PDB: 46169 resultsInfo pagesStatus searchChemie searchBIRD

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4EZ9	Bacillus DNA Polymerase I Large Fragment Complex 2 Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE, DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3'), ... Authors: Wang, W, Beese, L.S. Deposit date: 2012-05-02 Release date: 2013-07-24 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.64 Å) Cite: Structures of a High-fidelity DNA Polymerase to be published
3GFI	Crystal structure of ST1710 complexed with its promoter DNA Descriptor: 146aa long hypothetical transcriptional regulator, 5'-D(*TP*AP*AP*CP*AP*AP*TP*AP*GP*CP*AP*AP*A)-3', 5'-D(*TP*TP*GP*CP*TP*AP*TP*TP*GP*T)-3' Authors: Kumarevel, T, Tanaka, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) Deposit date: 2009-02-26 Release date: 2009-08-25 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (2.1 Å) Cite: ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators. Nucleic Acids Res., 37, 2009
3PW2	Ternary complex of Aflatoxin B1 Adduct modified DNA (AFB1-FAPY) with DNA Polymerase IV and incoming dTTP Descriptor: CALCIUM ION, DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'), DNA (5'-D(*TP*TP*(PVX)P*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'), ... Authors: Banerjee, S. Deposit date: 2010-12-07 Release date: 2011-08-10 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (2.74 Å) Cite: Bypass of Aflatoxin B(1) Adducts by the Sulfolobus solfataricus DNA Polymerase IV. J.Am.Chem.Soc., 133, 2011
3PW5	Ternary complex of Aflatoxin B1 Adduct modified DNA (AFB1-N7-Gua) with DNA Polymerase IV and incoming dTTP Descriptor: 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1, CALCIUM ION, DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'), ... Authors: Banerjee, S. Deposit date: 2010-12-07 Release date: 2011-08-10 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (3 Å) Cite: Bypass of Aflatoxin B(1) Adducts by the Sulfolobus solfataricus DNA Polymerase IV. J.Am.Chem.Soc., 133, 2011
3PW4	Ternary complex of Aflatoxin B1 Adduct modified DNA (AFB1-N7-Gua) with DNA Polymerase IV and incoming dATP Descriptor: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1, CALCIUM ION, ... Authors: Banerjee, S. Deposit date: 2010-12-07 Release date: 2011-08-10 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (2.9 Å) Cite: Bypass of Aflatoxin B(1) Adducts by the Sulfolobus solfataricus DNA Polymerase IV. J.Am.Chem.Soc., 133, 2011
4DOC	Ternary complex of dna polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding of S-isomer Descriptor: 5'-O-[(R)-{[(S)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine, C C G A C C G C G C A T C A G C, CHLORIDE ION, ... Authors: Batra, V.K. Deposit date: 2012-02-09 Release date: 2012-06-13 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.949 Å) Cite: Beta,gamma-CHF- and beta,gamma-CHCl-dGTP Diastereomers: Synthesis, Discrete (31)P NMR Signatures, and Absolute Configurations of New Stereochemical Probes for DNA Polymerases J.Am.Chem.Soc., 134, 2012
3PW0	Ternary complex of Aflatoxin B1 Adduct modified DNA (AFB1-FAPY) with DNA Polymerase IV and incoming dATP Descriptor: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'), ... Authors: Banerjee, S. Deposit date: 2010-12-07 Release date: 2011-08-10 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (2.91 Å) Cite: Bypass of Aflatoxin B(1) Adducts by the Sulfolobus solfataricus DNA Polymerase IV. J.Am.Chem.Soc., 133, 2011
3PW7	Ternary complex of Aflatoxin B1 Adduct modified DNA (AFB1-N7-Gua) with DNA Polymerase IV and incoming dCTP Descriptor: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1, CALCIUM ION, ... Authors: Banerjee, S. Deposit date: 2010-12-07 Release date: 2011-08-10 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (2.9 Å) Cite: Bypass of Aflatoxin B(1) Adducts by the Sulfolobus solfataricus DNA Polymerase IV. J.Am.Chem.Soc., 133, 2011
