3ISC
| Binary complex of human DNA polymerase beta with an abasic site (THF) in the gapped DNA | 分子名称: | 5'-D(*CP*CP*GP*AP*CP*(3DR)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | 著者 | Beard, W.A, Shock, D.D, Batra, V.K, Pedersen, L.C, Wilson, S.H. | 登録日 | 2009-08-25 | 公開日 | 2009-09-15 | 最終更新日 | 2023-09-06 | 実験手法 | X-RAY DIFFRACTION (2 Å) | 主引用文献 | DNA polymerase beta substrate specificity: side chain modulation of the "A-rule". J.Biol.Chem., 284, 2009
|
|
3ISD
| Ternary complex of human DNA polymerase beta with an abasic site (THF): DAPCPP mismatch | 分子名称: | 1,2-ETHANEDIOL, 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine, 5'-D(*CP*CP*GP*AP*CP*(3DR)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', ... | 著者 | Beard, W.A, Shock, D.D, Batra, V.K, Pedersen, L.C, Wilson, S.H. | 登録日 | 2009-08-25 | 公開日 | 2009-09-15 | 最終更新日 | 2023-09-06 | 実験手法 | X-RAY DIFFRACTION (2.6 Å) | 主引用文献 | DNA polymerase beta substrate specificity: side chain modulation of the "A-rule". J.Biol.Chem., 284, 2009
|
|
3ISB
| Binary complex of human DNA polymerase beta with a gapped DNA | 分子名称: | 5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | 著者 | Beard, W.A, Shock, D.D, Batra, V.K, Pedersen, L.C, Wilson, S.H. | 登録日 | 2009-08-25 | 公開日 | 2009-09-15 | 最終更新日 | 2023-09-06 | 実験手法 | X-RAY DIFFRACTION (2 Å) | 主引用文献 | DNA polymerase beta substrate specificity: side chain modulation of the "A-rule". J.Biol.Chem., 284, 2009
|
|
4R63
| Binary complex crystal structure of R258A mutant of DNA polymerase Beta | 分子名称: | DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... | 著者 | Batra, V.K, Beard, W.A, Wilson, S.H. | 登録日 | 2014-08-22 | 公開日 | 2014-10-08 | 最終更新日 | 2023-09-20 | 実験手法 | X-RAY DIFFRACTION (1.85 Å) | 主引用文献 | Substrate-induced DNA Polymerase beta Activation. J.Biol.Chem., 289, 2014
|
|
4R65
| Ternary complex crystal structure of R258A mutant of DNA polymerase Beta | 分子名称: | 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | 著者 | Batra, V.K, Beard, W.A, Wilson, S.H. | 登録日 | 2014-08-22 | 公開日 | 2014-10-08 | 最終更新日 | 2024-02-28 | 実験手法 | X-RAY DIFFRACTION (1.95 Å) | 主引用文献 | Substrate-induced DNA Polymerase beta Activation. J.Biol.Chem., 289, 2014
|
|
4R64
| Binary complex crystal structure of E295K mutant of DNA polymerase Beta | 分子名称: | DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... | 著者 | Batra, V.K, Beard, W.A, Wilson, S.H. | 登録日 | 2014-08-22 | 公開日 | 2014-10-08 | 最終更新日 | 2023-09-20 | 実験手法 | X-RAY DIFFRACTION (2.2 Å) | 主引用文献 | Substrate-induced DNA Polymerase beta Activation. J.Biol.Chem., 289, 2014
|
|
4R66
| Ternary complex crystal structure of E295K mutant of DNA polymerase Beta | 分子名称: | 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | 著者 | Batra, V.K, Beard, W.A, Wilson, S.H. | 登録日 | 2014-08-22 | 公開日 | 2014-10-08 | 最終更新日 | 2024-02-28 | 実験手法 | X-RAY DIFFRACTION (2.25 Å) | 主引用文献 | Substrate-induced DNA Polymerase beta Activation. J.Biol.Chem., 289, 2014
|
|
6DIA
| DNA polymerase beta substrate complex with templating cytosine and incoming Fapy-dGTP analog | 分子名称: | 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, CALCIUM ION, DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | 著者 | Freudenthal, B.D, Smith, M.R, Wilson, S.H, Beard, W.A. | 登録日 | 2018-05-23 | 公開日 | 2019-01-30 | 最終更新日 | 2023-10-11 | 実験手法 | X-RAY DIFFRACTION (1.969 Å) | 主引用文献 | A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition. Nucleic Acids Res., 47, 2019
|
|
6DIC
| D276G DNA polymerase beta substrate complex with templating cytosine and incoming Fapy-dGTP analog | 分子名称: | 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, CALCIUM ION, CHLORIDE ION, ... | 著者 | Freudenthal, B.D, Smith, M.R, Wilson, S.H, Beard, W.A. | 登録日 | 2018-05-23 | 公開日 | 2019-01-30 | 最終更新日 | 2023-10-11 | 実験手法 | X-RAY DIFFRACTION (1.992 Å) | 主引用文献 | A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition. Nucleic Acids Res., 47, 2019
|
|
1MQ2
