PDB: 47011 resultsInfo pagesStatus searchChemie searchBIRD

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5TBB	Postcatalytic ternary complex of Human DNA Polymerase Beta with Gapped DNA substrate, incorporated (-)FTC and PPi. Descriptor: 10- MER PRIMER, 16- MER TEMPLATE, 5-MER PHOSPHORYLATED DOWNSTREAM PRIMER, ... Authors: Vyas, R, Suo, Z. Deposit date: 2016-09-11 Release date: 2017-01-11 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.39 Å) Cite: Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. J. Am. Chem. Soc., 139, 2017
5TBA	Postcatalytic ternary complex of Human DNA Polymerase Beta with Gapped DNA substrate, incorporated (-)3TC and PPi. Descriptor: 10-MER PRIMER, 16-MER TEMPLATE, 5-MER PHOSPHORYLATED DOWNSTREAM PRIMER, ... Authors: Vyas, R, Suo, Z. Deposit date: 2016-09-11 Release date: 2017-01-11 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.49 Å) Cite: Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. J. Am. Chem. Soc., 139, 2017
5TB8	Precatalytic ternary complex of Human DNA Polymerase Beta in closed conformation With Gapped DNA substrate incoming (-)3TC-TP and Mn2+. Descriptor: 10- MER PRIMER, 16- MER TEMPLATE, 5-MER PHOSPHORYLATED DOWNSTREAM PRIME, ... Authors: Vyas, R, Suo, Z. Deposit date: 2016-09-11 Release date: 2017-01-11 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2 Å) Cite: Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. J. Am. Chem. Soc., 139, 2017
5TBC	PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTRATE, INCORPORATED (-)3TC-MP AND AN ANOTHER INCOMING (-)3TC-TP NUCLEOTIDE. Descriptor: 10- MER PRIMER, 16- MER TEMPLATE, 5-MER PHOSPHORYLATED DOWNSTREAM PRIMER, ... Authors: Vyas, R, Suo, Z. Deposit date: 2016-09-11 Release date: 2017-01-11 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (1.85 Å) Cite: Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. J. Am. Chem. Soc., 139, 2017
9EZZ	Bacterial histone protein HBb from Bdellovibrio bacteriovorus bound to DNA Descriptor: DNA (5'-D(P*AP*GP*CP*CP*C)-3'), DNA (5'-D(P*GP*GP*GP*CP*T)-3'), PHOSPHATE ION, ... Authors: Hu, Y, Albrecht, R, Hartmann, M.D. Deposit date: 2024-04-14 Release date: 2024-06-26 Last modified: 2024-10-09 Method: X-RAY DIFFRACTION (1.95 Å) Cite: Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending. Nucleic Acids Res., 52, 2024
9F0E	Bacterial histone protein HBb from Bdellovibrio bacteriovorus bound to DNA Descriptor: DNA (5'-D(P*CP*GP*TP*TP*AP*AP*AP*GP*C)-3'), PHOSPHATE ION, Transcription factor CBF/NF-Y/archaeal histone domain-containing protein Authors: Hu, Y, Albrecht, R, Hartmann, M.D. Deposit date: 2024-04-15 Release date: 2024-06-26 Last modified: 2024-10-09 Method: X-RAY DIFFRACTION (1.85 Å) Cite: Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending. Nucleic Acids Res., 52, 2024
4WUL	Crystal structure of E. faecalis DNA binding domain LiaRD191N complexed with 26bp DNA Descriptor: DNA (26-MER), Response regulator receiver domain protein Authors: Davlieva, M, Shamoo, Y. Deposit date: 2014-11-02 Release date: 2015-05-06 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (2.4 Å) Cite: A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin. Nucleic Acids Res., 43, 2015
4WU4	Crystal structure of E. faecalis DNA binding domain LiaRD191N complexed with 22bp DNA Descriptor: DNA (5'-D(P*AP*AP*AP*TP*CP*GP*TP*TP*CP*TP*TP*AP*AP*GP*TP*CP*C)-3'), DNA (5'-D(P*GP*GP*AP*CP*TP*TP*AP*AP*GP*AP*AP*CP*GP*AP*TP*TP*T)-3'), GLYCEROL, ... Authors: Davlieva, M, Shamoo, Y. Deposit date: 2014-10-31 Release date: 2015-05-06 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (2.3 Å) Cite: A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin. Nucleic Acids Res., 43, 2015
7ICF	DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CDCL2 (0.1 MILLIMOLAR) (FOUR-DAY SOAK) Descriptor: CADMIUM ION, DNA (5'-D(*CP*AP*GP*AP*TP*G)-3'), DNA (5'-D(*CP*AP*TP*CP*TP*GP*T)-3'), ... Authors: Pelletier, H, Sawaya, M.R. Deposit date: 1996-04-19 Release date: 1996-11-15 Last modified: 2023-08-02 Method: X-RAY DIFFRACTION (3.1 Å) Cite: A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta Biochemistry, 35, 1996
