PDB: 45817 resultsInfo pagesStatus searchChemie searchBIRD

---

1CGP	CATABOLITE GENE ACTIVATOR PROTEIN (CAP)/DNA COMPLEX + ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE Descriptor: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE, DNA (5'-D(*GP*CP*GP*AP*AP*AP*AP*GP*TP*GP*TP*GP*AP*CP*AP*TP*AP*T)-3'), DNA (5'-D(*GP*TP*CP*AP*CP*AP*CP*TP*TP*TP*TP*CP*G)-3'), ... Authors: Schultz, S.C, Shields, G.C, Steitz, T.A. Deposit date: 1991-08-12 Release date: 1994-01-31 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (3 Å) Cite: Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science, 253, 1991
4NOE	Crystal structure of DdrB bound to 30b ssDNA Descriptor: 5'-D(*TP*TP*GP*CP*GP*CP*TP*TP*GP*CP*GP*CP*TP*TP*GP*CP*GP*CP*TP*TP*GP*CP*GP*CP*TP*TP*GP*CP*GP*CP)-3', CALCIUM ION, Single-stranded DNA-binding protein DdrB Authors: Sugiman-Marangos, S.N, Weiss, Y.M, Junop, M.S. Deposit date: 2013-11-19 Release date: 2015-05-20 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Mechanism for accurate, protein-assisted DNA annealing by Deinococcus radiodurans DdrB. Proc.Natl.Acad.Sci.USA, 113, 2016
3BS1	Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold with a Novel Mode of Binding Descriptor: Accessory gene regulator protein A, DNA (5'-D(*DAP*DAP*(BRU)P*DAP*DCP*DTP*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DTP*DAP*DA)-3'), DNA (5'-D(*DTP*DTP*DTP*DAP*DAP*DCP*DAP*DGP*DTP*DTP*DAP*DAP*DGP*(BRU)P*DAP*DT)-3'), ... Authors: Sidote, D.J, Barbieri, C, Wu, T, Stock, A.M. Deposit date: 2007-12-21 Release date: 2008-04-08 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (1.6 Å) Cite: Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold with an Unusual Mode of Binding. Structure, 16, 2008
5MF7	New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-GADD45) Descriptor: Cellular tumor antigen p53, DI(HYDROXYETHYL)ETHER, DNA, ... Authors: Rozenberg, H, Diskin-Posner, Y, Golovenko, D, Shakked, Z. Deposit date: 2016-11-17 Release date: 2018-05-30 Last modified: 2024-01-17 Method: X-RAY DIFFRACTION (1.59 Å) Cite: New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins. Structure, 26, 2018
3D1E	Crystal structure of E. coli sliding clamp (beta) bound to a polymerase II peptide Descriptor: DNA polymerase III subunit beta, decamer from polymerase II C-terminal Authors: Georgescu, R.E, Yurieva, O, Seung-Sup, K, Kuriyan, J, Kong, X.-P, O'Donnell, M. Deposit date: 2008-05-05 Release date: 2008-07-29 Last modified: 2023-08-30 Method: X-RAY DIFFRACTION (1.9 Å) Cite: Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp. Proc.Natl.Acad.Sci.Usa, 105, 2008
4PGQ	Structure of human DNA polymerase beta complexed with G in the template base paired with incoming non-hydrolyzable TTP Descriptor: 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine, DNA (5'-D(*CP*CP*GP*AP*CP*GP*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: Koag, M.C, Lee, S. Deposit date: 2014-05-02 Release date: 2014-10-01 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (2.3 Å) Cite: The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase beta. Nucleic Acids Res., 42, 2015
4PGX	Structure of human DNA polymerase beta complexed with G in the template base paired with incoming non-hydrolyzable TTP and MANGANESE Descriptor: 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine, DNA (5'-D(*CP*CP*GP*AP*CP*GP*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: Koag, M.C, Lee, S. Deposit date: 2014-05-03 Release date: 2014-09-24 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (2.077 Å) Cite: The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase beta. Nucleic Acids Res., 42, 2015
5YTE	Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with with natural dT:dATP base pair Descriptor: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, DNA (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'), ... Authors: Zeng, H, Mondal, M, Song, R.Y, Zhang, J, Xia, B, Gao, Y.Q, Yi, C.Q. Deposit date: 2017-11-17 Release date: 2018-11-21 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (2.21 Å) Cite: Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Angew. Chem. Int. Ed. Engl., 58, 2019
