6MR8
| D276G DNA polymerase beta substrate complex with templating adenine and incoming Fapy-dGTP analog | Descriptor: | 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, ... | Authors: | Freudenthal, B.D, Smith, M.R, Wilson, S.H, Beard, W.A. | Deposit date: | 2018-10-11 | Release date: | 2019-01-30 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (1.897 Å) | Cite: | 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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6MR7
| DNA polymerase beta substrate complex with templating adenine and incoming Fapy-dGTP analog | Descriptor: | 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, ... | Authors: | Freudenthal, B.D, Smith, M.R, Wilson, S.H, Beard, W.A. | Deposit date: | 2018-10-11 | Release date: | 2019-01-30 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (2.144 Å) | Cite: | 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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7LPH
| APE1 Mn-bound product complex with abasic ribonucleotide DNA | 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'-R(P*N)-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ... | Authors: | Freudenthal, B.D, Hoitsma, N.M. | Deposit date: | 2021-02-11 | Release date: | 2021-08-04 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.99 Å) | Cite: | Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker. Comput Struct Biotechnol J, 19, 2021
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7LPJ
| APE1 Mn-bound phosphorothioate substrate complex with abasic ribonucleotide DNA | Descriptor: | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-R(P*(YA4))-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*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-(apurinic or apyrimidinic site) lyase, ... | Authors: | Freudenthal, B.D, Hoitsma, N.M. | Deposit date: | 2021-02-11 | Release date: | 2021-08-04 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.56 Å) | Cite: | Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker. Comput Struct Biotechnol J, 19, 2021
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7LPG
| APE1 product complex with abasic ribonucleotide DNA | 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'-R(P*N)-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ... | Authors: | Freudenthal, B.D, Hoitsma, N.M. | Deposit date: | 2021-02-11 | Release date: | 2021-08-04 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.08 Å) | Cite: | Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker. Comput Struct Biotechnol J, 19, 2021
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7LPI
| APE1 phosphorothioate substrate complex with abasic ribonucleotide DNA | Descriptor: | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-R(P*(YA4))-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*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-(apurinic or apyrimidinic site) lyase | Authors: | Freudenthal, B.D, Hoitsma, N.M. | Deposit date: | 2021-02-11 | Release date: | 2021-08-04 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.05 Å) | Cite: | Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker. Comput Struct Biotechnol J, 19, 2021
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7S9L
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6BOT
| Human APE1 substrate complex with an C/C mismatch adjacent the THF | Descriptor: | 1,2-ETHANEDIOL, 21-mer DNA, DNA-(apurinic or apyrimidinic site) lyase | Authors: | Freudenthal, B.D, Whitaker, A.M, Fairlamb, M.S. | Deposit date: | 2017-11-20 | Release date: | 2018-08-15 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches. Acta Crystallogr D Struct Biol, 74, 2018
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6BOQ
| Human APE1 substrate complex with an A/A mismatch adjacent the THF | Descriptor: | 1,2-ETHANEDIOL, 21-mer DNA, DNA-(apurinic or apyrimidinic site) lyase | Authors: | Freudenthal, B.D, Whitaker, A.M, Fairlamb, M.S. | Deposit date: | 2017-11-20 | Release date: | 2018-08-15 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (1.96 Å) | Cite: | Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches. Acta Crystallogr D Struct Biol, 74, 2018
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6BOW
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6BOU
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6BOV
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6BOS
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6BOR
| Human APE1 substrate complex with an G/G mismatch adjacent the THF | Descriptor: | 1,2-ETHANEDIOL, 21-mer DNA, CHLORIDE ION, ... | Authors: | Freudenthal, B.D, Whitaker, A.M, Fairlamb, M.S. | Deposit date: | 2017-11-20 | Release date: | 2018-08-15 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (1.84 Å) | Cite: | Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches. Acta Crystallogr D Struct Biol, 74, 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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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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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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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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