:37 or .A:40 or .A:271 or .A:295; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2'-deoxy-5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]adenosine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CH-CH3, beta, gamma dATP analogue | PDB:6CR6 | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HGV or .HGV2 or .HGV3 or :3HGV;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2'-deoxy-5'-O-[(R)-hydroxy({(S)-hydroxy[(1R)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]guanosine | Ligand Info | |||||
| Structure Description | Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-MonoMethyl Methylene triphosphate | PDB:3JPP | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [17] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .G1M or .G1M2 or .G1M3 or :3G1M;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(1-methyl-1-phosphonoethyl)phosphoryl]oxy}phosphoryl]guanosine | Ligand Info | |||||
| Structure Description | Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-dimethyl methylene triphosphate | PDB:3JPR | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [17] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .G2M or .G2M2 or .G2M3 or :3G2M;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2'-Deoxyguanosine-5'-diphosphate | Ligand Info | |||||
| Structure Description | Human DNA polymerase beta ternary complex with templating cytosine and incoming deoxyguanosine diphosphate | PDB:7K96 | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [28] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DGI or .DGI2 or .DGI3 or :3DGI;style chemicals stick;color identity;select .A:179 or .A:180 or .A:183 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]thymidine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCH3, beta, gamma dTTP analogue | PDB:6CTJ | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FDV or .FDV2 or .FDV3 or :3FDV;style chemicals stick;color identity;select .A:40 or .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 5-Fluorodeoxyuridine triphosphate | Ligand Info | |||||
| Structure Description | DNA polymerase beta substrate complex with incoming 5-FdUTP | PDB:5WNY | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [14] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .B7P or .B7P2 or .B7P3 or :3B7P;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2'-deoxy-5'-O-[(S)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine | Ligand Info | |||||
| Structure Description | Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-dichloro methylene triphosphate | PDB:3JPN | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [17] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .G2C or .G2C2 or .G2C3 or :3G2C;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-amino-7-benzyl-9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-6-oxo-6,9-dihydro-1H-purin-7-ium | Ligand Info | |||||
| Structure Description | Structure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable CTP WITH MANGANESE IN THE ACTIVE SITE | PDB:4YMO | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [26] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7BG or .7BG2 or .7BG3 or :37BG;style chemicals stick;color identity;select .A:37 or .A:40 or .A:271 or .A:276 or .A:277 or .A:279 or .A:280 or .A:283 or .A:284 or .A:287; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF-R/S isomers, beta, gamma dTTP analogue | PDB:6CTK | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FDY or .FDY2 or .FDY3 or :3FDY;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:181 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 5'-O-[(S)-{[(S)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine | Ligand Info | |||||
