PDB: 264 resultsInfo pagesStatus searchChemie searchBIRD

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4YFU	Crystal structure of open Bacillus fragment DNA polymerase bound to DNA and dTTP Descriptor: DNA polymerase, Primer DNA, SULFATE ION, ... Authors: Wu, E.Y. Deposit date: 2015-02-25 Release date: 2015-07-22 Last modified: 2022-04-13 Method: X-RAY DIFFRACTION (1.5 Å) Cite: The Closing Mechanism of DNA Polymerase I at Atomic Resolution. Structure, 23, 2015
3PV8	Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddTTP-dA in Closed Conformation Descriptor: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE, DNA (5'-D(*C*AP*TP*AP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3'), DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3'), ... Authors: Wang, W, Beese, L.S. Deposit date: 2010-12-06 Release date: 2011-10-19 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (1.52 Å) Cite: Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Proc.Natl.Acad.Sci.USA, 108, 2011
6FBC	KlenTaq DNA polymerase processing a modified primer - bearing the modification at the 3'-terminus of the primer. Descriptor: 1,2-ETHANEDIOL, 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine, DNA (5'-D(*AP*AP*AP*CP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), ... Authors: Kropp, H.M, Diederichs, K, Marx, A. Deposit date: 2017-12-19 Release date: 2018-09-26 Last modified: 2019-08-14 Method: X-RAY DIFFRACTION (1.54 Å) Cite: Snapshots of a modified nucleotide moving through the confines of a DNA polymerase. Proc. Natl. Acad. Sci. U.S.A., 115, 2018
2HHV	T:O6-methyl-guanine in the polymerase-2 basepair position Descriptor: 5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*CP*TP*TP*G)-3', 5'-D(*GP*TP*AP*CP*(6OG)P*AP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3', DNA Polymerase I, ... Authors: Warren, J.J, Forsberg, L.J, Beese, L.S. Deposit date: 2006-06-28 Release date: 2006-12-12 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (1.55 Å) Cite: The structural basis for the mutagenicity of O6-methyl-guanine lesions. Proc.Natl.Acad.Sci.Usa, 103, 2006
4BWJ	KlenTaq mutant in complex with DNA and ddCTP Descriptor: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, 5'-D(*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*CP)-3', 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOCP)-3', ... Authors: Blatter, N, Bergen, K, Welte, W, Diederichs, K, Marx, A. Deposit date: 2013-07-03 Release date: 2013-09-18 Last modified: 2023-12-20 Method: X-RAY DIFFRACTION (1.55 Å) Cite: Structure and Function of an RNA-Reading Thermostable DNA Polymerase. Angew.Chem.Int.Ed.Engl., 52, 2013
4C8M	Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair d5SICS-dNaM at the postinsertion site (sequence context 2) Descriptor: GLYCEROL, LARGE FRAGMENT OF TAQ DNA POLYMERASE I, MAGNESIUM ION, ... Authors: Betz, K, Malyshev, D.A, Lavergne, T, Welte, W, Diederichs, K, Romesberg, F.E, Marx, A. Deposit date: 2013-10-01 Release date: 2013-12-11 Last modified: 2017-08-23 Method: X-RAY DIFFRACTION (1.568 Å) Cite: Structural Insights Into DNA Replication without Hydrogen Bonds. J.Am.Chem.Soc., 135, 2013
4F3O	DNA Polymerase I Large Fragment Complex 5 Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE, DNA (5'-D(*C*AP*TP*GP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3'), ... Authors: Wang, W, Beese, L.S. Deposit date: 2012-05-09 Release date: 2013-07-24 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.57 Å) Cite: Structures of a High-fidelity DNA Polymerase to be published
4E0D	Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ... Authors: Wang, W, Beese, L.S. Deposit date: 2012-03-02 Release date: 2012-06-06 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.58 Å) Cite: Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. J.Biol.Chem., 287, 2012
3PX4	Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA Mismatch (wobble) in Ajar Conformation Descriptor: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, DNA (5'-D(*CP*AP*TP*AP*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: 2010-12-09 Release date: 2011-10-19 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.582 Å) Cite: Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Proc.Natl.Acad.Sci.USA, 108, 2011
6DSW	Bst DNA polymerase I pre-chemistry (n) structure Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*G)-3'), DNA (5'-D(P*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'), ... Authors: Chim, N, Jackson, L.N, Chaput, J.C. Deposit date: 2018-06-14 Release date: 2018-10-31 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (1.589 Å) Cite: Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway. Elife, 7, 2018