4P2H	Structure of human DNA polymerase complexed with N7MG in the template opposite to incoming non-hydrolyzable TTP with manganese in the active site Descriptor: 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine, DNA (5'-D(*CP*CP*GP*AP*CP*(FMG)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: Lee, S, Koag, M.C. Deposit date: 2014-03-04 Release date: 2014-06-25 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.987 Å) Cite: Transition-state destabilization reveals how human DNA polymerase beta proceeds across the chemically unstable lesion N7-methylguanine. Nucleic Acids Res., 42, 2014
5YTD	large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with the natural base pair 5fC:dGTP Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*AP*AP*AP*(5FC)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'), ... Authors: Zeng, H, Mondal, M, Song, R.Y, Zhang, J, Xia, B, Gao, Y.Q, Yi, C.Q. Deposit date: 2017-11-17 Release date: 2018-11-21 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (2 Å) Cite: Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Angew. Chem. Int. Ed. Engl., 58, 2019
8UVK	CosR DNA bound form II Descriptor: DI(HYDROXYETHYL)ETHER, DNA (5'-D(*AP*AP*TP*TP*AP*AP*GP*AP*TP*AP*TP*TP*AP*TP*TP*AP*AP*CP*CP*AP*A)-3'), DNA (5'-D(*TP*TP*GP*GP*TP*TP*AP*AP*TP*AP*AP*TP*AP*TP*CP*TP*TP*AP*AP*TP*T)-3'), ... Authors: Zhang, Z. Deposit date: 2023-11-03 Release date: 2024-01-31 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (2.21 Å) Cite: Structural basis of DNA recognition of the Campylobacter jejuni CosR regulator. Mbio, 15, 2024
4N5S	Ternary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant (Cs3C KlenTaq) with DNA and ddCTP Descriptor: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, 5'-D(*AP*A*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3', ... Authors: Wu, E.Y. Deposit date: 2013-10-10 Release date: 2015-01-21 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (1.67 Å) Cite: A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase. Biochemistry, 54, 2015
5YTC	Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with the unnatural base M-fC pair with dATP in the active site Descriptor: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, DNA (5'-D(*AP*AP*AP*(92F)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC)P*(DOC))-3'), ... Authors: Zeng, H, Mondal, M, Song, R.Y, Zhang, J, Xia, B, Yi, C.Q. Deposit date: 2017-11-17 Release date: 2018-11-21 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (2.28 Å) Cite: Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Angew. Chem. Int. Ed. Engl., 58, 2019
5YTF	Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base M-fC pair with dA Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*AP*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*(92F)P*GP*GP*TP*C)-3'), DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'), ... Authors: Zeng, H, Mondal, M, Song, R.Y, Zhang, J, Xia, B, Gao, Y.Q, Yi, C.Q. Deposit date: 2017-11-17 Release date: 2018-11-21 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (1.98 Å) Cite: Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Angew. Chem. Int. Ed. Engl., 58, 2019
5YTG	Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base I-fC pair with dA Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*AP*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*(94O)P*GP*GP*TP*C)-3'), DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'), ... Authors: Zeng, H, Mondal, M, Song, R.Y, Zhang, J, Xia, B, Gao, Y.Q, Yi, C.Q. Deposit date: 2017-11-17 Release date: 2018-11-21 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (2.07 Å) Cite: Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Angew. Chem. Int. Ed. Engl., 58, 2019
5YTH	Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base M-fC pair with dG Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*AP*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*(92F)P*GP*GP*TP*C)-3'), DNA (5'-D(*GP*AP*CP*CP*GP*CP*GP*GP*CP*GP*CP*(DOC))-3'), ... Authors: Zeng, H, Mondal, M, Song, R.Y, Zhang, J, Xia, B, Gao, Y.Q, Yi, C.Q. Deposit date: 2017-11-17 Release date: 2018-11-21 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (2.53 Å) Cite: Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Angew. Chem. Int. Ed. Engl., 58, 2019