| Structure Description | Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-fluoro chloro methylene triphosphate | PDB:3JPT | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [17] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GFC or .GFC2 or .GFC3 or :3GFC;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 9-{2-deoxy-5-O-[(S)-{[(S)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dATP analogue | PDB:6CRB | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [4] |
| PDB Sequence |
PQETLNGGIT
16 DMLTELANFE26 KNVSQAIHKY36 NAYRKAASVI46 AKYPHKIKSG56 AEAKKLPGVG 66 TKIAEKIDEF76 LATGKLRKLE86 KIRQDDTSSS96 INFLTRVSGI106 GPSAARKFVD 116 EGIKTLEDLR126 KNEDKLNHHQ136 RIGLKYFGDF146 EKRIPREEML156 QMQDIVLNEV 166 KKVDSEYIAT176 VCGSFRRGAE186 SSGDMDVLLT196 HPSFTSESQP208 KLLHQVVEQL 218 QKVHFITDTL228 SKGETKFMGV238 CQLPSKNDEK248 EYPHRRIDIR258 LIPKDQYYCG 268 VLYFTGSDIF278 NKNMRAHALE288 KGFTINEYTI298 RPLGVTGVAG308 EPLPVDSEKD 318 IFDYIQWKYR328 EPKDRSE
|
|||||
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .VA6 or .VA62 or .VA63 or :3VA6;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: [(~{S})-chloranyl-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methyl]phosphonic acid | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (S-isomer), beta, gamma dTTP analogue | PDB:6G2Q | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EJH or .EJH2 or .EJH3 or :3EJH;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:254 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5-FodCTP | Ligand Info | |||||
| Structure Description | DNA polymerase beta substrate complex with incoming 5-FodCTP | PDB:5WNZ | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [14] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGTGVAGEP310 LPVDSEKDIF 320 DYIQWKYREP330 KDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .B7J or .B7J2 or .B7J3 or :3B7J;style chemicals stick;color identity;select .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Phosphomethyl phosphonic acid deoxythymidylate ester | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CH2, beta, gamma dTTP analogue | PDB:6CTP | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 LEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TTE or .TTE2 or .TTE3 or :3TTE;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 9-{2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF, beta, gamma dATP analogue | PDB:6CR7 | ||||
| Method | X-ray diffraction | Resolution | 2.29 Å | Mutation | No | [4] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .V3A or .V3A2 or .V3A3 or :3V3A;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: [(2r,3s,4r,5r)-5-(6-Amino-9h-Purin-9-Yl)-3,4-Dihydroxytetrahydrofuran-2-Yl]methyl [(2r,3s)-3-Hydroxytetrahydrofuran-2-Yl]methyl Dihydrogen Diphosphate | Ligand Info | |||||
| Structure Description | Human DNA polymerase beta complexed with adenylated tetrahydrofuran (abasic site) containing DNA | PDB:4O9M | ||||
| Method | X-ray diffraction | Resolution | 2.29 Å | Mutation | No | [29] |
| PDB Sequence |
PQETLNGGIT
16 DMLTELANFE26 KNVSQAIHKY36 NAYRKAASVI46 AKYPHKIKSG56 AEAKKLPGVG 66 TKIAEKIDEF76 LATGKLRKLE86 KIRQDDTSSS96 INFLTRVSGI106 GPSAARKFVD 116 EGIKTLEDLR126 KNEDKLNHHQ136 RIGLKYFGDF146 EKRIPREEML156 QMQDIVLNEV 166 KKVDSEYIAT176 VCGSFRRGAE186 SSGDMDVLLT196 HPSFTSESPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2RW or .2RW2 or .2RW3 or :32RW;style chemicals stick;color identity;select .A:26 or .A:35 or .A:68 or .A:71 or .A:72 or .A:84; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2'-deoxy-5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CCL2, beta, gamma dATP analogue | PDB:6CRC | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [4] |
| PDB Sequence |
PQETLNGGIT
16 DMLTELANFE26 KNVSQAIHKY36 NAYRKAASVI46 AKYPHKIKSG56 AEAKKLPGVG 66 TKIAEKIDEF76 LATGKLRKLE86 KIRQDDTSSS96 INFLTRVSGI106 GPSAARKFVD 116 EGIKTLEDLR126 KNEDKLNHHQ136 RIGLKYFGDF146 EKRIPREEML156 QMQDIVLNEV 166 KKVDSEYIAT176 VCGSFRRGAE186 SSGDMDVLLT196 HPSFTSESQP208 KLLHQVVEQL 218 QKVHFITDTL228 SKGETKFMGV238 CQLPSKNDEK248 EYPHRRIDIR258 LIPKDQYYCG 268 VLYFTGSDIF278 NKNMRAHALE288 KGFTINEYTI298 RPLGVTGVAG308 EPLPVDSEKD 318 IFDYIQWKYR328 EPKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .VA7 or .VA72 or .VA73 or :3VA7;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:181 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5-Carboxy-2'-deoxycytidine monophosphate | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with 5-carboxy-dC (5-caC) at the templating position | PDB:6N2S | ||||