6FBE	KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the third primer nucleotide. Descriptor: 1,2-ETHANEDIOL, 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine, DNA (5'-D(*AP*AP*AP*CP*GP*GP*GP*TP*GP*CP*GP*TP*GP*GP*TP*C)-3'), ... Authors: Kropp, H.M, Diederichs, K, Marx, A. Deposit date: 2017-12-19 Release date: 2018-09-26 Last modified: 2019-08-14 Method: X-RAY DIFFRACTION (1.589 Å) Cite: Snapshots of a modified nucleotide moving through the confines of a DNA polymerase. Proc. Natl. Acad. Sci. U.S.A., 115, 2018
3PX6	Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA Mismatch (tautomer) in Closed Conformation Descriptor: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, DNA (5'-D(*C*AP*TP*AP*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: 2010-12-09 Release date: 2011-10-19 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.59 Å) Cite: Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Proc.Natl.Acad.Sci.USA, 108, 2011
4DQQ	Ternary complex of Bacillus DNA Polymerase I Large Fragment E658A, DNA duplex, and rCTP (paired with dG of template) in presence of Mg2+ Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CYTIDINE-5'-TRIPHOSPHATE, ... 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 (1.595 Å) Cite: Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. J.Biol.Chem., 287, 2012
1NK4	GUANINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE 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 (1.6 Å) Cite: Structures of mismatch replication errors observed in a DNA polymerase. Cell(Cambridge,Mass.), 116, 2004
4F4K	DNA Polymerase I Large Fragment Complex 6 Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*CP*AP*TP*TP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'), ... Authors: Wang, W, Beese, L.S. Deposit date: 2012-05-10 Release date: 2013-07-24 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.6 Å) Cite: Structures of a High-fidelity DNA Polymerase to be published
1U4B	Extension of an adenine-8oxoguanine mismatch Descriptor: DNA polymerase I, DNA primer strand, DNA template strand with 8-oxoguanine, ... Authors: Hsu, G.W, Ober, M, Carell, T, Beese, L.S. Deposit date: 2004-07-23 Release date: 2004-09-14 Last modified: 2023-08-23 Method: X-RAY DIFFRACTION (1.6 Å) Cite: Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. Nature, 431, 2004
6MU4	Bst DNA polymerase I FANA/DNA binary complex Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3'), DNA polymerase I, ... Authors: Jackson, L.N, Chim, N, Chaput, J.C. Deposit date: 2018-10-22 Release date: 2019-06-05 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (1.62 Å) Cite: Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase. Nucleic Acids Res., 47, 2019
4F2R	DNA Polymerase I Large Fragment complex 3 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: 2012-05-08 Release date: 2013-07-24 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.63 Å) Cite: Structures of a High-fidelity DNA Polymerase to be published
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
4F8R	Bacillus DNA Polymerase I Large Fragment complex 7 Descriptor: DNA (5'-D(*CP*AP*TP*TP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'), DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'), DNA polymerase, ... Authors: Wang, W, Beese, L.S. Deposit date: 2012-05-17 Release date: 2013-08-07 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.64 Å) Cite: Structures of a High-fidelity DNA Polymerase to be published
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
4DFK	large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(N-(10-hydroxydecanoyl)-aminopentinyl)-2-dUTP Descriptor: 1,2-ETHANEDIOL, 2'-deoxy-5-{5-[(10-hydroxydecanoyl)amino]pent-1-yn-1-yl}uridine 5'-(tetrahydrogen triphosphate), 5'-d(AAAAGGCGCCGTGGTC)-3', ... Authors: Bergen, K, Steck, A, Struett, S, Baccaro, A, Welte, W, Diederichs, K, Marx, A. Deposit date: 2012-01-24 Release date: 2012-05-16 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.647 Å) Cite: Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates. J.Am.Chem.Soc., 134, 2012
1NJX	THYMINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE 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 (1.65 Å) Cite: Structures of mismatch replication errors observed in a DNA polymerase. Cell(Cambridge,Mass.), 116, 2004
4F2S	DNA Polymerase I Large Fragment complex 4 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: 2012-05-08 Release date: 2013-07-24 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.651 Å) Cite: Structures of a High-fidelity DNA Polymerase to be published
4DQS	Binary complex of Bacillus DNA Polymerase I Large Fragment and duplex DNA with rC in primer terminus paired with dG of template Descriptor: CYTIDINE-5'-TRIPHOSPHATE, DNA (5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'), DNA polymerase, ... 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 (1.66 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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