PDB: 41207 resultsInfo pagesStatus searchChemie searchBIRD

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8U0P	Synaptic complex of human DNA polymerase Lambda DL variant engaged on a noncomplementary DNA double-strand break Descriptor: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, CHLORIDE ION, DNA (5'-D(*CP*AP*GP*TP*AP*C)-3'), ... Authors: Kaminski, A.M, Pedersen, L.C, Bebenek, K, Kunkel, T.A, Chiruvella, K.K, Ramsden, D.A. Deposit date: 2023-08-29 Release date: 2024-03-13 Method: X-RAY DIFFRACTION (1.9 Å) Cite: DNA polymerase lambda Loop1 variant yields unexpected gain-of-function capabilities in nonhomologous end-joining. DNA Repair (Amst), 136, 2024
8U0O	Synaptic complex of human DNA polymerase Lambda DL variant engaged on a DNA double-strand break containing an unpaired 3' primer terminus Descriptor: 1,2-ETHANEDIOL, CHLORIDE ION, DNA (5'-D(*AP*CP*GP*CP*GP*GP*CP*A)-3'), ... Authors: Kaminski, A.M, Pedersen, L.C, Bebenek, K, Kunkel, T.A, Chiruvella, K.K, Ramsden, D.A. Deposit date: 2023-08-29 Release date: 2024-03-13 Method: X-RAY DIFFRACTION (2.05 Å) Cite: DNA polymerase lambda Loop1 variant yields unexpected gain-of-function capabilities in nonhomologous end-joining. DNA Repair (Amst), 136, 2024
6P5C	Bacillus Fragment DNA polymerase mutant I716M Descriptor: DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*TP*GP*AP*TP*CP*G)-3'), DNA polymerase I, ... Authors: Wu, E.Y. Deposit date: 2019-05-30 Release date: 2020-03-25 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (2.2 Å) Cite: The importance of Ile716 toward the mutagenicity of 8-Oxo-2'-deoxyguanosine with Bacillus fragment DNA polymerase. DNA Repair (Amst.), 89, 2020
6UG1	Sequence impact in DNA duplex opening by the Rad4/XPC nucleotide excision repair complex Descriptor: DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3'), DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47)P*AP*CP*AP*TP*CP*CP*CP*CP*TP*AP*CP*AP*A)-3'), DNA repair protein RAD4, ... Authors: Paul, D, Min, J.-H. Deposit date: 2019-09-25 Release date: 2021-03-31 Last modified: 2021-09-08 Method: X-RAY DIFFRACTION (2.833 Å) Cite: Impact of DNA sequences on DNA 'opening' by the Rad4/XPC nucleotide excision repair complex. DNA Repair (Amst), 107, 2021
5T14	DNA polymerase kappa extending beyond a bulky major benzo[a]pyrene adduct Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, DNA, DNA polymerase kappa, ... Authors: Jha, V.K, Ling, H. Deposit date: 2016-08-17 Release date: 2016-12-21 Last modified: 2024-03-06 Method: X-RAY DIFFRACTION (3 Å) Cite: Structural basis of accurate replication beyond a bulky major benzo[a]pyrene adduct by human DNA polymerase kappa. DNA Repair (Amst.), 49, 2017
8E11	Structure of mouse DNA polymerase Beta (PolB) mutant Descriptor: ACETATE ION, DNA polymerase beta, MALONIC ACID Authors: Sharma, N, Thompson, M.K, Prakash, A. Deposit date: 2022-08-09 Release date: 2023-02-01 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Pol beta /XRCC1 heterodimerization dictates DNA damage recognition and basal Pol beta protein levels without interfering with mouse viability or fertility. DNA Repair (Amst), 123, 2023
2P66	Human DNA Polymerase beta complexed with tetrahydrofuran (abasic site) containing DNA Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*AP*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'), DNA (5'-D(P*(3DR)P*GP*TP*CP*GP*G)-3'), ... Authors: Prasad, R, Batra, V.K, Yang, X.-P, Krahn, J.M, Pedersen, L.C, Beard, W.A, Wilson, S.H. Deposit date: 2007-03-16 Release date: 2007-04-10 Last modified: 2023-08-30 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Structural insight into the DNA Polymerase beta deoxyribose phosphate lyase mechanism DNA REPAIR, 4, 2005
