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6N9V
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BU of 6n9v by Molmil
Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS1)
Descriptor: DNA primase/helicase, DNA-directed DNA polymerase, MAGNESIUM ION, ...
Authors:Gao, Y, Fox, T, Val, N, Yang, W.
Deposit date:2018-12-04
Release date:2019-03-06
Last modified:2019-12-18
Method:ELECTRON MICROSCOPY (4 Å)
Cite:Structures and operating principles of the replisome.
Science, 363, 2019
6N9U
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BU of 6n9u by Molmil
Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) interacting with primase domains of two gp4 subunits bound to an RNA/DNA hybrid and dTTP (from LagS1)
Descriptor: DNA (44-MER), DNA primase/helicase, DNA-directed DNA polymerase, ...
Authors:Gao, Y, Fox, T, Val, N, Yang, W.
Deposit date:2018-12-04
Release date:2019-03-06
Last modified:2019-12-18
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:Structures and operating principles of the replisome.
Science, 363, 2019
5Z3N
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BU of 5z3n by Molmil
Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base 5fC pair with dA
Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*AP*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*(5FC)P*GP*GP*TP*C)-3'), DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'), ...
Authors:Zeng, H, Mondal, M, Song, R.Y, Zhang, J, Xia, B, Gao, Y.Q, Yi, C.Q.
Deposit date:2018-01-08
Release date:2018-11-21
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry.
Angew. Chem. Int. Ed. Engl., 58, 2019
6N9X
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BU of 6n9x by Molmil
Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS3)
Descriptor: DNA primase/helicase, DNA-directed DNA polymerase, MAGNESIUM ION, ...
Authors:Gao, Y, Fox, T, Val, N, Yang, W.
Deposit date:2018-12-04
Release date:2019-03-06
Last modified:2019-12-18
Method:ELECTRON MICROSCOPY (4.1 Å)
Cite:Structures and operating principles of the replisome.
Science, 363, 2019
6N9W
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BU of 6n9w by Molmil
Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS2)
Descriptor: DNA primase/helicase, DNA-directed DNA polymerase, MAGNESIUM ION, ...
Authors:Gao, Y, Cui, Y, Zhou, Z, Yang, W.
Deposit date:2018-12-04
Release date:2019-03-06
Last modified:2019-12-18
Method:ELECTRON MICROSCOPY (4 Å)
Cite:Structures and operating principles of the replisome.
Science, 363, 2019
3RR7
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BU of 3rr7 by Molmil
Binary Structure of the large fragment of Taq DNA polymerase bound to an abasic site
Descriptor: (5'-D(*AP*AP*AP*(3DR)P*GP*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*(DOC))-3'), DNA polymerase I, ...
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 (1.95 Å)
Cite:Amino Acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase.
J.Biol.Chem., 287, 2012
3RR8
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BU of 3rr8 by Molmil
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
3RTV
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BU of 3rtv by Molmil
Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer/template DNA
Descriptor: (5'-D(*AP*AP*AP*GP*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'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, ...
Authors:Marx, A, Diederichs, K, Betz, K.
Deposit date:2011-05-04
Release date:2012-05-30
Last modified:2023-09-13
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.
Nat.Chem.Biol., 8, 2012
3T3F
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BU of 3t3f by Molmil
Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and dNITP
Descriptor: 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO -1H-INDOLE, 5'-D(*AP*AP*AP*(3DR)P*GP*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*(DOC))-3', ...
Authors:Marx, A, Diederichs, K, Obeid, S.
Deposit date:2011-07-25
Release date:2012-02-15
Last modified:2023-09-13
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase.
J.Biol.Chem., 287, 2012
3SYZ
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BU of 3syz by Molmil
Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase
Descriptor: (5'-D(*AP*AP*AP*(BMN)P*GP*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*(DOC))-3'), DNA polymerase I, ...
Authors:Betz, K, Diederichs, K, Marx, A.
Deposit date:2011-07-18
Release date:2012-06-06
Last modified:2023-09-13
Method:X-RAY DIFFRACTION (1.952 Å)
Cite:KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.
Nat.Chem.Biol., 8, 2012
3SV4
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BU of 3sv4 by Molmil
Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dT as templating nucleobase
Descriptor: (5'-D(*AP*AP*AP*TP*GP*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*(DOC))-3'), DNA polymerase I, ...
Authors:Betz, K, Diederichs, K, Marx, A.
Deposit date:2011-07-12
Release date:2012-06-06
Last modified:2023-09-13
Method:X-RAY DIFFRACTION (1.99 Å)
Cite:KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.
Nat.Chem.Biol., 8, 2012
3SZ2
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BU of 3sz2 by Molmil
Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dG as templating nucleobase
Descriptor: (5'-D(*AP*AP*AP*GP*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'), DNA polymerase I, ...