| Method | X-ray diffraction | Resolution | 2.46 Å | Mutation | No | [30] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1CC or .1CC2 or .1CC3 or :31CC;style chemicals stick;color identity;select .A:37 or .A:279 or .A:280 or .A:283 or .A:284 or .A:287 or .A:292; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5'-O-[(R)-{[(R)-[difluoro(Phosphono)methyl](Hydroxy)phosphoryl](Difluoro)methyl}(Hydroxy)phosphoryl]thymidine | Ligand Info | |||||
| Structure Description | DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P | PDB:3LK9 | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [31] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TFF or .TFF2 or .TFF3 or :3TFF;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2'-Deoxy-6-thioguanosine 5'-triphosphate | Ligand Info | |||||
| Structure Description | DNA polymerase beta substrate complex with incoming 6-TdGTP | PDB:5WNX | ||||
| Method | X-ray diffraction | Resolution | 2.55 Å | Mutation | No | [14] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGTGVAGEP310 LPVDSEKDIF 320 DYIQWKYREP330 KDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SGT or .SGT2 or .SGT3 or :3SGT;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1',2'-Dideoxyribofuranose-5'-phosphate | Ligand Info | |||||
| Structure Description | Ternary complex of human DNA polymerase beta with an abasic site (THF): DAPCPP mismatch | PDB:3ISD | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [32] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3DR or .3DR2 or .3DR3 or :33DR;style chemicals stick;color identity;select .A:37 or .A:280 or .A:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5-Hydroxymethyldeoxycytidylic acid | Ligand Info | |||||
| Structure Description | Ternary complex crystal structure of DNA polymerase Beta with 5-hydroxymethyl-dC (5-hmC) at the templating position | PDB:6N2T | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [30] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5HC or .5HC2 or .5HC3 or :35HC;style chemicals stick;color identity;select .A:37 or .A:40 or .A:279 or .A:280 or .A:283 or .A:284 or .A:287; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Combivir | Ligand Info | |||||
| Structure Description | DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF AZT-TP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) | PDB:8ICO | ||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | No | [1] |
| PDB Sequence |
ETLNGGITDM
18 LTELANFEKN28 VSQAIHKYNA38 YRKAASVIAK48 YPHKIKSGAE58 AKKLPGVGTK 68 IAEKIDEFLA78 TGKLRKLEKI88 RQDDTSSSIN98 FLTRVSGIGP108 SAARKFVDEG 118 IKTLEDLRKN128 EDKLNHHQRI138 GLKYFGDFEK148 RIPREEMLQM158 QDIVLNEVKK 168 VDSEYIATVC178 GSFRRGAESS188 GDMDVLLTHP198 SFTSESTKQP208 KLLHQVVEQL 218 QKVHFITDTL228 SKGETKFMGV238 CQLPSKNDEK248 EYPHRRIDIR258 LIPKDQYYCG 268 VLYFTGSDIF278 NKNMRAHALE288 KGFTINEYTI298 RPLGVTGVAG308 EPLPVDSEKD 318 IFDYIQWKYR328 EPKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AZT or .AZT2 or .AZT3 or :3AZT;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 8-Oxo-2'-deoxy-guanosine-5'-monophosphate | Ligand Info | |||||
| Structure Description | Human DNA polymerase beta 8-oxoG:dA extension with dTTP after 90 s | PDB:5VS3 | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [13] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8OG or .8OG2 or .8OG3 or :38OG;style chemicals stick;color identity;select .A:271 or .A:283 or .A:287 or .A:292 or .A:293 or .A:294 or .A:295; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2'-Deoxycytidine-5'-triphosphate | Ligand Info | |||||