4EZ6	Bacillus DNA Polymerase I Large Fragment Complex 1 Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*CP*AP*TP*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'), ... Authors: Wang, W, Beese, L.S. Deposit date: 2012-05-02 Release date: 2013-07-24 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.64 Å) Cite: Structures of a High-fidelity DNA Polymerase to be published
4JV1	Ternary complex of gamma-OHPDG adduct modified dna with dna (-1 primer) polymerase iv and incoming dgtp Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'), ... Authors: Banerjee, S, Shanmugam, G, Stone, M.P. Deposit date: 2013-03-25 Release date: 2013-08-28 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.3 Å) Cite: Ring-Opening of the gamma-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4. Chem.Res.Toxicol., 26, 2013
8OSJ	Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Descriptor: Basic helix-loop-helix ARNT-like protein 1, Circadian locomoter output cycles protein kaput, DNA (124-MER), ... Authors: Michael, A.K, Stoos, L, Kempf, G, Cavadini, S, Thoma, N.H. Deposit date: 2023-04-19 Release date: 2023-05-24 Last modified: 2024-07-24 Method: ELECTRON MICROSCOPY (6.2 Å) Cite: Cooperation between bHLH transcription factors and histones for DNA access. Nature, 619, 2023
4JUZ	Ternary complex of gamma-OHPDG adduct modified dna (zero primer) with dna polymerase iv and incoming dgtp Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3'), ... Authors: Banerjee, S, Shanmugam, G, Stone, M.P. Deposit date: 2013-03-25 Release date: 2013-08-28 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.65 Å) Cite: Ring-Opening of the gamma-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4. Chem.Res.Toxicol., 26, 2013
4JV2	Ternary complex of gamma-OHPDG adduct modified dna with dna (-1 primer) polymerase iv and incoming datp Descriptor: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'), ... Authors: Banerjee, S, Shanmugam, G, Stone, M.P. Deposit date: 2013-03-25 Release date: 2013-08-28 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.74 Å) Cite: Ring-Opening of the gamma-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4. Chem.Res.Toxicol., 26, 2013
4JV0	Ring-Opening of the -OH-PdG Adduct in Ternary Complexes with the Sulfolobus solfataricus DNA polymerase Dpo4 Descriptor: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3'), ... Authors: Banerjee, S, Shanmugam, G, Stone, M.P. Deposit date: 2013-03-25 Release date: 2013-08-28 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.95 Å) Cite: Ring-Opening of the gamma-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4. Chem.Res.Toxicol., 26, 2013
3MFK	Ets1 complex with stromelysin-1 promoter DNA Descriptor: Protein C-ets-1, stromelysin-1 promoter DNA Authors: Babayeva, N.D, Mino, K, Tahirov, T.H. Deposit date: 2010-04-02 Release date: 2010-08-18 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (3 Å) Cite: Structural basis of Ets1 cooperative binding to palindromic sequences on stromelysin-1 promoter DNA. Cell Cycle, 9, 2010
8J0R	Structure of human TFAP2A in complex with DNA Descriptor: DI(HYDROXYETHYL)ETHER, DNA (5'-D(*CP*TP*GP*CP*CP*TP*CP*AP*GP*GP*CP*AP*C)-3'), DNA (5'-D(*GP*TP*GP*CP*CP*TP*GP*AP*GP*GP*CP*AP*G)-3'), ... Authors: Liu, K, Xiao, Y.Q, Li, W.F, Min, J.R. Deposit date: 2023-04-11 Release date: 2023-07-05 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (2.1 Å) Cite: Structural basis for specific DNA sequence motif recognition by the TFAP2 transcription factors. Nucleic Acids Res., 51, 2023
4LNQ	Crystal structure of Ifi202 HINa domain in complex with 20bp dsDNA Descriptor: 20bp DNA, Interferon-activable protein 202 Authors: Li, H, Wang, Z.-X, Wu, J.-W. Deposit date: 2013-07-12 Release date: 2014-01-08 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2 Å) Cite: Structural mechanism of DNA recognition by the p202 HINa domain: insights into the inhibition of Aim2-mediated inflammatory signalling. Acta Crystallogr F Struct Biol Commun, 70, 2014
