PDB: 48855 resultsInfo pagesStatus searchChemie searchBIRD

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5J0W	Binary complex crystal structure of DNA polymerase Beta with T:C mismatch at the primer terminus Descriptor: DNA polymerase beta, Downstream Primer Strand, Primer Strand, ... Authors: Batra, V.K, Wilson, S.H. Deposit date: 2016-03-28 Release date: 2016-10-26 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism. Structure, 24, 2016
3GDX	Dna polymerase beta with a gapped DND substrate and dTMP(CF2)PP Descriptor: 5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... Authors: Wilson, S.H, Batra, V.K, Pedersen, L.C. Deposit date: 2009-02-24 Release date: 2009-05-05 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function Org.Lett., 11, 2009
5J0Y	Binary complex crystal structure of DNA polymerase Beta with T:T mismatch at the primer terminus Descriptor: DNA polymerase beta, Downstream Primer Strand, Primer Strand, ... Authors: Batra, V.K, Wilson, S.H. Deposit date: 2016-03-28 Release date: 2016-10-26 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (2 Å) Cite: Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism. Structure, 24, 2016
5J0P	Binary complex crystal structure of DNA polymerase Beta with A:C mismatch at the primer terminus Descriptor: DNA polymerase beta, Downstream Primer Strand, Primer Strand, ... Authors: Batra, V.K, Wilson, S.H. Deposit date: 2016-03-28 Release date: 2016-10-26 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism. Structure, 24, 2016
5J0S	Binary complex crystal structure of DNA polymerase Beta with C:T mismatch at the primer terminus Descriptor: DNA polymerase beta, Downstream Primer Strand, Primer Strand, ... Authors: Batra, V.K, Wilson, S.H. Deposit date: 2016-03-28 Release date: 2016-10-26 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (2 Å) Cite: Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism. Structure, 24, 2016
5J0Q	Binary complex crystal structure of DNA polymerase Beta with A:G mismatch at the primer terminus Descriptor: DNA polymerase beta, Downstream Primer Strand, Primer Strand, ... Authors: Batra, V.K, Wilson, S.H. Deposit date: 2016-03-28 Release date: 2016-10-26 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (2 Å) Cite: Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism. Structure, 24, 2016
5J0T	Binary complex crystal structure of DNA polymerase Beta with G:A mismatch at the primer terminus Descriptor: DNA polymerase beta, Downstream Primer Strand, Primer Strand, ... Authors: Batra, V.K, Wilson, S.H. Deposit date: 2016-03-28 Release date: 2016-10-26 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (2 Å) Cite: Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism. Structure, 24, 2016
5J0U	Binary complex crystal structure of DNA polymerase Beta with G:G mismatch at the primer terminus Descriptor: DNA polymerase beta, Downstream Primer Strand, Primer Strand, ... Authors: Batra, V.K, Wilson, S.H. Deposit date: 2016-03-28 Release date: 2016-10-26 Last modified: 2024-03-06 Method: X-RAY DIFFRACTION (2.1 Å) Cite: Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism. Structure, 24, 2016
8V55	Human mitochondrial DNA polymerase gamma bound to a replication fork in an open conformation Descriptor: DNA polymerase subunit gamma-1, DNA polymerase subunit gamma-2, mitochondrial, ... Authors: Riccio, A.A, Krahn, J.M, Bouvette, J, Borgnia, M.J, Copeland, W.C. Deposit date: 2023-11-30 Release date: 2024-07-10 Last modified: 2024-07-31 Method: ELECTRON MICROSCOPY (4.2 Å) Cite: Coordinated DNA polymerization by Pol gamma and the region of LonP1 regulated proteolysis. Nucleic Acids Res., 52, 2024
8V54	Engaged conformation of the human mitochondrial DNA polymerase gamma bound to DNA Descriptor: DNA (25-MER), DNA (44-MER), DNA polymerase subunit gamma-1, ... Authors: Riccio, A.A, Krahn, J.M, Bouvette, J, Borgnia, J.M, Copeland, W.C. Deposit date: 2023-11-30 Release date: 2024-07-10 Last modified: 2025-06-04 Method: ELECTRON MICROSCOPY (4.1 Å) Cite: Coordinated DNA polymerization by Pol gamma and the region of LonP1 regulated proteolysis. Nucleic Acids Res., 52, 2024