2PFP	DNA Polymerase lambda in complex with DNA and dCTP Descriptor: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, DNA polymerase lambda, Downstream Primer, ... Authors: Garcia-Diaz, M, Bebenek, K, Krahn, J.M, Pedersen, L.C, Kunkel, T.A. Deposit date: 2007-04-05 Release date: 2007-05-15 Last modified: 2023-08-30 Method: X-RAY DIFFRACTION (2.1 Å) Cite: Role of the catalytic metal during polymerization by DNA polymerase lambda. DNA Repair, 6, 2007
2PFO	DNA Polymerase lambda in complex with DNA and dUPNPP Descriptor: 1,2-ETHANEDIOL, 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, DNA polymerase lambda, ... Authors: Garcia-Diaz, M, Bebenek, K, Krahn, J.M, Pedersen, L.C, Kunkel, T.A. Deposit date: 2007-04-05 Release date: 2007-05-15 Last modified: 2023-08-30 Method: X-RAY DIFFRACTION (2 Å) Cite: Role of the catalytic metal during polymerization by DNA polymerase lambda. DNA Repair, 6, 2007
8E10	Structure of mouse polymerase beta Descriptor: DNA polymerase beta, MALONIC ACID Authors: Thompson, M.K, Sharma, N, Prakash, A. Deposit date: 2022-08-09 Release date: 2023-02-01 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (1.65 Å) Cite: Pol beta /XRCC1 heterodimerization dictates DNA damage recognition and basal Pol beta protein levels without interfering with mouse viability or fertility. DNA Repair (Amst), 123, 2023
4HSB	S. pombe 3-methyladenine DNA glycosylase-like protein Mag2 bound to damaged DNA Descriptor: DI(HYDROXYETHYL)ETHER, DNA (5'-D(P*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*C)-3'), DNA (5'-D(P*GP*GP*AP*CP*TP*(3DR)P*AP*CP*GP*GP*G)-3'), ... Authors: Adhikary, S, Eichman, B.F. Deposit date: 2012-10-29 Release date: 2013-01-23 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (1.9 Å) Cite: Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe. Dna Repair, 12, 2013
2PFQ	Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal Descriptor: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, DNA polymerase lambda, Downstream Primer, ... Authors: Garcia-Diaz, M, Bebenek, K, Krahn, J.M, Pedersen, L.C, Kunkel, T.A. Deposit date: 2007-04-05 Release date: 2007-05-15 Last modified: 2023-08-30 Method: X-RAY DIFFRACTION (2.1 Å) Cite: Role of the catalytic metal during polymerization by DNA polymerase lambda. DNA Repair, 6, 2007
2PFN	Na in the active site of DNA Polymerase lambda Descriptor: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, DNA polymerase lambda, Downstream Primer, ... Authors: Garcia-Diaz, M, Bebenek, K, Krahn, J.M, Pedersen, L.C, Kunkel, T.A. Deposit date: 2007-04-05 Release date: 2007-05-15 Last modified: 2023-08-30 Method: X-RAY DIFFRACTION (1.9 Å) Cite: Role of the catalytic metal during polymerization by DNA polymerase lambda. DNA Repair, 6, 2007
1Z56	Co-Crystal Structure of Lif1p-Lig4p Descriptor: DNA ligase IV, Ligase interacting factor 1 Authors: Dore, A.S, Furnham, N, Davies, O.R, Sibanda, B.L, Chirgadze, D.Y, Jackson, S.P, Pellegrini, L, Blundell, T.L. Deposit date: 2005-03-17 Release date: 2006-01-31 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (3.92 Å) Cite: Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode. DNA REPAIR, 5, 2006
7P8V	The structure of E. coli MutL bound to a 3' resected DNA end Descriptor: DNA mismatch repair protein MutL, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ... Authors: Borsellini, A, Lamers, M.H. Deposit date: 2021-07-23 Release date: 2022-06-29 Last modified: 2022-08-31 Method: ELECTRON MICROSCOPY (3.7 Å) Cite: MutL binds to 3' resected DNA ends and blocks DNA polymerase access. Nucleic Acids Res., 50, 2022
7P0L	Crystal structure of S.pombe Mdb1 BRCT domains in complex with a H2A phosphopeptide Descriptor: DNA damage response protein Mdb1, Histone H2A-beta Authors: Day, M, Oliver, A.W, Pearl, L.H. Deposit date: 2021-06-29 Release date: 2021-12-01 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (1.97 Å) Cite: Phosphorylation-dependent assembly of DNA damage response systems and the central roles of TOPBP1. DNA Repair (Amst), 108, 2021
