3TA5
 
 | | Cobalt bound structure of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family | | Descriptor: | ATP-dependent DNA ligase, N-terminal domain protein, COBALT (II) ION, ... | | Authors: | Das, U, Smith, P, Shuman, S. | | Deposit date: | 2011-08-03 | | Release date: | 2011-10-12 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.52 Å) | | Cite: | Structural insights to the metal specificity of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family.
Nucleic Acids Res., 40, 2012
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3TA7
 | | Zinc bound structure of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family | | Descriptor: | ATP-dependent DNA ligase, N-terminal domain protein, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Das, U, Smith, P, Shuman, S. | | Deposit date: | 2011-08-03 | | Release date: | 2011-10-12 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (1.48 Å) | | Cite: | Structural insights to the metal specificity of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family.
Nucleic Acids Res., 40, 2012
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6WBO
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7SX5
 | | Crystal structure of ligase I with nick duplexes containing mismatch A:C | | Descriptor: | ADENOSINE MONOPHOSPHATE, DNA chain 1, DNA chain 2, ... | | Authors: | Tang, Q, Gulkis, M, McKenna, R, Caglayan, M. | | Deposit date: | 2021-11-22 | | Release date: | 2022-07-13 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structures of LIG1 that engage with mutagenic mismatches inserted by pol beta in base excision repair.
Nat Commun, 13, 2022
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7SXE
 | | Crystal structure of ligase I with nick duplexes containing cognate G:T | | Descriptor: | ADENOSINE MONOPHOSPHATE, DNA chain 1, DNA chain 2, ... | | Authors: | Tang, Q, Gulkis, M, McKenna, R, Caglayan, M. | | Deposit date: | 2021-11-22 | | Release date: | 2022-07-13 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structures of LIG1 that engage with mutagenic mismatches inserted by pol beta in base excision repair.
Nat Commun, 13, 2022
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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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5V1I
 | | DNA polymerase beta ternary product complex with 8-oxoG:C and inserted dCTP | | Descriptor: | CHLORIDE ION, 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'), ... | | 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 (2.035 Å) | | Cite: | Capturing a mammalian DNA polymerase extending from an oxidized nucleotide.
Nucleic Acids Res., 45, 2017
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5V1R
 | | DNA polymerase beta reactant complex with 8-oxoG:C at the primer terminus and incoming dCTP | | Descriptor: | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, 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 (2.077 Å) | | Cite: | Capturing a mammalian DNA polymerase extending from an oxidized nucleotide.
Nucleic Acids Res., 45, 2017
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5V1O
 | | DNA polymerase beta product complex with 8-oxoG:A and inserted dCTP | | Descriptor: | CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*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'), ... | | 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 (1.801 Å) | | Cite: | Capturing a mammalian DNA polymerase extending from an oxidized nucleotide.
Nucleic Acids Res., 45, 2017
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5V1F
 | | DNA polymerase beta substrate complex with 8-oxoG at the primer terminus and incoming dCTP | | Descriptor: | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, CALCIUM 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, Schaich, M.A, Whitaker, A.M. | | Deposit date: | 2017-03-02 | | Release date: | 2017-05-10 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.181 Å) | | Cite: | Capturing a mammalian DNA polymerase extending from an oxidized nucleotide.
Nucleic Acids Res., 45, 2017
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6P1R
 | | Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and bound incoming AMPNPP | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, CHLORIDE ION, ... | | Authors: | Kaminski, A.M, Pedersen, L.C, Bebenek, K, Chiruvella, K.K, Ramsden, D.A, Kunkel, T.A. | | Deposit date: | 2019-05-20 | | Release date: | 2019-09-04 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.701 Å) | | Cite: | Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Nucleic Acids Res., 47, 2019
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7NFC
 | | Cryo-EM structure of NHEJ super-complex (dimer) | | Descriptor: | DNA (27-MER), DNA (28-MER), DNA ligase 4, ... | | Authors: | Chaplin, A.K, Hardwick, S.W, Kefala Stavridi, A, Chirgadze, D.Y, Blundell, T.L. | | Deposit date: | 2021-02-05 | | Release date: | 2021-08-18 | | Last modified: | 2024-07-10 | | Method: | ELECTRON MICROSCOPY (4.14 Å) | | Cite: | Cryo-EM of NHEJ supercomplexes provides insights into DNA repair.
Mol.Cell, 81, 2021
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7NFE
 | | Cryo-EM structure of NHEJ super-complex (monomer) | | Descriptor: | DNA (5'-D(P*AP*AP*TP*AP*AP*AP*CP*TP*AP*AP*AP*AP*AP*CP*TP*AP*TP*TP*AP*TP*TP*AP*TP*G)-3'), DNA (5'-D(P*TP*AP*AP*TP*AP*AP*TP*AP*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*AP*G)-3'), DNA ligase 4, ... | | Authors: | Chaplin, A.K, Hardwick, S.W, Kefala Stavridi, A, Chirgadze, D.Y, Blundell, T.L. | | Deposit date: | 2021-02-06 | | Release date: | 2021-08-18 | | Last modified: | 2024-07-10 | | Method: | ELECTRON MICROSCOPY (4.29 Å) | | Cite: | Cryo-EM of NHEJ supercomplexes provides insights into DNA repair.
