Target Binding Site Detail
| 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 | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | 2'-Deoxycytidine-5'-triphosphate | Ligand Info | |||
| Canonical SMILES | C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O | ||||
| InChI | 1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1 | ||||
| InChIKey | RGWHQCVHVJXOKC-SHYZEUOFSA-N | ||||
| PubChem Compound ID | 65091 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 4KLF DNA polymerase beta matched reactant complex with Mg2+, 20 s | ||||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [1] |
| 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
|
|||||
|
|
||||||
| PDB ID: 6CTQ Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with dCTP | ||||||
| Method | X-ray diffraction | Resolution | 1.87 Å | Mutation | No | [2] |
| 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
|
|||||
|
|
||||||
| PDB ID: 4KLD DNA polymerase beta matched substrate complex with Ca2+, 0 s | ||||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | No | [1] |
| 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
|
|||||
|
|
||||||
| PDB ID: 4KLE DNA polymerase beta matched reactant complex with Mg2+, 10 s | ||||||
| Method | X-ray diffraction | Resolution | 1.97 Å | Mutation | No | [1] |
| 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 .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
|
||||||
| PDB ID: 5V1N DNA polymerase beta substrate complex with 8-oxoG:A at the primer terminus and incoming dCTP | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [3] |
| PDB Sequence |
NGGIDMLTEL
22 ANFEKNVSQA32 IHKYNAYRKA42 ASVIAKYPHK52 IKSGAEAKLP63 GVGTKIAEKI 73 DEFLATGKLR83 KLEKIRQDDT93 SSSINFLTRV103 SGIGPSAARK113 FVDEGIKTLE 123 DLRKNEDKLN133 HHQRIGLKYF143 GDFEKRIPRE153 EMLQMQDIVL163 NEVKKVDSEY 173 IATVCGSFRR183 GAESSGDMDV193 LLTHPSFTSE203 STKQPKLLHQ213 VVEQLQKVHF 223 ITDTLSKGET233 KFMGVCQLPS243 KNDEKEYPHR253 RIDIRLIPKD263 QYYCGVLYFT 273 GSDIFNKNMR283 AHALEKGFTI293 NEYTIRPLTG305 VAGEPLPVDS315 EKDIFDYIQW 325 KYREPKDRSE335
|
|||||
|
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 #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 5V1R DNA polymerase beta reactant complex with 8-oxoG:C at the primer terminus and incoming dCTP | ||||||
| Method | X-ray diffraction | Resolution | 2.08 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
|
|||||
|
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
|
||||||
| PDB ID: 4M9L DNA Polymerase Beta E295K Soaked with dCTP | ||||||
| Method | X-ray diffraction | Resolution | 2.09 Å | Mutation | Yes | [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 FTSESKLLHQ213 VVEQLQKVHF 223 ITDTLSKGET233 KFMGVCQLPS243 EKEYPHRRID256 IRLIPKDQYY266 CGVLYFTGSD 276 IFNKNMRAHA286 LEKGFTINKY296 TIRPVAGEPL311 PVSEKDIFDY322 IQWKYREPKD 332 RSE
|
|||||
|
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: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
|
||||||
| PDB ID: 3RH5 DNA Polymerase Beta Mutant (Y271) with a dideoxy-terminated primer with an incoming deoxynucleotide (dCTP) | ||||||
| Method | X-ray diffraction | Resolution | 2.10 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 LAFTGSDIFN279 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 .DCP or .DCP2 or .DCP3 or :3DCP;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: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
|
ARG149
4.007
ILE174
3.117
ALA175
3.919
THR176
2.749
GLY179
3.327
SER180
2.616
ARG182
4.173
ARG183
2.681
SER187
4.758
SER188
3.727
GLY189
3.183
ASP190
2.948
ASP192
2.881
LEU194
4.086
|
|||||
| PDB ID: 5V1F DNA polymerase beta substrate complex with 8-oxoG at the primer terminus and incoming dCTP | ||||||
| Method | X-ray diffraction | Resolution | 2.18 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 PLVAGEPLPV313 DSEKDIFDYI 323 QWKYREPKDR333 SE
|
|||||
|
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 #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 6PH6 Ternary complex crystal structure of DNA polymerase Beta with 2nt-gap with dCTP bound downstream | ||||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [6] |
| 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 .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: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
|
||||||
| PDB ID: 1MQ3 Human DNA Polymerase Beta Complexed With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine Template Paired with dCTP | ||||||
| Method | X-ray diffraction | Resolution | 2.80 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
|
|||||
|
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 or .A:280; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 8ICS DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DCTP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) | ||||||
| Method | X-ray diffraction | Resolution | 2.90 Å | Mutation | No | [8] |
| 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
|
|||||
|
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: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:274 or .A:276; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 9ICG DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DCTP (1 MILLIMOLAR) AND ZNCL2 (1 MILLIMOLAR) | ||||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | No | [9] |
| 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
|
|||||
|
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:271 or .A:272 or .A:273 or .A:274 or .A:276; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 9ICR DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DCTP AND MNCL2 | ||||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | No | [8] |
