PDB: 47011 resultsInfo pagesStatus searchChemie searchBIRD

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8K8A	Crystal structure of NFIL3 in complex with TTACGTAA DNA Descriptor: DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*G)-3'), Nuclear factor interleukin-3-regulated protein Authors: Min, J.R, Chen, S.Z, Liu, K. Deposit date: 2023-07-29 Release date: 2024-03-06 Last modified: 2024-03-27 Method: X-RAY DIFFRACTION (2.07 Å) Cite: Structural basis for specific DNA sequence recognition by the transcription factor NFIL3. J.Biol.Chem., 300, 2024
5TZV	Binary complex crystal structure of DNA Polymerase Beta with G:T mismatch at the primer terminus 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*T)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... Authors: Wilson, S.H, Batra, V.K. Deposit date: 2016-11-22 Release date: 2016-12-07 Last modified: 2023-10-04 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
4O5C	Structure of human DNA polymerase complexed with N7-MG as the template base in a 1-nucleotide gapped DNA Descriptor: 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'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... Authors: Koag, M.C, Lee, S. Deposit date: 2013-12-19 Release date: 2014-07-02 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.363 Å) Cite: Transition-state destabilization reveals how human DNA polymerase beta proceeds across the chemically unstable lesion N7-methylguanine. Nucleic Acids Res., 42, 2014
6NHX	mycobacterial DNA ligase D complexed with ATP and MES Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ADENOSINE-5'-TRIPHOSPHATE, ATP-dependent DNA ligase Authors: Shuman, S, Unciuleac, M, Goldgur, Y. Deposit date: 2018-12-24 Release date: 2019-02-13 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (1.4 Å) Cite: Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates. J. Biol. Chem., 294, 2019
1NKC	A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER FIVE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, DTTP, AND DATP. Descriptor: DNA POLYMERASE I, DNA PRIMER STRAND, DNA TEMPLATE STRAND, ... Authors: Johnson, S.J, Beese, L.S. Deposit date: 2003-01-02 Release date: 2004-03-30 Last modified: 2023-08-16 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Structures of mismatch replication errors observed in a DNA polymerase. Cell(Cambridge,Mass.), 116, 2004
5L6L	Structure of Caulobacter crescentus VapBC1 bound to operator DNA Descriptor: DNA (27-MER), Ribonuclease VapC, VapB family protein Authors: Bendtsen, K.L, Xu, K, Luckmann, M, Brodersen, D.E. Deposit date: 2016-05-30 Release date: 2016-12-28 Last modified: 2024-10-16 Method: X-RAY DIFFRACTION (2.7 Å) Cite: Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding. Nucleic Acids Res., 45, 2017
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
6NHZ	mycobacterial DNA ligase D complexed with ATP and Mg Descriptor: ADENOSINE-5'-TRIPHOSPHATE, ATP-dependent DNA ligase, MAGNESIUM ION Authors: Shuman, S, Unciuleac, M, Goldgur, Y. Deposit date: 2018-12-24 Release date: 2019-02-13 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates. J. Biol. Chem., 294, 2019
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
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
5X07	Crystal structure of FOXA2 DNA binding domain bound to a full consensus DNA site Descriptor: DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3'), DNA (5'-D(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3'), Hepatocyte nuclear factor 3-beta Authors: Li, J, Guo, M, Zhou, Z, Jiang, L, Chen, X, Qu, L, Wu, D, Chen, Z, Chen, L, Chen, Y. Deposit date: 2017-01-20 Release date: 2017-08-16 Last modified: 2017-09-27 Method: X-RAY DIFFRACTION (2.796 Å) Cite: Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site Biochemistry, 56, 2017
7KR3	Human DNA Ligase 1(E346A/E592A) Bound to a bulged DNA substrate Descriptor: ACETATE ION, ADENOSINE MONOPHOSPHATE, DNA (5'-D(*AP*AP*TP*GP*TP*CP*TP*GP*CP*CP*CP*C)-3'), ... Authors: Tumbale, P.P, Williams, R.S. Deposit date: 2020-11-18 Release date: 2021-02-03 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (2.778 Å) Cite: High-fidelity DNA ligation enforces accurate Okazaki fragment maturation during DNA replication. Nat Commun, 12, 2021
7KR4	Human DNA Ligase 1(E346A/E592A) Bound to a nicked DNA substrate control duplex Descriptor: ACETATE ION, ADENOSINE MONOPHOSPHATE, DNA (5'-D(*AP*AP*TP*GP*TP*CP*TP*GP*CP*CP*C)-3'), ... Authors: Tumbale, P.P, Williams, R.S. Deposit date: 2020-11-18 Release date: 2021-02-03 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (2.2 Å) Cite: High-fidelity DNA ligation enforces accurate Okazaki fragment maturation during DNA replication. Nat Commun, 12, 2021