7ICJ	DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CUCL2 (0.1 MILLIMOLAR) Descriptor: COPPER (II) ION, DNA (5'-D(*CP*AP*GP*AP*TP*G)-3'), DNA (5'-D(*CP*AP*TP*CP*TP*G)-3'), ... Authors: Pelletier, H, Sawaya, M.R. Deposit date: 1996-04-19 Release date: 1996-11-15 Last modified: 2023-08-02 Method: X-RAY DIFFRACTION (3.5 Å) Cite: A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta Biochemistry, 35, 1996
7ICU	DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CDCL2 (0.1 MILLIMOLAR) Descriptor: CADMIUM ION, DNA (5'-D(*CP*AP*GP*AP*TP*G)-3'), DNA (5'-D(*CP*AP*TP*CP*TP*GP*T)-3'), ... Authors: Pelletier, H, Sawaya, M.R. Deposit date: 1996-04-19 Release date: 1996-11-15 Last modified: 2023-08-02 Method: X-RAY DIFFRACTION (3.3 Å) Cite: A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta. Biochemistry, 35, 1996
1SKN	THE BINDING DOMAIN OF SKN-1 IN COMPLEX WITH DNA: A NEW DNA-BINDING MOTIF Descriptor: DNA (5'-D(*CP*AP*GP*GP*GP*AP*TP*GP*AP*CP*AP*TP*TP*GP*T)-3'), DNA (5'-D(*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*TP*CP*CP*C)-3'), DNA-BINDING DOMAIN OF SKN-1, ... Authors: Rupert, P.B, Daughdrill, G.W, Bowerman, B, Matthews, B.W. Deposit date: 1998-03-30 Release date: 1998-06-24 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (2.5 Å) Cite: A new DNA-binding motif in the Skn-1 binding domain-DNA complex. Nat.Struct.Biol., 5, 1998
6T8H	Cryo-EM structure of the DNA-bound PolD-PCNA processive complex from P. abyssi Descriptor: DNA polymerase II small subunit, DNA polymerase sliding clamp, DNA primer, ... Authors: Madru, C, Raia, P, Hugonneau Beaufet, I, Pehau-Arnaudet, G, England, P, Lindhal, E, Delarue, M, Carroni, M, Sauguet, L. Deposit date: 2019-10-24 Release date: 2020-03-04 Last modified: 2020-04-08 Method: ELECTRON MICROSCOPY (3.77 Å) Cite: Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA. Nat Commun, 11, 2020
2IIE	single chain Integration Host Factor protein (scIHF2) in complex with DNA Descriptor: DNA (5'-D(*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DC)-3'), DNA (5'-D(*DGP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DAP*DAP*DGP*DCP*DAP*DTP*DT)-3'), Integration host factor, ... Authors: Bao, Q, Droege, P, Davey, C.A. Deposit date: 2006-09-28 Release date: 2007-02-20 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.41 Å) Cite: A Divalent Metal-mediated Switch Controlling Protein-induced DNA Bending J.Mol.Biol., 367, 2007
2IIF	single chain Integration Host Factor mutant protein (scIHF2-K45aE) in complex with DNA Descriptor: DNA (5'-D(*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DC)-3'), DNA (5'-D(*DGP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DAP*DAP*DGP*DCP*DAP*DTP*DT)-3'), Integration host factor, ... Authors: Bao, Q, Droege, P, Davey, C.A. Deposit date: 2006-09-28 Release date: 2007-02-20 Last modified: 2024-05-29 Method: X-RAY DIFFRACTION (2.72 Å) Cite: A Divalent Metal-mediated Switch Controlling Protein-induced DNA Bending J.Mol.Biol., 367, 2007
4QTR	Computational design of co-assembling protein-DNA nanowires Descriptor: DNA (5'-D(P*CP*GP*GP*AP*AP*AP*TP*TP*AP*AP*AP*TP*TP*AP*CP*A)-3'), DNA (5'-D(P*GP*TP*GP*TP*AP*AP*TP*TP*TP*AP*AP*TP*TP*TP*CP*C)-3'), dualENH Authors: Mou, Y, Mayo, S.L. Deposit date: 2014-07-08 Release date: 2015-07-29 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (3.2 Å) Cite: Computational design of co-assembling protein-DNA nanowires. Nature, 525, 2015
7PBK	Vibriophage phiVC8 family A DNA polymerase (DpoZ), two conformations: thumb-exo open and thumb-exo closed Descriptor: DNA polymerase I Authors: Czernecki, D, Hu, H, Romoli, F, Delarue, M. Deposit date: 2021-08-02 Release date: 2021-11-17 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (2.8 Å) Cite: Structural dynamics and determinants of 2-aminoadenine specificity in DNA polymerase DpoZ of vibriophage phi VC8. Nucleic Acids Res., 49, 2021