9FJR	Cryo-EM structure of Mycobacterium tuberculosis sigma-B RNA polymerase bound to -10 promoter element ssDNA oligo - sigma-B docked conformation Descriptor: DNA (17-MER), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Brodolin, K, Blaise, M. Deposit date: 2024-05-31 Release date: 2025-05-07 Method: ELECTRON MICROSCOPY (3.43 Å) Cite: Single-stranded DNA drives sigma subunit loading onto mycobacterial RNA polymerase to unlock initiation-competent conformations. Nucleic Acids Res., 53, 2025
8OJ6	HSV-1 DNA polymerase-processivity factor complex in pre-translocation state Descriptor: DNA (22-MER), DNA (48-MER), DNA polymerase catalytic subunit, ... Authors: Gustavsson, E, Grunewald, K, Elias, P, Hallberg, B.M. Deposit date: 2023-03-24 Release date: 2024-04-03 Last modified: 2024-07-17 Method: ELECTRON MICROSCOPY (2.41 Å) Cite: Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM. Nucleic Acids Res., 52, 2024
4JL3	Crystal structure of ms6564-dna complex Descriptor: DNA (31-MER), Transcriptional regulator, TetR family Authors: Yang, S.F, Gao, Z.Q, He, Z.G, Dong, Y.H. Deposit date: 2013-03-12 Release date: 2013-06-26 Last modified: 2024-11-27 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Structural basis for interaction between Mycobacterium smegmatis Ms6564, a TetR family master regulator, and its target DNA. J.Biol.Chem., 288, 2013
1GLU	CRYSTALLOGRAPHIC ANALYSIS OF THE INTERACTION OF THE GLUCOCORTICOID RECEPTOR WITH DNA Descriptor: DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*GP*AP*TP*GP*TP*TP*C P*TP*G)-3'), PROTEIN (GLUCOCORTICOID RECEPTOR), ZINC ION Authors: Luisi, B.F, Xu, W.X, Otwinowski, Z, Freedman, L.P, Yamamoto, K.R, Sigler, P.B. Deposit date: 1992-08-30 Release date: 1994-01-31 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (2.9 Å) Cite: Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature, 352, 1991
5DB9	Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dG Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*GP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*(FMG)P*AP*TP*GP*CP*GP*A)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... Authors: Koag, M.C, Lee, S. Deposit date: 2015-08-21 Release date: 2015-11-11 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (2.45 Å) Cite: N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA. J.Am.Chem.Soc., 137, 2015
2KEK	Solution structure of a dimer of LAC repressor DNA-binding domain complexed to its natural operator O3 Descriptor: DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*GP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*AP*AP*TP*TP*C)-3'), DNA (5'-D(P*GP*AP*AP*TP*TP*GP*CP*GP*TP*TP*GP*CP*GP*CP*TP*CP*AP*CP*TP*GP*CP*CP*G)-3'), Lactose operon repressor Authors: Romanuka, J, Folkers, G, Biris, N, Tishchenko, E, Wienk, H, Kaptein, R, Boelens, R. Deposit date: 2009-01-30 Release date: 2009-05-19 Last modified: 2024-11-20 Method: SOLUTION NMR Cite: Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes. J.Mol.Biol., 390, 2009
2KEI	Refined Solution Structure of a Dimer of LAC repressor DNA-Binding domain complexed to its natural operator O1 Descriptor: DNA (5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP*AP*AP*TP*TP*T)-3'), DNA (5'-D(P*AP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3'), Lactose operon repressor Authors: Romanuka, J, Folkers, G, Biris, N, Tishchenko, E, Wienk, H, Kaptein, R, Boelens, R. Deposit date: 2009-01-30 Release date: 2009-05-19 Last modified: 2024-11-20 Method: SOLUTION NMR Cite: Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes. J.Mol.Biol., 390, 2009
