7S9L
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7T1B
| Rev1 Ternary Complex with rCTP and Ca2+ | Descriptor: | CALCIUM ION, CYTIDINE-5'-TRIPHOSPHATE, DNA (5'-D(*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3'), ... | Authors: | Freudenthal, B.D, Weaver, T.M. | Deposit date: | 2021-12-01 | Release date: | 2022-05-25 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1. Nat Commun, 13, 2022
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7T1A
| Rev1 Ternary Complex with dATP and Ca2+ | Descriptor: | 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3'), ... | Authors: | Freudenthal, B.D, Weaver, T.M. | Deposit date: | 2021-12-01 | Release date: | 2022-05-25 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.81 Å) | Cite: | Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1. Nat Commun, 13, 2022
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7T18
| Rev1 Ternary Complex with dTTP and Ca2+ | Descriptor: | CALCIUM ION, DNA (5'-D(*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3'), DNA (5'-D(P*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*G)-3'), ... | Authors: | Freudenthal, B.D, Weaver, T.M. | Deposit date: | 2021-12-01 | Release date: | 2022-05-25 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1. Nat Commun, 13, 2022
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7T19
| Rev1 Ternary Complex with dGTP and Ca2+ | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(*CP*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3'), ... | Authors: | Freudenthal, B.D, Weaver, T.M. | Deposit date: | 2021-12-01 | Release date: | 2022-05-25 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.01 Å) | Cite: | Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1. Nat Commun, 13, 2022
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7U53
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7U52
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7U51
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7TR7
| APE1 product complex with abasic ssDNA | Descriptor: | DNA (5'-D(P*(3DR)P*CP*GP*AP*TP*GP*C)-3'), DNA-(apurinic or apyrimidinic site) lyase, MAGNESIUM ION | Authors: | Freudenthal, B.D, Hoitsma, N.M. | Deposit date: | 2022-01-28 | Release date: | 2023-04-12 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Mechanistic insight into AP-endonuclease 1 cleavage of abasic sites at stalled replication fork mimics. Nucleic Acids Res., 51, 2023
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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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7S9M
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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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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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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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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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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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7S9O
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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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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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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
| 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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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
| 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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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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5V1P
| DNA polymerase beta substrate complex with 8-oxoG:C at the primer terminus and 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*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-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 (1.991 Å) | Cite: | Capturing a mammalian DNA polymerase extending from an oxidized nucleotide. Nucleic Acids Res., 45, 2017
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