1HCQ	THE CRYSTAL STRUCTURE OF THE ESTROGEN RECEPTOR DNA-BINDING DOMAIN BOUND TO DNA: HOW RECEPTORS DISCRIMINATE BETWEEN THEIR RESPONSE ELEMENTS Descriptor: DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP*CP*CP*T P*G)-3'), DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*TP*GP*TP*GP*AP*CP*CP*T P*G)-3'), PROTEIN (ESTROGEN RECEPTOR), ... Authors: Schwabe, J.W.R, Chapman, L, Finch, J.T, Rhodes, D. Deposit date: 1995-01-04 Release date: 1995-11-23 Last modified: 2024-11-06 Method: X-RAY DIFFRACTION (2.4 Å) Cite: The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements. Cell(Cambridge,Mass.), 75, 1993
4TUP	Structure of human DNA polymerase beta complexed with GG as the template (GG0b) in a 1-nucleotide gapped DNA Descriptor: DNA (5'-D(*CP*CP*CP*AP*CP*GP*GP*CP*CP*CP*AP*TP*CP*AP*CP*C)-3'), DNA (5'-D(*GP*GP*TP*GP*AP*TP*GP*GP*GP*C)-3'), DNA (5'-D(P*GP*TP*GP*GP*G)-3'), ... Authors: Koag, M.C, Lee, S. Deposit date: 2014-06-24 Release date: 2014-10-01 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Structural Basis for the Inefficient Nucleotide Incorporation Opposite Cisplatin-DNA Lesion by Human DNA Polymerase beta. J.Biol.Chem., 289, 2014
1OCT	CRYSTAL STRUCTURE OF THE OCT-1 POU DOMAIN BOUND TO AN OCTAMER SITE: DNA RECOGNITION WITH TETHERED DNA-BINDING MODULES Descriptor: DNA (5'-D(*AP*CP*CP*TP*TP*AP*TP*TP*TP*GP*CP*AP*TP*AP*C)-3'), DNA (5'-D(*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*TP*AP*AP*GP*G)-3'), PROTEIN (OCT-1 POU DOMAIN) Authors: Klemm, J.D, Rould, M.A, Aurora, R, Herr, W, Pabo, C.O. Deposit date: 1994-05-09 Release date: 1994-08-31 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (3 Å) Cite: Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell(Cambridge,Mass.), 77, 1994
8V6G	DNA initiation complex (configuration 1) of Xenopus laevis DNA polymerase alpha-primase Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA polymerase alpha catalytic subunit, DNA polymerase alpha subunit B, ... Authors: Mullins, E.A, Durie, C.L, Ohi, M.D, Chazin, W.J, Eichman, B.F. Deposit date: 2023-12-01 Release date: 2023-12-20 Last modified: 2024-05-29 Method: ELECTRON MICROSCOPY (11.16 Å) Cite: A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase. Nat.Struct.Mol.Biol., 31, 2024
8V6H	DNA initiation complex (configuration 2) of Xenopus laevis DNA polymerase alpha-primase Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA polymerase alpha catalytic subunit, DNA polymerase alpha subunit B, ... Authors: Mullins, E.A, Durie, C.L, Ohi, M.D, Chazin, W.J, Eichman, B.F. Deposit date: 2023-12-01 Release date: 2023-12-20 Last modified: 2024-05-29 Method: ELECTRON MICROSCOPY (11.11 Å) Cite: A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase. Nat.Struct.Mol.Biol., 31, 2024
7OPL	CryoEM structure of DNA Polymerase alpha - primase bound to SARS CoV nsp1 Descriptor: DNA polymerase alpha catalytic subunit, DNA polymerase alpha subunit B, DNA primase large subunit, ... Authors: Kilkenny, M.L, Pellegrini, L. Deposit date: 2021-06-01 Release date: 2021-11-10 Last modified: 2024-07-17 Method: ELECTRON MICROSCOPY (4.12 Å) Cite: Structural basis for the interaction of SARS-CoV-2 virulence factor nsp1 with DNA polymerase alpha-primase. Protein Sci., 31, 2022
6N2S	Ternary complex crystal structure of DNA polymerase Beta with 5-carboxy-dC (5-caC) at the templating position Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine, DNA (5'-D(*CP*CP*GP*AP*CP*(1CC)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), ... Authors: Batra, V.K, Wilson, S.H. Deposit date: 2018-11-14 Release date: 2019-03-27 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (2.457 Å) Cite: Molecular basis for the faithful replication of 5-methylcytosine and its oxidized forms by DNA polymerase beta. J.Biol.Chem., 294, 2019
1LBG	LACTOSE OPERON REPRESSOR BOUND TO 21-BASE PAIR SYMMETRIC OPERATOR DNA, ALPHA CARBONS ONLY Descriptor: DNA (5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3'), PROTEIN (LACTOSE OPERON REPRESSOR) Authors: Lewis, M, Chang, G, Horton, N.C, Kercher, M.A, Pace, H.C, Lu, P. Deposit date: 1996-01-03 Release date: 1996-02-17 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (4.8 Å) Cite: Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science, 271, 1996

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