Mol.Cell, 81, 2021
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8EZB
 | | NHEJ Long-range complex with ATP | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, DNA (30-MER), DNA (31-MER), ... | | Authors: | Chen, S, He, Y. | | Deposit date: | 2022-10-31 | | Release date: | 2023-06-14 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (8.9 Å) | | Cite: | Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ.
Sci Adv, 9, 2023
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8EZA
 | | NHEJ Long-range complex with PAXX | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, DNA (30-MER), DNA (31-MER), ... | | Authors: | Chen, S, He, Y. | | Deposit date: | 2022-10-31 | | Release date: | 2023-06-14 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (4.39 Å) | | Cite: | Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ.
Sci Adv, 9, 2023
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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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7SUM
 | | Crystal structure of human ligase I with nick duplexes containing cognate A:T | | Descriptor: | ADENOSINE MONOPHOSPHATE, DNA ligase 1, DNA(5'-*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*A-3'), ... | | Authors: | Tang, Q, Gulkis, M, McKenna, R, Caglayan, M. | | Deposit date: | 2021-11-17 | | Release date: | 2022-07-13 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Structures of LIG1 that engage with mutagenic mismatches inserted by pol beta in base excision repair.
Nat Commun, 13, 2022
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5VEZ
 | | DNA polymerase beta substrate complex with 8-oxoG:A at the primer terminus and incoming dCTP analog | | Descriptor: | 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine, DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3'), ... | | Authors: | Freudenthal, B.D, Schaich, M.A, Whitaker, A.M, Smith, M.R. | | Deposit date: | 2017-04-06 | | Release date: | 2017-05-10 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.039 Å) | | Cite: | Capturing a mammalian DNA polymerase extending from an oxidized nucleotide.
Nucleic Acids Res., 45, 2017
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5WNX
 | | DNA polymerase beta substrate complex with incoming 6-TdGTP | | Descriptor: | 2-amino-9-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-1,9-dihydro-6H-purine-6-thione, CALCIUM ION, CHLORIDE ION, ... | | Authors: | Schaich, M.A, Smith, M.R, Cloud, A.S, Holloran, S.M, Freudenthal, B.D. | | Deposit date: | 2017-08-01 | | Release date: | 2017-09-13 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues.
Chem. Res. Toxicol., 30, 2017
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5WO0
 | | DNA polymerase beta substrate complex with incoming 5-FodUTP | | Descriptor: | 2'-deoxy-5-formyluridine 5'-(tetrahydrogen triphosphate), CALCIUM ION, CHLORIDE ION, ... | | Authors: | Schaich, M.A, Smith, M.R, Cloud, A.S, Holloran, S.M, Freudenthal, B.D. | | Deposit date: | 2017-08-01 | | Release date: | 2017-09-13 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues.
Chem. Res. Toxicol., 30, 2017
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5WNY
 | | DNA polymerase beta substrate complex with incoming 5-FdUTP | | Descriptor: | 2'-deoxy-5-fluorouridine 5'-(tetrahydrogen triphosphate), CALCIUM ION, CHLORIDE ION, ... | | Authors: | Schaich, M.A, Smith, M.R, Cloud, A.S, Holloran, S.M, Freudenthal, B.D. | | Deposit date: | 2017-08-01 | | Release date: | 2017-09-13 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues.
Chem. Res. Toxicol., 30, 2017
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5WNZ
 | | DNA polymerase beta substrate complex with incoming 5-FodCTP | | Descriptor: | 2'-deoxy-5-formylcytidine 5'-(tetrahydrogen triphosphate), CALCIUM ION, CHLORIDE ION, ... | | Authors: | Schaich, M.A, Smith, M.R, Cloud, A.S, Holloran, S.M, Freudenthal, B.D. | | Deposit date: | 2017-08-01 | | Release date: | 2017-09-13 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues.
Chem. Res. Toxicol., 30, 2017
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7SGL
 | | DNA-PK complex of DNA end processing | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, DNA-dependent protein kinase catalytic subunit, Hairpin_1, ... | | Authors: | Liu, L, Li, J, Chen, X, Yang, W, Gellert, M. | | Deposit date: | 2021-10-06 | | Release date: | 2022-01-12 | | Last modified: | 2022-01-19 | | Method: | ELECTRON MICROSCOPY (3 Å) | | Cite: | Autophosphorylation transforms DNA-PK from protecting to processing DNA ends.
Mol.Cell, 82, 2022
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6P1S
 | | Post-catalytic nicked complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and newly incorporated AMP | | Descriptor: | 1,2-ETHANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ADENOSINE-5'-TRIPHOSPHATE, ... | | Authors: | Kaminski, A.M, Pedersen, L.C, Bebenek, K, Chiruvella, K.K, Ramsden, D.A, Kunkel, T.A. | | Deposit date: | 2019-05-20 | | Release date: | 2019-09-04 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Nucleic Acids Res., 47, 2019
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6P1O
 | | Post-catalytic nicked complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and newly incorporated dAMP | | Descriptor: | 1,2-ETHANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ADENOSINE-5'-TRIPHOSPHATE, ... | | Authors: | Kaminski, A.M, Pedersen, L.C, Bebenek, K, Chiruvella, K.K, Ramsden, D.A, Kunkel, T.A. | | Deposit date: | 2019-05-20 | | Release date: | 2019-09-04 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Nucleic Acids Res., 47, 2019
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