| Structure Description | Human DNA polymerase beta crosslinked ternary complex 2 | PDB:7RBH | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [33] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DCP or .DCP2 or .DCP3 or :3DCP;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: [(2R,3S)-2,5-dihydroxy-1-phosphonooxypentan-3-yl] dihydrogen phosphate | Ligand Info | |||||
| Structure Description | Human DNA polymerase beta crosslinked ternary complex 2 | PDB:7RBH | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [33] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QPJ or .QPJ2 or .QPJ3 or :3QPJ;style chemicals stick;color identity;select .A:26 or .A:35 or .A:39 or .A:68 or .A:72 or .A:84; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: [[(2r,5s)-5-(4-Azanyl-5-Fluoranyl-2-Oxidanylidene-Pyrimidin-1-Yl)-1,3-Oxathiolan-2-Yl]methoxy-Oxidanyl-Phosphoryl] Phosphono Hydrogen Phosphate | Ligand Info | |||||
| Structure Description | Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate incoming (-)FTC-TP and Ca2+. | PDB:5U2T | ||||
| Method | X-ray diffraction | Resolution | 1.79 Å | Mutation | No | [34] |
| PDB Sequence |
APQETLNGGI
15 TDMLTELANF25 EKNVSQAIHK35 YNAYRKAASV45 IAKYPHKIKS55 GAEAKKLPGV 65 GTKIAEKIDE75 FLATGKLRKL85 EKIRQDDTSS95 SINFLTRVSG105 IGPSAARKFV 115 DEGIKTLEDL125 RKNEDKLNHH135 QRIGLKYFGD145 FEKRIPREEM155 LQMQDIVLNE 165 VKKVDSEYIA175 TVCGSFRRGA185 ESSGDMDVLL195 THPSFTSESP208 KLLHQVVEQL 218 QKVHFITDTL228 SKGETKFMGV238 CQLPSKNDEK248 EYPHRRIDIR258 LIPKDQYYCG 268 VLYFTGSDIF278 NKNMRAHAKG290 FTINEYTIRP300 LGVTGVAGEP310 LPVDSEKDIF 320 DYIQWKYREP330 KDRS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1RY or .1RY2 or .1RY3 or :31RY;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 4-Amino-1-{2-Deoxy-5-O-[(R)-Hydroxy{[(S)-Hydroxy(Phosphonooxy)phosphoryl]oxy}phosphoryl]-Beta-L-Erythro-Pentofuranosyl}pyrimidin-2(1h)-One | Ligand Info | |||||
| Structure Description | PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTARTE, INCOMING L-DCTP AND CA2+ | PDB:5U2R | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [34] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSEHH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1S0 or .1S02 or .1S03 or :31S0;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Lamivudine Triphosphate | Ligand Info | |||||
| Structure Description | PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTRATE, INCORPORATED (-)3TC-MP AND AN ANOTHER INCOMING (-)3TC-TP NUCLEOTIDE. | PDB:5TBC | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [35] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESPKLLH212 QVVEQLQKVH 222 FITDTLSKGE232 TKFMGVCQLP242 SKNDEKEYPH252 RRIDIRLIPK262 DQYYCGVLYF 272 TGSDIFNKNM282 RNEYTVDSEK317 DIFDYYREPK331 DR
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1RZ or .1RZ2 or .1RZ3 or :31RZ;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: [(2r,5s)-5-(4-Amino-2-Oxopyrimidin-1(2h)-Yl)-1,3-Oxathiolan-2-Yl]methyl Dihydrogen Phosphate | Ligand Info | |||||
| Structure Description | PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTRATE, INCORPORATED (-)3TC-MP AND AN ANOTHER INCOMING (-)3TC-TP NUCLEOTIDE. | PDB:5TBC | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [35] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESPKLLH212 QVVEQLQKVH 222 FITDTLSKGE232 TKFMGVCQLP242 SKNDEKEYPH252 RRIDIRLIPK262 DQYYCGVLYF 272 TGSDIFNKNM282 RNEYTVDSEK317 DIFDYYREPK331 DR
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .42E or .42E2 or .42E3 or :342E;style chemicals stick;color identity;select .A:190 or .A:192 or .A:258 or .A:271 or .A:272; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: [(2r,5s)-5-(4-Amino-5-Fluoro-2-Oxopyrimidin-1(2h)-Yl)-1,3-Oxathiolan-2-Yl]methyl Dihydrogen Phosphate | Ligand Info | |||||
| Structure Description | Postcatalytic ternary complex of Human DNA Polymerase Beta with Gapped DNA substrate, incorporated (-)FTC and PPi. | PDB:5TBB | ||||
