1MQ2
 
 | | Human DNA Polymerase Beta Complexed With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine and dAMP | | Descriptor: | 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', ... | | Authors: | Krahn, J.M, Beard, W.A, Miller, H, Grollman, A.P, Wilson, S.H. | | Deposit date: | 2002-09-13 | | Release date: | 2003-01-28 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | Structure of DNA Polymerase beta with the Mutagenic DNA Lesion 8-oxodeoxyguanine Reveals
Structural Insights into its Coding Potential
Structure, 11, 2003
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4F5O
 | | Open ternary complex of R283K DNA polymerase beta with a one metal bound 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*(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'), ... | | 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 Å) | | Cite: | Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly.
Structure, 20, 2012
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4F5Q
 | | Closed ternary complex of R283K DNA polymerase beta | | 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(P*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 (2.25 Å) | | Cite: | Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly.
Structure, 20, 2012
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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
 | | 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
 | | 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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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
 | | 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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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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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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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
 | | 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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4UB5
 | | DNA polymerase beta substrate complex with a templating cytosine, incoming 8-oxodGTP, and Mn2+, 5 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: | 2014-08-11 | | Release date: | 2014-11-12 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide.
Nature, 517, 2015
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4UB2
 | | DNA polymerase beta product complex with a templating cytosine and 8-oxodGMP, 120 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 (2.51 Å) | | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide.
Nature, 517, 2015
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4UB1
 | | DNA polymerase beta product complex with a templating adenine and 8-oxodGMP, 90 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 (2.341 Å) | | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide.
Nature, 517, 2015
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4UB4
 | | DNA polymerase beta substrate complex with a templating cytosine and incoming dGTP, 0 s | | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 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', ... | | 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 (1.954 Å) | | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide.
Nature, 517, 2015
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2FMS
 | | DNA Polymerase beta with a gapped DNA substrate and dUMPNPP with magnesium in the catalytic site | | Descriptor: | 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', ... | | Authors: | Batra, V.K, Beard, W.A, Shock, D.D, Krahn, J.M, Pedersen, L.C, Wilson, S.H. | | Deposit date: | 2006-01-09 | | Release date: | 2006-04-25 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Magnesium-induced assembly of a complete DNA polymerase catalytic complex.
Structure, 14, 2006
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2FMQ
 | | Sodium in active site of DNA Polymerase Beta | | Descriptor: | 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', ... | | Authors: | Batra, V.K, Beard, W.A, Shock, D.D, Krahn, J.M, Pedersen, L.C, Wilson, S.H. | | Deposit date: | 2006-01-09 | | Release date: | 2006-04-25 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Magnesium-induced assembly of a complete DNA polymerase catalytic complex.
Structure, 14, 2006
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2FMP
 | | DNA Polymerase beta with a terminated gapped DNA substrate and ddCTP with sodium in the catalytic site | | Descriptor: | 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', ... | | Authors: | Batra, V.K, Beard, W.A, Shock, D.D, Krahn, J.M, Pedersen, L.C, Wilson, S.H. | | Deposit date: | 2006-01-09 | | Release date: | 2006-04-25 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Magnesium-induced assembly of a complete DNA polymerase catalytic complex.
Structure, 14, 2006
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3RJJ
 | | Ternary complex crystal structure of DNA Polymerase Beta with template 8odG provides insight into mutagenic lesion bypass | | Descriptor: | 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'), ... | | Authors: | Batra, V.K, Beard, W.A, Wilson, S.H. | | Deposit date: | 2011-04-15 | | Release date: | 2012-01-18 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | 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) | | Descriptor: | 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', ... | | Authors: | Cavanaugh, N.A, Beard, W.A, Batra, V.K, Perera, L, Pedersen, L.G, Wilson, S.H. | | Deposit date: | 2011-04-11 | | Release date: | 2011-07-06 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.918 Å) | | Cite: | 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 | | Descriptor: | 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'), ... | | Authors: | Batra, V.K, Beard, W.A, Wilson, S.H. | | Deposit date: | 2011-04-15 | | Release date: | 2012-01-18 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | 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) | | Descriptor: | 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'), ... | | Authors: | Batra, V.K, Beard, W.A, Wilson, S.H. | | Deposit date: | 2011-04-15 | | Release date: | 2012-01-18 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | 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 | | Descriptor: | 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'), ... | | Authors: | Batra, V.K, Beard, W.A, Wilson, S.H. | | Deposit date: | 2011-04-15 | | Release date: | 2012-01-18 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | 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) | | Descriptor: | 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'), ... | | Authors: | Batra, V.K, Beard, W.A, Wilson, S.H. | | Deposit date: | 2011-04-15 | | Release date: | 2012-01-18 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | 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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