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
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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
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3RJJ
| Ternary complex crystal structure of DNA Polymerase Beta with template 8odG provides insight into mutagenic lesion bypass | 分子名称: | DNA (5'-D(*CP*CP*GP*AP*CP*GP*(8OG)P*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 | 2011-04-15 | 公開日 | 2012-01-18 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (2 Å) | 主引用文献 | Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion. Proc.Natl.Acad.Sci.USA, 109, 2012
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3RH4
| DNA Polymerase Beta with a dideoxy-terminated primer with an incoming ribonucleotide (rCTP) | 分子名称: | 5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DDG))-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | 著者 | Cavanaugh, N.A, Beard, W.A, Batra, V.K, Perera, L, Pedersen, L.G, Wilson, S.H. | 登録日 | 2011-04-11 | 公開日 | 2011-07-06 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (1.918 Å) | 主引用文献 | Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. J.Biol.Chem., 286, 2011
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3RJK
| Ternary complex of DNA Polymerase Beta with a gapped DNA containing 8odG:dC base pair at primer terminus and dG:dCMP(CF2)PP in the active site | 分子名称: | 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*GP*(8OG)P*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | 著者 | Batra, V.K, Beard, W.A, Wilson, S.H. | 登録日 | 2011-04-15 | 公開日 | 2012-01-18 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (2.1 Å) | 主引用文献 | Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion. Proc.Natl.Acad.Sci.USA, 109, 2012
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3RJH
| Ternary complex of DNA Polymerase Beta with a gapped DNA containing (syn)8odG:dA at primer terminus and dG:dCMP(CF2)PPin the active site | 分子名称: | 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*GP*(8OG)P*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | 著者 | Batra, V.K, Beard, W.A, Wilson, S.H. | 登録日 | 2011-04-15 | 公開日 | 2012-01-18 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (2.2 Å) | 主引用文献 | Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion Proc.Natl.Acad.Sci.USA, 109, 2012
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3RJI
| Ternary complex of DNA Polymerase Beta with a gapped DNA containing 8odG at template position paired with non-hydrolyzable dCTP analog (dCMP(CF2)PP) | 分子名称: | 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | 著者 | Batra, V.K, Beard, W.A, Wilson, S.H. | 登録日 | 2011-04-15 | 公開日 | 2012-01-18 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | 主引用文献 | Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion Proc.Natl.Acad.Sci.USA, 109, 2012
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3RJF
| Ternary complex of DNA Polymerase Beta with a gapped DNA containing (syn)8odG at template position paired with non-hydrolyzable dATP analog (dApCPP) | 分子名称: | 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | 著者 | Batra, V.K, Beard, W.A, Wilson, S.H. | 登録日 | 2011-04-15 | 公開日 | 2012-01-18 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | 主引用文献 | Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion Proc.Natl.Acad.Sci.USA, 109, 2012
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3RH5
| DNA Polymerase Beta Mutant (Y271) with a dideoxy-terminated primer with an incoming deoxynucleotide (dCTP) | 分子名称: | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, 5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DDG))-3', ... | 著者 | Cavanaugh, N.A, Beard, W.A, Batra, V.K, Perera, L, Pedersen, L.G, Wilson, S.H. | 登録日 | 2011-04-11 | 公開日 | 2011-07-06 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (2.096 Å) | 主引用文献 | Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. J.Biol.Chem., 286, 2011
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3RJE
| Ternary complex of DNA Polymerase Beta with a gapped DNA containing 8odG at template position | 分子名称: | 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'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... | 著者 | Batra, V.K, Beard, W.A, Wilson, S.H. | 登録日 | 2011-04-15 | 公開日 | 2012-01-18 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (2.1 Å) | 主引用文献 | Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion Proc.Natl.Acad.Sci.USA, 109, 2012
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3RH6
| DNA Polymerase Beta Mutant (Y271) with a dideoxy-terminated primer with an incoming ribonucleotide (rCTP) | 分子名称: | (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DDG))-3'), (5'-D(P*GP*TP*CP*GP*G)-3'), 5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', ... | 著者 | Cavanaugh, N.A, Beard, W.A, Batra, V.K, Perera, L, Pedersen, L.G, Wilson, S.H. | 登録日 | 2011-04-11 | 公開日 | 2011-07-06 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (2.048 Å) | 主引用文献 | Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. J.Biol.Chem., 286, 2011
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3RJG
| Binary complex of DNA Polymerase Beta with a gapped DNA containing 8odG:dA base-pair at primer Terminus | 分子名称: | DNA (5'-D(*CP*CP*GP*AP*CP*GP*(8OG)P*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-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 | 2011-04-15 | 公開日 | 2012-01-18 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (2 Å) | 主引用文献 | Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion Proc.Natl.Acad.Sci.USA, 109, 2012
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3TFR
| Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, b dAMP(CF2)PP in the active site | 分子名称: | 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*TP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | 著者 | Chamberlain, B.T, Batra, V.K, Beard, W.A, Kadina, A.P, Shock, D.D, Kashemirov, B.A, McKenna, C.E, Goodman, M.F, Wilson, S.H. | 登録日 | 2011-08-16 | 公開日 | 2012-03-21 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (2 Å) | 主引用文献 | Stereospecific Formation of a Ternary Complex of (S)-alpha, beta-Fluoromethylene-dATP with DNA Pol beta. Chembiochem, 13, 2012
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3TFS
| 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 | 分子名称: | 2'-deoxy-5'-O-[(S)-{(S)-fluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*TP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | 著者 | Chamberlain, B.T, Batra, V.K, Beard, W.A, Kadina, A.P, Shock, D.D, Kashemirov, B.A, McKenna, C.E, Goodman, M.F, Wilson, S.H. | 登録日 | 2011-08-16 | 公開日 | 2012-03-21 | 最終更新日 | 2023-09-13 | 実験手法 | X-RAY DIFFRACTION (2 Å) | 主引用文献 | Stereospecific Formation of a Ternary Complex of (S)-alpha, beta-Fluoromethylene-dATP with DNA Pol beta. Chembiochem, 13, 2012
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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
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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
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4JWM
| Ternary complex of D256E 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, Perera, L, Ping, L, Shock, D.D, Beard, W.A, Pedersen, L.C, Pedersen, L.G, Wilson, S.H. | 登録日 | 2013-03-27 | 公開日 | 2013-06-26 | 最終更新日 | 2023-09-20 | 実験手法 | X-RAY DIFFRACTION (2 Å) | 主引用文献 | Amino Acid Substitution in the Active Site of DNA Polymerase beta Explains the Energy Barrier of the Nucleotidyl Transfer Reaction. J.Am.Chem.Soc., 135, 2013
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5U9H
| DNA polymerase beta product complex with inserted Sp-isomer of dCTP-alpha-S | 分子名称: | 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*CP*(C7R))-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... | 著者 | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | 登録日 | 2016-12-16 | 公開日 | 2017-02-08 | 最終更新日 | 2023-10-04 | 実験手法 | X-RAY DIFFRACTION (1.85 Å) | 主引用文献 | Revealing the role of the product metal in DNA polymerase beta catalysis. Nucleic Acids Res., 45, 2017
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5UGO
| DNA polymerase beta nick complex with imidodiphosphate | 分子名称: | CALCIUM ION, 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*CP*C)-3'), ... | 著者 | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | 登録日 | 2017-01-09 | 公開日 | 2017-07-26 | 最終更新日 | 2024-03-06 | 実験手法 | X-RAY DIFFRACTION (1.897 Å) | 主引用文献 | Modulating the DNA polymerase beta reaction equilibrium to dissect the reverse reaction. Nat. Chem. Biol., 13, 2017
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4JWN
| Ternary complex of D256A 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, Perera, L, Ping, L, Shock, D.D, Beard, W.A, Pedersen, L.C, Pedersen, L.G, Wilson, S.H. | 登録日 | 2013-03-27 | 公開日 | 2013-06-26 | 最終更新日 | 2023-09-20 | 実験手法 | X-RAY DIFFRACTION (2.39 Å) | 主引用文献 | Amino Acid Substitution in the Active Site of DNA Polymerase beta Explains the Energy Barrier of the Nucleotidyl Transfer Reaction. J.Am.Chem.Soc., 135, 2013
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4KLH
| DNA polymerase beta matched product complex with Mn2+, 40 s | 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*CP*C)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | 著者 | Freudenthal, B.D, Beard, W.A, Shock, D.D, Wilson, S.H. | 登録日 | 2013-05-07 | 公開日 | 2013-07-17 | 最終更新日 | 2023-09-20 | 実験手法 | X-RAY DIFFRACTION (1.876 Å) | 主引用文献 | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
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4KLT
| DNA polymerase beta mismatched product complex with Mn2+, 30 min | 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*CP*A)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | 著者 | Freudenthal, B.D, Beard, W.A, Shock, D.D, Wilson, S.H. | 登録日 | 2013-05-07 | 公開日 | 2013-07-17 | 最終更新日 | 2023-09-20 | 実験手法 | X-RAY DIFFRACTION (1.979 Å) | 主引用文献 | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
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5UGP
| DNA polymerase beta complex with a 1nt gap and dCMPPNP | 分子名称: | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}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, Wilson, S.H, Beard, W.A. | 登録日 | 2017-01-09 | 公開日 | 2017-07-26 | 最終更新日 | 2023-10-04 | 実験手法 | X-RAY DIFFRACTION (1.955 Å) | 主引用文献 | Modulating the DNA polymerase beta reaction equilibrium to dissect the reverse reaction. Nat. Chem. Biol., 13, 2017
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4KLL
| DNA polymerase beta matched product complex with Mg2+, 45 min | 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*CP*C)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | 著者 | Freudenthal, B.D, Beard, W.A, Shock, D.D, Wilson, S.H. | 登録日 | 2013-05-07 | 公開日 | 2013-07-17 | 最終更新日 | 2023-09-20 | 実験手法 | X-RAY DIFFRACTION (1.841 Å) | 主引用文献 | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
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4KLU
| DNA polymerase beta mismatched product complex with Mn2+, 15 h | 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*CP*A)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | 著者 | Freudenthal, B.D, Beard, W.A, Shock, D.D, Wilson, S.H. | 登録日 | 2013-05-07 | 公開日 | 2013-07-17 | 最終更新日 | 2023-09-20 | 実験手法 | X-RAY DIFFRACTION (1.97 Å) | 主引用文献 | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
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