PDB: 13252 resultsInfo pagesStatus searchChemie searchBIRD

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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
6UES	Apo SAM-IV Riboswitch Descriptor: RNA (119-MER) Authors: Zhang, K, Li, S, Kappel, K, Pintilie, G, Su, Z, Mou, T, Schmid, M, Das, R, Chiu, W. Deposit date: 2019-09-23 Release date: 2019-12-18 Last modified: 2024-03-20 Method: ELECTRON MICROSCOPY (3.7 Å) Cite: Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 angstrom resolution. Nat Commun, 10, 2019
6UET	SAM-bound SAM-IV riboswitch Descriptor: RNA (119-MER), S-ADENOSYLMETHIONINE Authors: Zhang, K, Li, S, Kappel, K, Pintilie, G, Su, Z, Mou, T, Schmid, M, Das, R, Chiu, W. Deposit date: 2019-09-23 Release date: 2019-12-18 Last modified: 2024-03-20 Method: ELECTRON MICROSCOPY (4.1 Å) Cite: Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 angstrom resolution. Nat Commun, 10, 2019
5DKW	Ternary crystal structure of polymerase lambda with a GA mispair at the primer terminus with Ca2+ in the active Descriptor: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(*CP*AP*GP*TP*AP*C)-3'), ... Authors: Liu, M.S, Tsai, M.D. Deposit date: 2015-09-04 Release date: 2016-02-24 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (2.689 Å) Cite: Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda J.Am.Chem.Soc., 138, 2016
1OR7	Crystal Structure of Escherichia coli sigmaE with the Cytoplasmic Domain of its Anti-sigma RseA Descriptor: RNA polymerase sigma-E factor, Sigma-E factor negative regulatory protein Authors: Campbell, E.A, Tupy, J.L, Gruber, T.M, Wang, S, Sharp, M.M, Gross, C.A, Darst, S.A. Deposit date: 2003-03-12 Release date: 2003-04-15 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (2 Å) Cite: Crystal structure of Escherichia coli sigmaE with the cytoplasmic domain of its anti-sigma RseA. Mol.Cell, 11, 2003
2MQT	Solution NMR structure of the U5-primer binding site (U5-PBS) domain of murine leukemia virus RNA genome Descriptor: RNA (68-MER) Authors: D'Souza, V, Yildiz, Z. Deposit date: 2014-06-26 Release date: 2014-09-10 Last modified: 2024-05-01 Method: SOLUTION NMR Cite: A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing. Nature, 515, 2014
17RA	BRANCHPOINT HELIX FROM YEAST AND BINDING SITE FOR PHAGE GA/MS2 COAT PROTEINS, NMR, 12 STRUCTURES Descriptor: RNA Authors: Nikonowicz, E.P, Smith, J.S. Deposit date: 1998-08-04 Release date: 1999-04-20 Last modified: 2024-05-22 Method: SOLUTION NMR Cite: NMR structure and dynamics of an RNA motif common to the spliceosome branch-point helix and the RNA-binding site for phage GA coat protein. Biochemistry, 37, 1998
4DO9	Ternary complex of dna polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monofluoromethylene triphosphate: stereoselective binding of r-isomer Descriptor: 2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE, 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
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
3RRG	Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddGTP Descriptor: (5'-D(*AP*AP*AP*(3DR)P*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3'), 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, ... Authors: Marx, A, Diederichs, K, Obeid, S. Deposit date: 2011-04-29 Release date: 2012-02-15 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.3 Å) Cite: Amino Acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase. J.Biol.Chem., 287, 2012
3RRH	Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddTTP Descriptor: (5'-D(*AP*AP*AP*(3DR)P*AP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DT))-3'), ACETATE ION, ... Authors: Marx, A, Diederichs, K, Obeid, S. Deposit date: 2011-04-29 Release date: 2012-02-15 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Amino Acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase. J.Biol.Chem., 287, 2012
4QW8	TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND D-DCTP Descriptor: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(P*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3'), ... Authors: Gaur, V, Suo, Z. Deposit date: 2014-07-16 Release date: 2014-08-27 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.29 Å) Cite: Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase. Nucleic Acids Res., 42, 2014
4QWA	TERNARY CRYSTAL STRUCTURES OF A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS in COMPLEX WITH DNA AND (-)3TC-DP Descriptor: CALCIUM ION, DNA (5'-D(P*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3'), DNA (5'-D(P*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3'), ... Authors: Gaur, V, Suo, Z. Deposit date: 2014-07-16 Release date: 2014-08-27 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase. Nucleic Acids Res., 42, 2014