| Method | X-ray diffraction | Resolution | 2.39 Å | Mutation | No | [35] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESQPKLL211 HQVVEQLQKV 221 HFITDTLSKG231 ETKFMGVCQL241 PSKNDEKEYP251 HRRIDIRLIP261 KDQYYCGVLY 271 FTGSDIFNKN281 NEYTVAGEPL311 PVDSEKDIFD321 YEPKDR
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .43X or .43X2 or .43X3 or :343X;style chemicals stick;color identity;select .A:190 or .A:192 or .A:256 or .A:258 or .A:271 or .A:272; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-amino-9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-7-methyl-6-oxo-6,9-dihydro-1H-purin-7-ium | Ligand Info | |||||
| Structure Description | Structure of human DNA polymerase complexed with N7MG in the template opposite to incoming non-hydrolyzable TTP with manganese in the active site | PDB:4P2H | ||||
| Method | X-ray diffraction | Resolution | 1.99 Å | Mutation | No | [36] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESQPKLL211 HQVVEQLQKV 221 HFITDTLSKG231 ETKFMGVCQL241 PSKNDEKEYP251 HRRIDIRLIP261 KDQYYCGVLY 271 FTGSDIFNKN281 MRAHALEKGF291 TINEYTIRPL301 GVTGVAGEPL311 PVDSEKDIFD 321 YIQWKYREPK331 DRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FMG or .FMG2 or .FMG3 or :3FMG;style chemicals stick;color identity;select .A:37 or .A:271; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-imidazo[4,5-c]pyridin-4-amine | Ligand Info | |||||
| Structure Description | Structure of human DNA polymerase beta complexed with dzA at N-1 of the template base paired with incoming dTTP | PDB:7MZ2 | ||||
| Method | X-ray diffraction | Resolution | 2.09 Å | Mutation | No | [37] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4DU or .4DU2 or .4DU3 or :34DU;style chemicals stick;color identity;select .A:271 or .A:283 or .A:287 or .A:292 or .A:293 or .A:294; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]thymidine | Ligand Info | |||||
| Structure Description | Dna polymerase beta with a gapped DND substrate and dTMP(CF2)PP | PDB:3GDX | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [38] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4BD or .4BD2 or .4BD3 or :34BD;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 6-O-Methyl guanosine-5'-monophosphate | Ligand Info | |||||
| Structure Description | Structure of human DNA polymerase beta complexed with O6MG in the template base paired with incoming non-hydrolyzable CTP | PDB:4MFC | ||||
| Method | X-ray diffraction | Resolution | 2.13 Å | Mutation | No | [39] |
| PDB Sequence |
LNGGITDMLT
20 ELANFEKNVS30 QAIHKYNAYR40 KAASVIAKYP50 HKIKSGAEAK60 KLPGVGTKIA 70 EKIDEFLATG80 KLRKLEKIRQ90 DDTSSSINFL100 TRVSGIGPSA110 ARKFVDEGIK 120 TLEDLRKNED130 KLNHHQRIGL140 KYFGDFEKRI150 PREEMLQMQD160 IVLNEVKKVD 170 SEYIATVCGS180 FRRGAESSGD190 MDVLLTHPSF200 TSEKLLHQVV215 EQLQKVHFIT 225 DTLSKGETKF235 MGVCQLPSDE247 KEYPHRRIDI257 RLIPKDQYYC267 GVLYFTGSDI 277 FNKNMRAHAL287 EKGFTINEYT297 IRPLGVTGVA307 GEPLPVDSEK317 DIFDYIQWKY 327 REPKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6OG or .6OG2 or .6OG3 or :36OG;style chemicals stick;color identity;select .A:37 or .A:271 or .A:295; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 8-Bromo-2'-deoxyguanosine-5'-monophosphate | Ligand Info | |||||
| Structure Description | structure of human DNA polymerase complexed with 8-BrG in the template base paired with incoming non-hydrolyzable GTP | PDB:4M47 | ||||
| Method | X-ray diffraction | Resolution | 2.37 Å | Mutation | No | [40] |
| PDB Sequence |
NGGITDMLTE
21 LANFEKNVSQ31 AIHKYNAYRK41 AASVIAKYPH51 KIKSGAEAKK61 LPGVGTKIAE 71 KIDEFLATGK81 LRKLEKIRQD91 DTSSSINFLT101 RVSGIGPSAA111 RKFVDEGIKT 121 LEDLRKNEDK131 LNHHQRIGLK141 YFGDFEKRIP151 REEMLQMQDI161 VLNEVKKVDS 171 EYIATVCGSF181 RRGAESSGDM191 DVLLTHPSFT201 SESKLLHQVV215 EQLQKVHFIT 225 DTLSKGETKF235 MGVCQLPSKE249 YPHRRIDIRL259 IPKDQYYCGV269 LYFTGSDIFN 279 KNMRAHALEK289 GFTINEYTIR299 PLTGVAGEPL311 PVDSEKDIFD321 YIQWKYREPK 331 DRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGM or .BGM2 or .BGM3 or :3BGM;style chemicals stick;color identity;select .A:37 or .A:271 or .A:280 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 8-chloro-2'-deoxyguanosine 5'-(dihydrogen phosphate) | Ligand Info | |||||