| Human DNA Polymerase Beta Complexed With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine and dAMP | 分子名称: | 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE, 5'-D(*CP*CP*GP*AP*CP*(8OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(2DA))-3', ... | 著者 | Krahn, J.M, Beard, W.A, Miller, H, Grollman, A.P, Wilson, S.H. | 登録日 | 2002-09-13 | 公開日 | 2003-01-28 | 最終更新日 | 2024-05-29 | 実験手法 | X-RAY DIFFRACTION (3.1 Å) | 主引用文献 | Structure of DNA Polymerase beta with the Mutagenic DNA Lesion 8-oxodeoxyguanine Reveals
Structural Insights into its Coding Potential Structure, 11, 2003
|
|
2FMS
| DNA Polymerase beta with a gapped DNA substrate and dUMPNPP with magnesium in the catalytic site | 分子名称: | 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, 5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3', ... | 著者 | Batra, V.K, Beard, W.A, Shock, D.D, Krahn, J.M, Pedersen, L.C, Wilson, S.H. | 登録日 | 2006-01-09 | 公開日 | 2006-04-25 | 最終更新日 | 2023-08-30 | 実験手法 | X-RAY DIFFRACTION (2 Å) | 主引用文献 | Magnesium-induced assembly of a complete DNA polymerase catalytic complex. Structure, 14, 2006
|
|
2FMQ
| Sodium in active site of DNA Polymerase Beta | 分子名称: | 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, 5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3', ... | 著者 | Batra, V.K, Beard, W.A, Shock, D.D, Krahn, J.M, Pedersen, L.C, Wilson, S.H. | 登録日 | 2006-01-09 | 公開日 | 2006-04-25 | 最終更新日 | 2023-08-30 | 実験手法 | X-RAY DIFFRACTION (2.2 Å) | 主引用文献 | Magnesium-induced assembly of a complete DNA polymerase catalytic complex. Structure, 14, 2006
|
|
2FMP
| DNA Polymerase beta with a terminated gapped DNA substrate and ddCTP with sodium in the catalytic site | 分子名称: | 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, 5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3', ... | 著者 | Batra, V.K, Beard, W.A, Shock, D.D, Krahn, J.M, Pedersen, L.C, Wilson, S.H. | 登録日 | 2006-01-09 | 公開日 | 2006-04-25 | 最終更新日 | 2023-08-30 | 実験手法 | X-RAY DIFFRACTION (1.65 Å) | 主引用文献 | Magnesium-induced assembly of a complete DNA polymerase catalytic complex. Structure, 14, 2006
|
|
3C2L
| Ternary complex of DNA POLYMERASE BETA with a C:DAPCPP mismatch in the active site | 分子名称: | 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine, DNA (5'-D(*DCP*DCP*DGP*DAP*DCP*DCP*DGP*DCP*DGP*DCP*DAP*DTP*DCP*DAP*DGP*DC)-3'), DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DTP*DGP*DCP*DGP*DC)-3'), ... | 著者 | Batra, V.K, Beard, W.A, Shock, D.D, Pedersen, L.C, Wilson, S.H. | 登録日 | 2008-01-25 | 公開日 | 2008-05-20 | 最終更新日 | 2023-08-30 | 実験手法 | X-RAY DIFFRACTION (2.6 Å) | 主引用文献 | Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation. Mol.Cell, 30, 2008
|
|
2PXI
| Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monofluoromethylene triphosphate | 分子名称: | 2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE, 5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3', ... | 著者 | McKenna, C.E, Batra, V.K, Beard, W.A, Pedersen, L.C, Wilson, S.H. | 登録日 | 2007-05-14 | 公開日 | 2008-01-08 | 最終更新日 | 2023-08-30 | 実験手法 | X-RAY DIFFRACTION (2.1 Å) | 主引用文献 | (R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta. J.Am.Chem.Soc., 129, 2007
|
|
2P66
| Human DNA Polymerase beta complexed with tetrahydrofuran (abasic site) containing DNA | 分子名称: | DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3'), DNA (5'-D(P*(3DR)P*GP*TP*CP*GP*G)-3'), ... | 著者 | Prasad, R, Batra, V.K, Yang, X.-P, Krahn, J.M, Pedersen, L.C, Beard, W.A, Wilson, S.H. | 登録日 | 2007-03-16 | 公開日 | 2007-04-10 | 最終更新日 | 2023-08-30 | 実験手法 | X-RAY DIFFRACTION (2.5 Å) | 主引用文献 | Structural insight into the DNA Polymerase beta deoxyribose phosphate lyase mechanism DNA REPAIR, 4, 2005
|
|
4F5O
| Open ternary complex of R283K DNA polymerase beta with a one metal bound dCTP analog | 分子名称: | 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine, DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'), ... | 著者 | Freudenthal, B.D, Beard, W.A, Wilson, S.H. | 登録日 | 2012-05-13 | 公開日 | 2012-12-12 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (2 Å) | 主引用文献 | Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Structure, 20, 2012