3RR8	Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddGTP Descriptor: (5'-D(*AP*AP*AP*(3DR)P*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3'), 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, ... Authors: Marx, A, Diederichs, K, Obeid, S. Deposit date: 2011-04-29 Release date: 2012-02-15 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Amino Acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase. J.Biol.Chem., 287, 2012
2M23	NMR solution structure of the d3'-hairpin of the group II intron Sc.ai5gamma including EBS1 bound to IBS1 Descriptor: RNA (29-MER), RNA_(5'-R(*CP*AP*GP*UP*GP*UP*C)-3')_ Authors: Kruschel, D, Skilandat, M, Sigel, R.K.O. Deposit date: 2012-12-12 Release date: 2013-12-18 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: NMR structure of the 5' splice site in the group IIB intron Sc.ai5 gamma--conformational requirements for exon-intron recognition. Rna, 20, 2014
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
2AHQ	Solution Structure of the C-terminal RpoN Domain of Sigma-54 from Aquifex aeolicus Descriptor: RNA polymerase sigma factor RpoN Authors: Doucleff, M, Malak, L.T, Pelton, J.G, Wemmer, D.E. Deposit date: 2005-07-28 Release date: 2005-10-11 Last modified: 2024-05-22 Method: SOLUTION NMR Cite: The C-terminal RpoN domain of sigma54 forms an unpredicted helix-turn-helix motif similar to domains of sigma70. J.Biol.Chem., 280, 2005
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
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
4R65	Ternary complex crystal structure of R258A mutant of DNA polymerase Beta Descriptor: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... Authors: Batra, V.K, Beard, W.A, Wilson, S.H. Deposit date: 2014-08-22 Release date: 2014-10-08 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (1.95 Å) Cite: Substrate-induced DNA Polymerase beta Activation. J.Biol.Chem., 289, 2014
4DS4	Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and rCTP in presence of Mn2+ Descriptor: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3'), DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3'), DNA polymerase, ... Authors: Wang, W, Beese, L.S. Deposit date: 2012-02-17 Release date: 2012-06-06 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.681 Å) Cite: Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. J.Biol.Chem., 287, 2012
4DQP	Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG of template) Descriptor: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, DNA (5'-D(*C*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3'), DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3'), ... Authors: Wang, W, Beese, L.S. Deposit date: 2012-02-16 Release date: 2012-06-06 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.74 Å) Cite: Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. J.Biol.Chem., 287, 2012
4DSE	Ternary complex of Bacillus DNA Polymerase I Large Fragment F710Y, DNA duplex, and rCTP (paired with dG of template) in presence of Mg2+ Descriptor: CYTIDINE-5'-TRIPHOSPHATE, DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3'), DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3'), ... Authors: Wang, W, Beese, L.S. Deposit date: 2012-02-18 Release date: 2012-06-06 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.67 Å) Cite: Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. J.Biol.Chem., 287, 2012
4DQI	Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and dCTP (paired with dG of template) Descriptor: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, DNA (5'-D(*C*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3'), DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3'), ... Authors: Wang, W, Beese, L.S. Deposit date: 2012-02-15 Release date: 2012-06-06 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.69 Å) Cite: Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. J.Biol.Chem., 287, 2012
4DS5	Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and rCTP in presence of Mg2+ Descriptor: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3'), DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*C)-3'), DNA polymerase, ... Authors: Wang, W, Beese, L.S. Deposit date: 2012-02-17 Release date: 2012-06-06 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.68 Å) Cite: Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. J.Biol.Chem., 287, 2012

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