6BOW
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![BU of 6bow by Molmil](/molmil-images/mine/6bow) | |
5WN0
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![BU of 5wn0 by Molmil](/molmil-images/mine/5wn0) | APE1 exonuclease substrate complex with a C/G match | Descriptor: | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ... | Authors: | Freudenthal, B.D, Whitaker, A.M. | Deposit date: | 2017-07-31 | Release date: | 2018-02-28 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Molecular snapshots of APE1 proofreading mismatches and removing DNA damage. Nat Commun, 9, 2018
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5UGO
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![BU of 5ugo by Molmil](/molmil-images/mine/5ugo) | DNA polymerase beta nick complex with imidodiphosphate | Descriptor: | 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'), ... | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | Deposit date: | 2017-01-09 | Release date: | 2017-07-26 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (1.897 Å) | Cite: | Modulating the DNA polymerase beta reaction equilibrium to dissect the reverse reaction. Nat. Chem. Biol., 13, 2017
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5U9H
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![BU of 5u9h by Molmil](/molmil-images/mine/5u9h) | DNA polymerase beta product complex with inserted Sp-isomer of dCTP-alpha-S | Descriptor: | 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'), ... | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | Deposit date: | 2016-12-16 | Release date: | 2017-02-08 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Revealing the role of the product metal in DNA polymerase beta catalysis. Nucleic Acids Res., 45, 2017
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5V1G
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![BU of 5v1g by Molmil](/molmil-images/mine/5v1g) | DNA polymerase beta binary complex with 8-oxoG at the primer terminus | Descriptor: | DNA (5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... | Authors: | Freudenthal, B.D, Smith, M.R, Whitaker, A.M, Schaich, M.A. | Deposit date: | 2017-03-02 | Release date: | 2017-05-10 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (1.798 Å) | Cite: | Capturing a mammalian DNA polymerase extending from an oxidized nucleotide. Nucleic Acids Res., 45, 2017
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5V1N
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![BU of 5v1n by Molmil](/molmil-images/mine/5v1n) | DNA polymerase beta substrate complex with 8-oxoG:A at the primer terminus and incoming dCTP | Descriptor: | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, CALCIUM ION, CHLORIDE ION, ... | Authors: | Freudenthal, B.D, Schaich, M.A, Whitaker, A.M, Smith, M.R. | Deposit date: | 2017-03-02 | Release date: | 2017-05-10 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (2.005 Å) | Cite: | Capturing a mammalian DNA polymerase extending from an oxidized nucleotide. Nucleic Acids Res., 45, 2017
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5UGP
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![BU of 5ugp by Molmil](/molmil-images/mine/5ugp) | DNA polymerase beta complex with a 1nt gap and dCMPPNP | Descriptor: | 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'), ... | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | Deposit date: | 2017-01-09 | Release date: | 2017-07-26 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (1.955 Å) | Cite: | Modulating the DNA polymerase beta reaction equilibrium to dissect the reverse reaction. Nat. Chem. Biol., 13, 2017
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5UGN
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![BU of 5ugn by Molmil](/molmil-images/mine/5ugn) | DNA polymerase beta imidodiphosphate reactant complex | Descriptor: | 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*CP*C)-3'), ... | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | Deposit date: | 2017-01-09 | Release date: | 2017-07-26 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (1.997 Å) | Cite: | Modulating the DNA polymerase beta reaction equilibrium to dissect the reverse reaction. Nat. Chem. Biol., 13, 2017
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5V1J
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![BU of 5v1j by Molmil](/molmil-images/mine/5v1j) | DNA polymerase beta open product complex with 8-oxoG:C and inserted dCTP | Descriptor: | DNA (5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG)P*C)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... | Authors: | Freudenthal, B.D, Smith, M.R, Whitaker, A.M, Schaich, M.A. | Deposit date: | 2017-03-02 | Release date: | 2017-05-10 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (2.616 Å) | Cite: | Capturing a mammalian DNA polymerase extending from an oxidized nucleotide. Nucleic Acids Res., 45, 2017
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7S9M
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![BU of 7s9m by Molmil](/molmil-images/mine/7s9m) | |
7S9N
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![BU of 7s9n by Molmil](/molmil-images/mine/7s9n) | Binary complex of DNA Polymerase Beta with Fapy-dG in the template position | Descriptor: | DNA (5'-D(*CP*CP*GP*AP*CP*(FAP)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'), ... | Authors: | Freudenthal, B.D, Ryan, B.J, Smith, M.R. | Deposit date: | 2021-09-21 | Release date: | 2022-08-03 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.71 Å) | Cite: | Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication. J.Am.Chem.Soc., 144, 2022
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7S9J
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![BU of 7s9j by Molmil](/molmil-images/mine/7s9j) | Crystal Structure of DNA Polymerase Beta with Fapy-dG base-paired with a dC | Descriptor: | DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*(FAP)P*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*CP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... | Authors: | Freudenthal, B.D, Ryan, B.J. | Deposit date: | 2021-09-21 | Release date: | 2022-08-03 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.91 Å) | Cite: | Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication. J.Am.Chem.Soc., 144, 2022
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7S9P