Authors:Betz, K, Marx, A, Diederichs, K.
Deposit date:2011-07-18
Release date:2012-06-06
Last modified:2023-09-13
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.
Nat.Chem.Biol., 8, 2012
3SV3
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BU of 3sv3 by Molmil
Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dNaM-d5SICSTP
Descriptor: (5'-D(*AP*AP*AP*(BMN)P*GP*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*(DOC))-3'), 2-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-6-methylisoquinoline-1(2H)-thione, ...
Authors:Betz, K, Diederichs, K, Marx, A.
Deposit date:2011-07-12
Release date:2012-06-06
Last modified:2023-09-13
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.
Nat.Chem.Biol., 8, 2012
6VDE
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BU of 6vde by Molmil
Full-length M. smegmatis Pol1
Descriptor: DNA polymerase I, MANGANESE (II) ION
Authors:Shuman, S, Goldgur, Y, Ghosh, S.
Deposit date:2019-12-24
Release date:2020-02-12
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.713 Å)
Cite:Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO-POL enzyme.
Nucleic Acids Res., 48, 2020
4ELU
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BU of 4elu by Molmil
Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines
Descriptor: 2'-deoxy-5-[(4-ethynylphenyl)ethynyl]cytidine 5'-(tetrahydrogen triphosphate), ACETATE ION, DNA (5'-D(*AP*AP*AP*GP*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), ...
Authors:Marx, A, Diederichs, K, Obeid, S.
Deposit date:2012-04-11
Release date:2013-03-27
Last modified:2023-09-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Interactions of non-polar and "Click-able" nucleotides in the confines of a DNA polymerase active site.
Chem.Commun.(Camb.), 48, 2012
4KTQ
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BU of 4ktq by Molmil
BINARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM T. AQUATICUS BOUND TO A PRIMER/TEMPLATE DNA
Descriptor: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'), DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), PROTEIN (LARGE FRAGMENT OF DNA POLYMERASE I)
Authors:Li, Y, Waksman, G.
Deposit date:1998-09-09
Release date:1999-01-13
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation.
EMBO J., 17, 1998
6FBI
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BU of 6fbi by Molmil
KlenTaq DNA polymerase in a closed, ternary complex with dGpNHpp bound in the active site
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 (1.9 Å)
Cite:Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.
Proc. Natl. Acad. Sci. U.S.A., 115, 2018
6FBE
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BU of 6fbe by Molmil
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
6FBC
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BU of 6fbc by Molmil
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
6FBF
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BU of 6fbf by Molmil
KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the fourth primer nucleotide.
Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine, DNA (5'-D(*AP*AP*AP*CP*GP*CP*GP*GP*TP*GP*CP*TP*GP*GP*TP*C)-3'), DNA (5'-D(*GP*AP*CP*CP*AP*GP*CP*AP*(OH3)P*CP*GP*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 (2.001 Å)
Cite:Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.
Proc. Natl. Acad. Sci. U.S.A., 115, 2018
6FBD
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BU of 6fbd by Molmil
KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the second primer nucleotide.
Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine, DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*AP*(OH3)P*C)-3'), DNA (5'-D(P*AP*AP*AP*CP*GP*GP*TP*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 (2.099 Å)
Cite:Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.
Proc. Natl. Acad. Sci. U.S.A., 115, 2018
6FBG
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BU of 6fbg by Molmil
KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the fifth 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*CP*CP*GP*GP*TP*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 (1.702 Å)
Cite:Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.
Proc. Natl. Acad. Sci. U.S.A., 115, 2018
6FBH
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BU of 6fbh by Molmil
KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the sixth 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*TP*CP*CP*GP*GP*TP*GP*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 (1.8 Å)
Cite:Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.
Proc. Natl. Acad. Sci. U.S.A., 115, 2018
1JXE
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BU of 1jxe by Molmil
STOFFEL FRAGMENT OF TAQ DNA POLYMERASE I
Descriptor: TAQ DNA POLYMERASE I
Authors:Oefner, C, Gelfand, D.H, Stoffel, S, Winkler, F.K.
Deposit date:1996-10-09
Release date:1997-03-12
Last modified:2024-02-07
Method:X-RAY DIFFRACTION (2.85 Å)
Cite:

1KLN
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BU of 1kln by Molmil
DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX
Descriptor: DNA (5'-D(*GP*CP*CP*GP*CP*GP*AP*GP*GP*C)-3'), DNA (5'-D(*GP*CP*CP*TP*CP*GP*CP*GP*GP*CP*GP*GP*C)-3'), PROTEIN (DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7)), ...
Authors:Beese, L.S, Derbyshire, V, Steitz, T.A.
Deposit date:1994-05-24
Release date:1994-11-30
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Structure of DNA polymerase I Klenow fragment bound to duplex DNA.
Science, 260, 1993

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