| Structure Description | Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable CTP | PDB:6CPQ | ||||
| Method | X-ray diffraction | Resolution | 1.93 Å | Mutation | No | [20] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .F74 or .F742 or .F743 or :3F74;style chemicals stick;color identity;select .A:271 or .A:276 or .A:279 or .A:280 or .A:283 or .A:284 or .A:287; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 3-deaza-3-methyladenine | Ligand Info | |||||
| Structure Description | Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) in the template base paired with incoming dTTP | PDB:7MZ4 | ||||
| Method | X-ray diffraction | Resolution | 2.08 Å | Mutation | No | [41] |
| PDB Sequence |
PQETLNGGIT
16 DMLTELANFE26 KNVSQAIHKY36 NAYRKAASVI46 AKYPHKIKSG56 AEAKKLPGVG 66 TKIAEKIDEF76 LATGKLRKLE86 KIRQDDTSSS96 INFLTRVSGI106 GPSAARKFVD 116 EGIKTLEDLR126 KNEDKLNHHQ136 RIGLKYFGDF146 EKRIPREEML156 QMQDIVLNEV 166 KKVDSEYIAT176 VCGSFRRGAE186 SSGDMDVLLT196 HPSFTSESQP208 KLLHQVVEQL 218 QKVHFITDTL228 SKGETKFMGV238 CQLPSKDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DZM or .DZM2 or .DZM3 or :3DZM;style chemicals stick;color identity;select .A:34 or .A:37 or .A:271 or .A:280 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: N-[(5S)-2-amino-5-formamido-6-oxo-5,6-dihydropyrimidin-4-yl]-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine | Ligand Info | |||||
| Structure Description | Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dCTP analog | PDB:7S9P | ||||
| Method | X-ray diffraction | Resolution | 1.86 Å | Mutation | No | [7] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8NI or .8NI2 or .8NI3 or :38NI;style chemicals stick;color identity;select .A:33 or .A:37 or .A:271 or .A:276 or .A:279 or .A:280 or .A:283 or .A:284 or .A:287; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta. Biochemistry. 1996 Oct 1;35(39):12762-77. | ||||
| REF 2 | Structural basis for the inefficient nucleotide incorporation opposite cisplatin-DNA lesion by human DNA polymerase beta. J Biol Chem. 2014 Nov 7;289(45):31341-8. | ||||
| REF 3 | Magnesium-induced assembly of a complete DNA polymerase catalytic complex. Structure. 2006 Apr;14(4):757-66. | ||||
| REF 4 | Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs. Biochemistry. 2018 Jul 3;57(26):3934-3944. | ||||
| REF 5 | Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography. Biochemistry. 2020 Mar 3;59(8):955-963. | ||||
| REF 6 | Structures of dNTP intermediate states during DNA polymerase active site assembly. Structure. 2012 Nov 7;20(11):1829-37. | ||||
| REF 7 | Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication. J Am Chem Soc. 2022 May 11;144(18):8054-8065. | ||||
| REF 8 | Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. J Biol Chem. 2011 Sep 9;286(36):31650-60. | ||||
| REF 9 | Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase beta. J Biol Chem. 2020 Feb 7;295(6):1613-1622. | ||||
| REF 10 | Intrinsic mutagenic properties of 5-chlorocytosine: A mechanistic connection between chronic inflammation and cancer. Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):E4571-80. | ||||
| REF 11 | Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis. Biochemistry. 1996 Oct 1;35(39):12778-87. | ||||
| REF 12 | Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential. Structure. 2003 Jan;11(1):121-7. | ||||
| REF 13 | Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta. J Am Chem Soc. 2017 Jul 19;139(28):9684-9690. | ||||
| REF 14 | Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues. Chem Res Toxicol. 2017 Nov 20;30(11):1993-2001. | ||||
| REF 15 | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature. 2015 Jan 29;517(7536):635-9. | ||||