5MCV	New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-LWC1) Descriptor: 1,2-ETHANEDIOL, ACETATE ION, Cellular tumor antigen p53, ... Authors: Golovenko, D, Rozenberg, H, Shakked, Z. Deposit date: 2016-11-10 Release date: 2018-06-13 Last modified: 2024-01-17 Method: X-RAY DIFFRACTION (1.6 Å) Cite: New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins. Structure, 26, 2018
4GZ0	Mus Musculus Tdp2-DNA Substrate Analog (5'-6-aminohexanol) Complex Descriptor: 1,2-ETHANEDIOL, 6-aminohexan-1-ol, ACETATE ION, ... Authors: Schellenberg, M.J, Williams, R.S. Deposit date: 2012-09-05 Release date: 2012-10-31 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.113 Å) Cite: Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2. Nat.Struct.Mol.Biol., 19, 2012
5Z3N	Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base 5fC pair with dA Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*AP*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*(5FC)P*GP*GP*TP*C)-3'), DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'), ... Authors: Zeng, H, Mondal, M, Song, R.Y, Zhang, J, Xia, B, Gao, Y.Q, Yi, C.Q. Deposit date: 2018-01-08 Release date: 2018-11-21 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (1.91 Å) Cite: Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Angew. Chem. Int. Ed. Engl., 58, 2019
7MCA	Structure of the S. cerevisiae origin recognition complex bound to the replication initiator Cdc6 and the ARS1 origin DNA. Descriptor: Cell division control protein 6, DNA (85-MER), MAGNESIUM ION, ... Authors: Feng, X, Li, H. Deposit date: 2021-04-01 Release date: 2021-06-02 Last modified: 2024-05-29 Method: ELECTRON MICROSCOPY (3.6 Å) Cite: The structure of ORC-Cdc6 on an origin DNA reveals the mechanism of ORC activation by the replication initiator Cdc6. Nat Commun, 12, 2021
7R3X	The crystal structure of the L439V variant of Pol2CORE in complex with DNA and an incoming nucleotide Descriptor: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, ACETATE ION, CALCIUM ION, ... Authors: Barbari, S.R, Beach, A.K, Markgren, J.G, Parkash, V, Johansson, E, Shcherbakova, P.V. Deposit date: 2022-02-08 Release date: 2022-07-27 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (2.46 Å) Cite: Enhanced polymerase activity permits efficient synthesis by cancer-associated DNA polymerase ε variants at low dNTP levels. Nucleic Acids Res., 50, 2022
1I7D	NONCOVALENT COMPLEX OF E.COLI DNA TOPOISOMERASE III WITH AN 8-BASE SINGLE-STRANDED DNA OLIGONUCLEOTIDE Descriptor: 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3', CHLORIDE ION, DNA TOPOISOMERASE III, ... Authors: Changela, A, DiGate, R.J, Mondragon, A. Deposit date: 2001-03-08 Release date: 2001-06-29 Last modified: 2023-08-09 Method: X-RAY DIFFRACTION (2.05 Å) Cite: Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule. Nature, 411, 2001
7R3Y	The crystal structure of the V426L variant of Pol2CORE in complex with DNA and an incoming nucleotide Descriptor: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, CALCIUM ION, DNA Primer, ... Authors: Barbari, S.R, Beach, A.K, Markgren, J.G, Parkash, V, Johansson, E, Shcherbakova, P.V. Deposit date: 2022-02-08 Release date: 2022-07-27 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (2.6 Å) Cite: Enhanced polymerase activity permits efficient synthesis by cancer-associated DNA polymerase ε variants at low dNTP levels. Nucleic Acids Res., 50, 2022
2ZO1	Mouse NP95 SRA domain DNA specific complex 2 Descriptor: 1,2-ETHANEDIOL, DNA (5'-D(*DGP*DTP*DCP*DAP*DGP*(5CM)P*DGP*DCP*DAP*DAP*DTP*DGP*DG)-3'), DNA (5'-D(*DTP*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP*DAP*DC)-3'), ... Authors: Hashimoto, H, Horton, J.R, Cheng, X. Deposit date: 2008-05-05 Release date: 2008-09-09 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (1.96 Å) Cite: The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix Nature, 455, 2008
3CMX	Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures Descriptor: ADENOSINE-5'-DIPHOSPHATE, DNA (5'-D(*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DA)-3'), DNA (5'-D(*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DT)-3'), ... Authors: Pavletich, N.P. Deposit date: 2008-03-24 Release date: 2008-05-20 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (3.4 Å) Cite: Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature, 453, 2008

<135136137138139140141142143144145146147148149150>