7YWH	Six DNA Helix Bundle nanopore - State 1 Descriptor: DNA (50-MER) Authors: Javed, A, Ahmad, K, Lanphere, C, Coveney, P, Howorka, S, Orlova, E.V. Deposit date: 2022-02-14 Release date: 2023-05-24 Last modified: 2023-07-05 Method: ELECTRON MICROSCOPY (8 Å) Cite: Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations. Nat Commun, 14, 2023
7YWI	Six DNA duplex bundle nanopore - State 2 Descriptor: DNA (50-MER) Authors: Javed, A, Ahmad, K, Lanphere, C, Coveney, P, Howorka, S, Orlova, E.V. Deposit date: 2022-02-14 Release date: 2023-05-24 Last modified: 2023-07-05 Method: ELECTRON MICROSCOPY (8 Å) Cite: Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations. Nat Commun, 14, 2023
7YWN	Six DNA Helix Bundle nanopore - State 4 Descriptor: DNA (50-MER) Authors: Javed, A, Ahmad, K, Lanphere, C, Orlova, E.V, Coveney, P, Howorka, S. Deposit date: 2022-02-14 Release date: 2023-05-24 Last modified: 2023-07-05 Method: ELECTRON MICROSCOPY (8 Å) Cite: Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations. Nat Commun, 14, 2023
7YWL	Six DNA Helix Bundle nanopore - State 3 Descriptor: DNA (50-MER) Authors: Javed, A, Ahmad, K, Lanphere, C, Coveney, P, Howorka, S, Orlova, E.V. Deposit date: 2022-02-14 Release date: 2023-05-24 Last modified: 2023-07-05 Method: ELECTRON MICROSCOPY (8 Å) Cite: Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations. Nat Commun, 14, 2023
7YWO	Six DNA Helix Bundle nanopore - State 5 Descriptor: DNA (50-MER) Authors: Javed, A, Ahmad, K, Lanphere, C, Coveney, P, Howorka, S, Orlova, E.V. Deposit date: 2022-02-14 Release date: 2023-05-24 Last modified: 2023-07-05 Method: ELECTRON MICROSCOPY (8 Å) Cite: Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations. Nat Commun, 14, 2023
2LIB	DNA sequence context conceals alpha anomeric lesion Descriptor: DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3'), DNA (5'-D(*GP*TP*CP*CP*(A3A)P*GP*GP*AP*CP*G)-3') Authors: Johnson, C.N, Spring, A.M, Cunningham, R.P, Germann, M.W. Deposit date: 2011-08-27 Release date: 2012-08-08 Method: SOLUTION NMR Cite: DNA sequence context conceals alpha-anomeric lesions. J.Mol.Biol., 416, 2012
122D	DNA HELIX STRUCTURE AND REFINEMENT ALGORITHM: COMPARISON OF MODELS FOR D(CCAGGCM==5==CTGG) DERIVED FROM NUCLSQ, TNT, AND X-PLOR Descriptor: DNA (5'-D(*CP*CP*AP*GP*GP*CP*(5CM)P*TP*GP*G)-3') Authors: Hahn, M, Heinemann, U. Deposit date: 1993-05-03 Release date: 1993-10-15 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (1.7 Å) Cite: DNA helix structure and refinement algorithm: comparison of models for d(CCAGGCm5CTGG) derived from NUCLSQ, TNT and X-PLOR. Acta Crystallogr.,Sect.D, 49, 1993
123D	DNA HELIX STRUCTURE AND REFINEMENT ALGORITHM: COMPARISON OF MODELS FOR D(CCAGGCM==5==CTGG) DERIVED FROM NUCLSQ, TNT, AND X-PLOR Descriptor: DNA (5'-D(*CP*CP*AP*GP*GP*CP*(5CM)P*TP*GP*G)-3') Authors: Hahn, M, Heinemann, U. Deposit date: 1993-05-03 Release date: 1993-10-15 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (1.7 Å) Cite: DNA helix structure and refinement algorithm: comparison of models for d(CCAGGCm5CTGG) derived from NUCLSQ, TNT and X-PLOR. Acta Crystallogr.,Sect.D, 49, 1993
104D	DNA DUPLEXES FLANKED BY HYBRID DUPLEXES: THE SOLUTION STRUCTURE OF CHIMERIC JUNCTIONS IN Descriptor: DNA/RNA (5'-R(*CP*GP*CP*G)-D(P*TP*AP*TP*AP*CP*GP*CP*G)-3') Authors: Zhu, L, Salazar, M, Reid, B.R. Deposit date: 1994-12-16 Release date: 1995-03-31 Last modified: 2022-02-16 Method: SOLUTION NMR Cite: DNA duplexes flanked by hybrid duplexes: the solution structure of chimeric junctions in [r(cgcg)d(TATACGCG)]2. Biochemistry, 34, 1995

 

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