2F03	Crystal structure of tetrameric restriction endonuclease SfiI in complex with cognate DNA (partial bound form) Descriptor: CALCIUM ION, DNA (5'-D(*AP*AP*TP*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*AP*CP*AP*T)-3'), DNA (5'-D(*AP*TP*G*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*TP*AP*TP*T)-3'), ... Authors: Aggarwal, A.K, Vanamee, E.S, Viadiu, H Deposit date: 2005-11-11 Release date: 2007-01-16 Last modified: 2015-09-09 Method: X-RAY DIFFRACTION (3.05 Å) Cite: A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA. Embo J., 24, 2005
1KO9	Native Structure of the Human 8-oxoguanine DNA Glycosylase hOGG1 Descriptor: 8-oxoguanine DNA glycosylase, SULFATE ION Authors: Bjoras, M, Seeberg, E, Luna, L, Pearl, L.H, Barrett, T.E. Deposit date: 2001-12-20 Release date: 2002-01-09 Last modified: 2023-08-16 Method: X-RAY DIFFRACTION (2.15 Å) Cite: Reciprocal "flipping" underlies substrate recognition and catalytic activation by the human 8-oxo-guanine DNA glycosylase. J.Mol.Biol., 317, 2002
4DOB	Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate: Stereoselective binding of R-isomer Descriptor: 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine, C C G A C C G C G C A T C A G C, CHLORIDE ION, ... Authors: Batra, V.K. Deposit date: 2012-02-09 Release date: 2012-06-13 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.05 Å) Cite: Beta,Gamma-CHF- and beta,gamma-CHCl-dGTP Diastereomers: Synthesis, Discrete (31)P NMR Signatures, and Absolute Configurations of New Stereochemical Probes for DNA Polymerases J.Am.Chem.Soc., 134, 2012
7OXA	Target-bound SpCas9 complex with AAVS1 chimeric RNA-DNA guide Descriptor: AAVS1 non-target DNA strand, AAVS1 target DNA strand, CRISPR-associated endonuclease Cas9/Csn1, ... Authors: Donohoue, P, Pacesa, M, Lau, E, Vidal, B, Irby, M.J, Nyer, D.B, Rotstein, T, Banh, L, Toh, M.T, Gibson, J, Kohrs, B, Baek, K, Owen, A.L.G, Slorach, E.M, van Overbeek, M, Fuller, C.K, May, A.P, Jinek, M, Cameron, P. Deposit date: 2021-06-22 Release date: 2021-09-15 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (2.15 Å) Cite: Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells. Mol.Cell, 81, 2021
7OX7	Target-bound SpCas9 complex with TRAC chimeric RNA-DNA guide Descriptor: CRISPR-associated endonuclease Cas9/Csn1, MAGNESIUM ION, POTASSIUM ION, ... Authors: Donohoue, P, Pacesa, M, Lau, E, Vidal, B, Irby, M.J, Nyer, D.B, Rotstein, T, Banh, L, Toh, M.T, Gibson, J, Kohrs, B, Baek, K, Owen, A.L.G, Slorach, E.M, van Overbeek, M, Fuller, C.K, May, A.P, Jinek, M, Cameron, P. Deposit date: 2021-06-22 Release date: 2021-09-15 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (2.6 Å) Cite: Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells. Mol.Cell, 81, 2021
4I9Q	Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine, CALCIUM ION, DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3'), ... Authors: Guja, K.E, Jacewicz, A, Trzemecka, A, Plochocka, D, Yakubovskaya, E, Bebenek, A, Garcia-Diaz, M. Deposit date: 2012-12-05 Release date: 2013-10-09 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.3 Å) Cite: A Remote Palm Domain Residue of RB69 DNA Polymerase Is Critical for Enzyme Activity and Influences the Conformation of the Active Site. Plos One, 8, 2013
6IUD	Structure of Helicobacter pylori Soj-ADP complex bound to DNA Descriptor: ADENOSINE-5'-DIPHOSPHATE, DNA (5'-D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP*GP*A)-3'), DNA (5'-D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP*CP*T)-3'), ... Authors: Yen, C.Y, Chu, C.H, Sun, Y.J. Deposit date: 2018-11-28 Release date: 2019-02-13 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (2.506 Å) Cite: Crystal structures of HpSoj-DNA complexes and the nucleoid-adaptor complex formation in chromosome segregation. Nucleic Acids Res., 47, 2019
1NKE	A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A CYTOSINE-THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP. Descriptor: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, DNA POLYMERASE I, DNA PRIMER 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

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