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![BU of 7s9p by Molmil](/molmil-images/mine/7s9p) | Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dCTP analog | Descriptor: | 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*(FAP)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | Authors: | Freudenthal, B.D, Ryan, B.J, Smith, M.R. | Deposit date: | 2021-09-21 | Release date: | 2022-08-03 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.86 Å) | Cite: | Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication. J.Am.Chem.Soc., 144, 2022
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7S9K
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![BU of 7s9k by Molmil](/molmil-images/mine/7s9k) | Crystal Structure of DNA Polymerase Beta with Fapy-dG base-paired with a dA | Descriptor: | DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*(FAP)P*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*AP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... | Authors: | Freudenthal, B.D, Ryan, B.J. | Deposit date: | 2021-09-21 | Release date: | 2022-08-03 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.97 Å) | Cite: | Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication. J.Am.Chem.Soc., 144, 2022
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7S9Q
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![BU of 7s9q by Molmil](/molmil-images/mine/7s9q) | Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dATP analog | Descriptor: | 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine, DNA (5'-D(*CP*CP*GP*AP*CP*(FAP)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'), ... | Authors: | Freudenthal, B.D, Ryan, B.J, Smith, M.R. | Deposit date: | 2021-09-21 | Release date: | 2022-08-03 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication. J.Am.Chem.Soc., 144, 2022
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7S9O
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![BU of 7s9o by Molmil](/molmil-images/mine/7s9o) | |
4UBC
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![BU of 4ubc by Molmil](/molmil-images/mine/4ubc) | DNA polymerase beta substrate complex with a templating cytosine and incoming 8-oxodGTP, 0 s | Descriptor: | 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*C)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | Deposit date: | 2014-08-12 | Release date: | 2014-11-12 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature, 517, 2015
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4UAZ
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![BU of 4uaz by Molmil](/molmil-images/mine/4uaz) | DNA polymerase beta reactant complex with a templating adenine and incoming 8-oxodGTP, 20 s | Descriptor: | 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*CP*(8OG))-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | Deposit date: | 2014-08-11 | Release date: | 2014-11-12 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.88 Å) | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature, 517, 2015
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4F5N
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![BU of 4f5n by Molmil](/molmil-images/mine/4f5n) | Open ternary complex of R283K DNA polymerase beta with a metal free dCTP analog | Descriptor: | 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'), ... | Authors: | Freudenthal, B.D, Beard, W.A, Wilson, S.H. | Deposit date: | 2012-05-13 | Release date: | 2012-12-12 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Structure, 20, 2012
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4F5R
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![BU of 4f5r by Molmil](/molmil-images/mine/4f5r) | Open and closed ternary complex of R283K DNA polymerase beta with a dCTP analog in the same asymmetric unit | Descriptor: | 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'), ... | Authors: | Freudenthal, B.D, Beard, W.A, Wilson, S.H. | Deposit date: | 2012-05-13 | Release date: | 2012-12-12 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Structure, 20, 2012
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4F5P
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![BU of 4f5p by Molmil](/molmil-images/mine/4f5p) | Open ternary mismatch complex of R283K DNA polymerase beta with a dATP analog | Descriptor: | 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'), ... | Authors: | Freudenthal, B.D, Beard, W.A, Wilson, S.H. | Deposit date: | 2012-05-13 | Release date: | 2012-12-12 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Structure, 20, 2012
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4UB3
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![BU of 4ub3 by Molmil](/molmil-images/mine/4ub3) | DNA polymerase beta closed product complex with a templating cytosine and 8-oxodGMP, 60 s | Descriptor: | 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*CP*(8OG))-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | Deposit date: | 2014-08-11 | Release date: | 2014-11-12 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (2.06 Å) | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature, 517, 2015
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4UBB
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![BU of 4ubb by Molmil](/molmil-images/mine/4ubb) | DNA polymerase beta reactant complex with a templating cytosine and incoming 8-oxodGTP, 40 s | Descriptor: | 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*CP*(8OG))-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | Deposit date: | 2014-08-12 | Release date: | 2014-11-12 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature, 517, 2015
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4UAY
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![BU of 4uay by Molmil](/molmil-images/mine/4uay) | DNA polymerase beta product complex with a templating adenine and inserted 8-oxodGMP, 40 s | Descriptor: | 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*CP*(8OG))-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | Deposit date: | 2014-08-11 | Release date: | 2014-11-12 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.984 Å) | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature, 517, 2015
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4UAW
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![BU of 4uaw by Molmil](/molmil-images/mine/4uaw) | DNA polymerase beta substrate complex with a templating adenine and incoming 8-oxodGTP, 0 s | Descriptor: | 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', 5'-D(P*GP*TP*CP*GP*G)-3', ... | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | Deposit date: | 2014-08-11 | Release date: | 2014-11-12 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature, 517, 2015
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