1HF0	Crystal structure of the DNA-binding domain of Oct-1 bound to DNA as a dimer Descriptor: DNA 5'-D(*CP*AP*CP*AP*TP*TP*TP*GP*AP*AP*AP*GP*GP* CP*AP*AP*AP*TP*GP*GP*AP*G)-3', DNA 5'-D(*CP*TP*CP*CP*AP*TP*TP*TP*GP*CP*CP*TP*TP* TP*CP*AP*AP*AP*TP*GP*TP*G)-3', OCTAMER-BINDING TRANSCRIPTION FACTOR 1 Authors: Remenyi, A, Tomilin, A, Pohl, E, Scholer, H.R, Wilmanns, M. Deposit date: 2000-11-27 Release date: 2001-11-10 Last modified: 2024-05-08 Method: X-RAY DIFFRACTION (2.7 Å) Cite: Differential Dimer Activities of the Transcription Factor Oct-1 by DNA-Induced Interface Swapping Mol.Cell, 8, 2001
5VXN	Structure of two RcsB dimers bound to two parallel DNAs. Descriptor: DNA (5'-D(*GP*AP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*AP*TP*A)-3'), DNA (5'-D(*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*A)-3'), Transcriptional regulatory protein RcsB Authors: Filippova, E.V, Minasov, G, Pshenychnyi, S, Anderson, W.F, Center for Structural Genomics of Infectious Diseases (CSGID) Deposit date: 2017-05-23 Release date: 2018-03-07 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (3.375 Å) Cite: Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB. MBio, 9, 2018
4X0Q	Ternary complex of human DNA polymerase theta C-terminal domain binding ddGTP opposite dCMP Descriptor: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3'), DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3'), ... Authors: Zahn, K.E, Doublie, S. Deposit date: 2014-11-22 Release date: 2015-03-18 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (3.9 Å) Cite: Human DNA polymerase theta grasps the primer terminus to mediate DNA repair. Nat.Struct.Mol.Biol., 22, 2015
2IRF	CRYSTAL STRUCTURE OF AN IRF-2/DNA COMPLEX. Descriptor: DNA (5'-D(*TP*TP*CP*AP*CP*TP*TP*TP*CP*AP*CP*(5IU)P*T)-3'), DNA (5'-D(P*AP*AP*GP*TP*GP*AP*AP*AP*GP*(5IU)P*GP*A)-3'), INTERFERON REGULATORY FACTOR 2, ... Authors: Fujii, Y, Shimizu, T, Kusumoto, M, Kyogoku, Y, Taniguchi, T, Hakoshima, T. Deposit date: 1999-05-30 Release date: 1999-10-08 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences. EMBO J., 18, 1999
5DBB	Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dA Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*AP*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: Koag, M.C, Lee, S. Deposit date: 2015-08-21 Release date: 2015-11-11 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (2.25 Å) Cite: N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA. J.Am.Chem.Soc., 137, 2015
4X0P	Ternary complex of human DNA polymerase theta C-terminal domain binding ddATP opposite a tetrahydrofuran AP site analog Descriptor: 2',3'-dideoxyadenosine triphosphate, CALCIUM ION, DNA (5'-D(*CP*GP*TP*TP*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3'), ... Authors: Zahn, K.E, Doublie, S. Deposit date: 2014-11-21 Release date: 2015-03-18 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (3.911 Å) Cite: Human DNA polymerase theta grasps the primer terminus to mediate DNA repair. Nat.Struct.Mol.Biol., 22, 2015
2KEJ	Solution structure of a dimer of LAC repressor DNA-binding domain complexed to its natural operator O2 Descriptor: DNA (5'-D(*GP*AP*AP*AP*TP*GP*TP*GP*AP*GP*CP*GP*AP*GP*TP*AP*AP*CP*AP*AP*CP*CP*G)-3'), DNA (5'-D(P*CP*GP*GP*TP*TP*GP*TP*TP*AP*CP*TP*CP*GP*CP*TP*CP*AP*CP*AP*TP*TP*TP*C)-3'), Lactose operon repressor Authors: Romanuka, J, Folkers, G, Biris, N, Tishchenko, E, Wienk, H, Kaptein, R, Boelens, R. Deposit date: 2009-01-30 Release date: 2009-05-19 Last modified: 2024-11-20 Method: SOLUTION NMR Cite: Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes. J.Mol.Biol., 390, 2009
1JEY	Crystal Structure of the Ku heterodimer bound to DNA Descriptor: DNA (34-MER), DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3'), Ku70, ... Authors: Walker, J.R, Corpina, R.A, Goldberg, J. Deposit date: 2001-06-19 Release date: 2001-08-10 Last modified: 2023-08-16 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature, 412, 2001

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