5U8G	DNA Polymerase Beta crystallized in PEG 400 Descriptor: CHLORIDE ION, 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*C)-3'), ... Authors: Eckenroth, B.E, Doublie, S. Deposit date: 2016-12-14 Release date: 2017-04-26 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (2.166 Å) Cite: Remote Mutations Induce Functional Changes in Active Site Residues of Human DNA Polymerase beta. Biochemistry, 56, 2017
1AHD	DETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX Descriptor: DNA (5'-D(*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3'), DNA (5'-D(*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3'), Homeotic protein antennapedia Authors: Billeter, M, Qian, Y.Q, Otting, G, Muller, M, Gehring, W.J, Wuthrich, K. Deposit date: 1993-04-02 Release date: 1993-10-31 Last modified: 2024-04-10 Method: SOLUTION NMR Cite: Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex. J.Mol.Biol., 234, 1993
4GFH	Topoisomerase II-DNA-AMPPNP complex Descriptor: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3'), DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3'), DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3'), ... Authors: Schmidt, B.H, Osheroff, N, Berger, J.M. Deposit date: 2012-08-03 Release date: 2012-10-03 Last modified: 2019-07-31 Method: X-RAY DIFFRACTION (4.408 Å) Cite: Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity. Nat.Struct.Mol.Biol., 19, 2012
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
2ZO0	mouse NP95 SRA domain DNA specific complex 1 Descriptor: 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'), E3 ubiquitin-protein ligase UHRF1 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 (2.19 Å) Cite: The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix Nature, 455, 2008
3OGU	DNA Polymerase beta mutant 5P20 complexed with 6bp of DNA Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 5'-D(*CP*AP*TP*CP*TP*G)-3', 5'-D(P*CP*AP*GP*AP*TP*G)-3', ... Authors: Marx, A, Diederichs, K, Bergen, K. Deposit date: 2010-08-17 Release date: 2010-11-24 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (1.845 Å) Cite: Human DNA polymerase beta mutations allowing efficient abasic site bypass. J.Biol.Chem., 286, 2011
4NXZ	DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable TTP with manganese in the active site Descriptor: 5'-D(*CP*CP*GP*AP*CP*(6OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... Authors: Koag, M.-C, Min, K, Monzingo, A.F, Lee, S. Deposit date: 2013-12-09 Release date: 2014-04-16 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.557 Å) Cite: Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase beta. J.Am.Chem.Soc., 136, 2014
4NY8	DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, 5'-D(*CP*CP*GP*AP*CP*(6OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3', ... Authors: Koag, M.-C, Min, K, Monzingo, A.F, Lee, S. Deposit date: 2013-12-10 Release date: 2014-04-16 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.246 Å) Cite: Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase beta. J.Am.Chem.Soc., 136, 2014
1ZQF	DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CSCL (150 MILLIMOLAR) Descriptor: CESIUM ION, DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3'), DNA (5'-D(*TP*CP*TP*AP*AP*TP*G)-3'), ... Authors: Pelletier, H, Sawaya, M.R. Deposit date: 1996-04-12 Release date: 1996-11-15 Last modified: 2023-08-02 Method: X-RAY DIFFRACTION (2.9 Å) Cite: Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis. Biochemistry, 35, 1996
1ZQB	DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF BACL2 (150 MILLIMOLAR) Descriptor: BARIUM ION, DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3'), DNA (5'-D(*TP*CP*TP*AP*AP*TP*G)-3'), ... Authors: Pelletier, H, Sawaya, M.R. Deposit date: 1996-04-12 Release date: 1996-11-15 Last modified: 2023-08-02 Method: X-RAY DIFFRACTION (3.2 Å) Cite: Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis. Biochemistry, 35, 1996
1ZQJ	DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CACL2 (15 MILLIMOLAR) AND MGCL2 (15 MILLIMOLAR) Descriptor: CALCIUM ION, DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3'), DNA (5'-D(*TP*CP*TP*AP*AP*TP*G)-3'), ... Authors: Pelletier, H, Sawaya, M.R. Deposit date: 1996-04-12 Release date: 1996-11-15 Last modified: 2023-08-02 Method: X-RAY DIFFRACTION (3.3 Å) Cite: Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis. Biochemistry, 35, 1996
1ZQE	DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CRCL3 (SATURATED SOLUTION) Descriptor: CHROMIUM ION, DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3'), DNA (5'-D(*TP*CP*TP*AP*AP*TP*G)-3'), ... Authors: Pelletier, H, Sawaya, M.R. Deposit date: 1996-04-12 Release date: 1996-04-12 Last modified: 2023-08-02 Method: X-RAY DIFFRACTION (3.7 Å) Cite: Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis. Biochemistry, 35, 1996

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