| REF 16 | A guardian residue hinders insertion of a Fapy?dGTP analog by modulating the open-closed DNA polymerase transition. Nucleic Acids Res. 2019 Apr 8;47(6):3197-3207. | ||||
| REF 17 | Halogenated beta,gamma-methylene- and ethylidene-dGTP-DNA ternary complexes with DNA polymerase beta: structural evidence for stereospecific binding of the fluoromethylene analogues. J Am Chem Soc. 2010 Jun 9;132(22):7617-25. | ||||
| REF 18 | Modulating the DNA polymerase beta reaction equilibrium to dissect the reverse reaction. Nat Chem Biol. 2017 Oct;13(10):1074-1080. | ||||
| REF 19 | Two Scaffolds from Two Flips: (Alpha,beta)/(beta,Gamma) CH2/NH "Met-Im" Analogues of dTTP. Org Lett. 2015 Jun 5;17(11):2586-9. | ||||
| REF 20 | Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable CTP | ||||
| REF 21 | beta,Gamma-CHF- and beta,Gamma-CHCl-dGTP diastereomers: synthesis, discrete 31P NMR signatures, and absolute configurations of new stereochemical probes for DNA polymerases. J Am Chem Soc. 2012 May 30;134(21):8734-7. | ||||
| REF 22 | Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-oxoadenine by Human DNA Polymerases. J Am Chem Soc. 2019 Mar 20;141(11):4584-4596. | ||||
| REF 23 | Stereospecific formation of a ternary complex of (S)-Alpha,beta-fluoromethylene-dATP with DNA pol beta. Chembiochem. 2012 Mar 5;13(4):528-30. | ||||
| REF 24 | Structure of a DNA polymerase abortive complex with the 8OG:dA base pair at the primer terminus. Commun Biol. 2020 Jul 3;3(1):348. | ||||
| REF 25 | Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable ATP and MANGANESE | ||||
| REF 26 | Structural and Kinetic Studies of the Effect of Guanine N7 Alkylation and Metal Cofactors on DNA Replication. Biochemistry. 2018 Aug 28;57(34):5105-5116. | ||||
| REF 27 | Structure of DNA polymerase beta with a benzo[c]phenanthrene diol epoxide-adducted template exhibits mutagenic features. Proc Natl Acad Sci U S A. 2006 Nov 14;103(46):17231-6. | ||||
| REF 28 | Mechanism of Deoxyguanosine Diphosphate Insertion by Human DNA Polymerase beta. Biochemistry. 2021 Feb 9;60(5):373-380. | ||||
| REF 29 | Role of polymerase beta in complementing aprataxin deficiency during abasic-site base excision repair. Nat Struct Mol Biol. 2014 May;21(5):497-9. | ||||
| REF 30 | Molecular basis for the faithful replication of 5-methylcytosine and its oxidized forms by DNA polymerase beta. J Biol Chem. 2019 May 3;294(18):7194-7201. | ||||
| REF 31 | Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid. Proc Natl Acad Sci U S A. 2010 Sep 7;107(36):15693-8. | ||||
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| REF 33 | Interlocking activities of DNA polymerase beta in the base excision repair pathway. Proc Natl Acad Sci U S A. 2022 Mar 8;119(10):e2118940119. | ||||
| REF 34 | Structural basis for the D-stereoselectivity of human DNA polymerase beta. Nucleic Acids Res. 2017 Jun 2;45(10):6228-6237. | ||||
| REF 35 | Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. J Am Chem Soc. 2017 Jan 11;139(1):465-471. | ||||
| REF 36 | Transition-state destabilization reveals how human DNA polymerase beta proceeds across the chemically unstable lesion N7-methylguanine. Nucleic Acids Res. 2014 Jul;42(13):8755-66. | ||||
| REF 37 | Structure of human DNA polymerase beta complexed with dzA at N-1 of the template base paired with incoming dTTP | ||||
| REF 38 | Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function. Org Lett. 2009 May 7;11(9):1883-6. | ||||
| REF 39 | Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase beta. J Am Chem Soc. 2014 Apr 16;136(15):5709-21. | ||||
| REF 40 | Structural basis for promutagenicity of 8-halogenated guanine. J Biol Chem. 2014 Feb 28;289(9):6289-98. | ||||
| REF 41 | Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) in the template base paired with incoming dTTP | ||||
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