|
|
4F5Q
| Closed ternary complex of R283K DNA polymerase beta | 分子名称: | 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine, DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), ... | 著者 | Freudenthal, B.D, Beard, W.A, Wilson, S.H. | 登録日 | 2012-05-13 | 公開日 | 2012-12-12 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (2.25 Å) | 主引用文献 | Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Structure, 20, 2012
|
|
4F5N
| Open ternary complex of R283K DNA polymerase beta with a metal free dCTP analog | 分子名称: | 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine, DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), ... | 著者 | Freudenthal, B.D, Beard, W.A, Wilson, S.H. | 登録日 | 2012-05-13 | 公開日 | 2012-12-12 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (1.8 Å) | 主引用文献 | Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Structure, 20, 2012
|
|
4F5R
| Open and closed ternary complex of R283K DNA polymerase beta with a dCTP analog in the same asymmetric unit | 分子名称: | 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine, DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), ... | 著者 | Freudenthal, B.D, Beard, W.A, Wilson, S.H. | 登録日 | 2012-05-13 | 公開日 | 2012-12-12 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (2.2 Å) | 主引用文献 | Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Structure, 20, 2012
|
|
4F5P
| Open ternary mismatch complex of R283K DNA polymerase beta with a dATP analog | 分子名称: | 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine, DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), ... | 著者 | Freudenthal, B.D, Beard, W.A, Wilson, S.H. | 登録日 | 2012-05-13 | 公開日 | 2012-12-12 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (1.85 Å) | 主引用文献 | Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Structure, 20, 2012
|
|
6MR8
| D276G DNA polymerase beta substrate complex with templating adenine and incoming Fapy-dGTP analog | 分子名称: | 1,2-ETHANEDIOL, 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, CALCIUM ION, ... | 著者 | Freudenthal, B.D, Smith, M.R, Wilson, S.H, Beard, W.A. | 登録日 | 2018-10-11 | 公開日 | 2019-01-30 | 最終更新日 | 2023-10-11 | 実験手法 | X-RAY DIFFRACTION (1.897 Å) | 主引用文献 | A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition. Nucleic Acids Res., 47, 2019
|
|
6MR7
| DNA polymerase beta substrate complex with templating adenine and incoming Fapy-dGTP analog | 分子名称: | 1,2-ETHANEDIOL, 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, CALCIUM ION, ... | 著者 | Freudenthal, B.D, Smith, M.R, Wilson, S.H, Beard, W.A. | 登録日 | 2018-10-11 | 公開日 | 2019-01-30 | 最終更新日 | 2023-10-11 | 実験手法 | X-RAY DIFFRACTION (2.144 Å) | 主引用文献 | A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition. Nucleic Acids Res., 47, 2019
|
|
3LK9
| DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P | 分子名称: | 5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl](difluoro)methyl}(hydroxy)phosphoryl]thymidine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | 著者 | Zibinsky, M, Surya Prakash, G.K, Upton, T.G, Kashemirov, B.A, McKenna, C.E, Oertell, K, Goodman, M.F, Batra, V.K, Pedersen, L.C, Beard, W.A, Wilson, S.H. | 登録日 | 2010-01-27 | 公開日 | 2011-01-12 | 最終更新日 | 2023-09-06 | 実験手法 | X-RAY DIFFRACTION (2.5 Å) | 主引用文献 | Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid. Proc.Natl.Acad.Sci.USA, 107, 2010
|
|
3MBY
| Ternary complex of DNA Polymerase BETA with template base A and 8oxodGTP in the active site with a dideoxy terminated primer | 分子名称: | 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | 著者 | Batra, V.K, Beard, W.A, Hou, E.W, Pedersen, L.C, Prasad, R, Wilson, S.H. | 登録日 | 2010-03-26 | 公開日 | 2010-06-09 | 最終更新日 | 2023-09-06 | 実験手法 | X-RAY DIFFRACTION (2 Å) | 主引用文献 | Mutagenic conformation of 8-oxo-7,8-dihydro-2'-dGTP in the confines of a DNA polymerase active site. Nat.Struct.Mol.Biol., 17, 2010
|
|