| 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
|
|||||
|
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: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
|
||||||
| PDB ID: 8ICT DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DCTP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) | ||||||
| Method | X-ray diffraction | Resolution | 3.10 Å | Mutation | No | [8] |
| 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
|
|||||
|
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:271 or .A:272 or .A:273 or .A:274 or .A:276; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 7RBH Human DNA polymerase beta crosslinked ternary complex 2 | ||||||
| Method | X-ray diffraction | Resolution | 1.75 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 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 .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
|
||||||
| PDB ID: 7RBG Human DNA polymerase beta crosslinked ternary complex 1 | ||||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [10] |
| 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 CQLPSKEYPH252 RRIDIRLIPK262 DQYYCGVLYF 272 TGSDIFNKNM282 RAHALEKGFT292 INEYTIRPLG302 VTGVAGEPLP312 VDSEKDIFDY 322 IQWKYREPKD332 RSE
|
|||||
|
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: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
|
||||||
| PDB ID: 7RBJ Human DNA polymerase beta crosslinked complex, 30 s Ca to Mg exchange | ||||||
| Method | X-ray diffraction | Resolution | 1.91 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 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 .DCP or .DCP2 or .DCP3 or :3DCP;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: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
|
||||||
| PDB ID: 7RBI Human DNA polymerase beta crosslinked complex, 20 s Ca to Mg exchange | ||||||
| Method | X-ray diffraction | Resolution | 1.93 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 FTSESTKLLH212 QVVEQLQKVH 222 FITDTLSKGE232 TKFMGVCQLP242 SKNKEYPHRR254 IDIRLIPKDQ264 YYCGVLYFTG 274 SDIFNKNMRA284 HALEKGFTIN294 EYTIRPLGVT304 GVAGEPLPVD314 SEKDIFDYIQ 324 WKYREPKDRS334 E
|
|||||
|
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 #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 7RBK Human DNA polymerase beta crosslinked complex, 40 s Ca to Mg exchange | ||||||
| Method | X-ray diffraction | Resolution | 2.20 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 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 .DCP or .DCP2 or .DCP3 or :3DCP;style chemicals stick;color identity;select .A:174 or .A:175 or .A:176 or .A:182 or .A:194 or .A:195 or .A:196 or .A:262 or .A:265 or .A:266 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: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
|
ILE174
3.162
ALA175
4.318
THR176
2.936
ARG182
4.626
LEU194
3.776
LEU195
4.960
THR196
2.643
LYS262
2.794
TYR265
3.212
TYR266
3.292
ARG149
3.383
GLY179
3.594
SER180
2.564
|
|||||
| PDB ID: 4RPX Precatalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG) and dCTP in the presence of CaCl2 | ||||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [11] |
| 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 .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 #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 4RPY Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG) and dCTP soaked with MgCl2 for 30 s | ||||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [11] |
| 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 .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: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
|
||||||
| PDB ID: 4RPZ Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 60 s | ||||||
| Method | X-ray diffraction | Resolution | 2.19 Å | Mutation | No | [11] |
| 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 .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 #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 4RQ0 Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 80 s | ||||||
| Method | X-ray diffraction | Resolution | 2.20 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
|
|||||
|
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:123 or .A:124 or .A:127; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Observing a DNA polymerase choose right from wrong. Cell. 2013 Jul 3;154(1):157-68. | ||||
| REF 2 | 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 3 | Capturing a mammalian DNA polymerase extending from an oxidized nucleotide. Nucleic Acids Res. 2017 Jun 20;45(11):6934-6944. | ||||
| REF 4 | The E295K cancer variant of human polymerase beta favors the mismatch conformational pathway during nucleotide selection. J Biol Chem. 2013 Nov 29;288(48):34850-60. | ||||
| REF 5 | Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. J Biol Chem. 2011 Sep 9;286(36):31650-60. | ||||
| REF 6 | DNA polymerase beta nucleotide-stabilized template misalignment fidelity depends on local sequence context. J Biol Chem. 2020 Jan 10;295(2):529-538. | ||||
| REF 7 | 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 8 | A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta. Biochemistry. 1996 Oct 1;35(39):12762-77. | ||||
| REF 9 | 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 10 | 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 11 | Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography. J Am Chem Soc. 2015 Apr 22;137(15):5225-30. | ||||
If You Find Any Error in Data or Bug in Web Service, Please Kindly Report It to Dr. Zhou and Dr. Zhang.