3SUN
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3sun by Molmil](/molmil-images/mine/3sun) | RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite 2AP (AT rich sequence) | Descriptor: | 5'-D(*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*(2DA))-3', 5'-D(P*CP*(2PR)P*TP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*G)-3', CALCIUM ION, ... | Authors: | Xia, S, Konigsberg, W.H, Wang, J. | Deposit date: | 2011-07-11 | Release date: | 2011-11-09 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (2.42 Å) | Cite: | Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase. Biochemistry, 50, 2011
|
|
2R8G
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2r8g by Molmil](/molmil-images/mine/2r8g) | Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2-Propanodeoxyguanosine (PdG) by the Sulfolobus solfataricus DNA Polymerase Dpo4 Polymerase | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*DGP*DGP*DGP*DGP*DGP*DAP*DAP*DGP*DGP*DAP*DTP*DTP*DT)-3', 5'-D(*DTP*DCP*DAP*DCP*(P)P*DGP*DAP*DAP*DAP*DTP*DCP*DCP*DTP*DTP*DCP*DCP*DCP*DCP*DC)-3', ... | Authors: | Wang, Y, Saleh, S, Marnette, L.J, Egli, M, Stone, M.P. | Deposit date: | 2007-09-10 | Release date: | 2008-07-22 | Last modified: | 2024-02-21 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Insertion of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct by Sulfolobus solfataricus P2 DNA polymerase IV Biochemistry, 47, 2008
|
|
3SUP
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3sup by Molmil](/molmil-images/mine/3sup) | RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite 2AP (GC rich sequence) | Descriptor: | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, 5'-D(*CP*GP*CP*GP*CP*GP*GP*CP*GP*GP*CP*GP*(2DA))-3', 5'-D(P*CP*(2PR)P*TP*CP*GP*CP*CP*GP*CP*CP*GP*CP*GP*CP*GP*G)-3', ... | Authors: | Xia, S, Konigsberg, W.H, Wang, J. | Deposit date: | 2011-07-11 | Release date: | 2011-11-09 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (2.32 Å) | Cite: | Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase. Biochemistry, 50, 2011
|
|
6HMF
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6hmf by Molmil](/molmil-images/mine/6hmf) | D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease) H451 proof-reading deficient variant | Descriptor: | ACETATE ION, CACODYLATE ION, CALCIUM ION, ... | Authors: | Raia, P, Delarue, M, Sauguet, L. | Deposit date: | 2018-09-12 | Release date: | 2019-01-30 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases. PLoS Biol., 17, 2019
|
|
3Q06
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3q06 by Molmil](/molmil-images/mine/3q06) | |
2XHB
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2xhb by Molmil](/molmil-images/mine/2xhb) | Crystal structure of DNA polymerase from Thermococcus gorgonarius in complex with hypoxanthine-containing DNA | Descriptor: | 5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*A)-3', DNA POLYMERASE, HYPOXANTHINE-CONTAINING DNA, ... | Authors: | Killelea, T, Ghosh, S, Tan, S.S, Heslop, P, Firbank, S.J, Kool, E.T, Connolly, B.A. | Deposit date: | 2010-06-14 | Release date: | 2010-07-21 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (2.72 Å) | Cite: | Probing the Interaction of Archaeal DNA Polymerases with Deaminated Bases Using X-Ray Crystallography and Non-Hydrogen Bonding Isosteric Base Analogues. Biochemistry, 49, 2010
|
|
7OMG
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7omg by Molmil](/molmil-images/mine/7omg) | Crystal structure of KOD DNA Polymerase in a ternary complex with an Uracil containing template | Descriptor: | 1,2-ETHANEDIOL, 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, CALCIUM ION, ... | Authors: | Betz, K, Kropp, H.M, Diederichs, K, Marx, A. | Deposit date: | 2021-05-22 | Release date: | 2021-10-13 | Last modified: | 2024-01-31 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase. Chembiochem, 22, 2021
|
|
7OMB
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7omb by Molmil](/molmil-images/mine/7omb) | Crystal structure of KOD DNA Polymerase in a ternary complex with a p/t duplex containing an extended 5' single stranded template overhang | Descriptor: | 1,2-ETHANEDIOL, 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, DNA polymerase, ... | Authors: | Betz, K, Kropp, H.M, Diederichs, K, Marx, A. | Deposit date: | 2021-05-21 | Release date: | 2021-10-13 | Last modified: | 2024-01-31 | Method: | X-RAY DIFFRACTION (2.01 Å) | Cite: | Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase. Chembiochem, 22, 2021
|
|
7OM3
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7om3 by Molmil](/molmil-images/mine/7om3) | Crystal structure of KOD DNA Polymerase in a binary complex with Hypoxanthine containing template | Descriptor: | 1,2-ETHANEDIOL, 21nt Template, BROMIDE ION, ... | Authors: | Betz, K, Kropp, H.M, Diederichs, K, Marx, A. | Deposit date: | 2021-05-21 | Release date: | 2021-10-13 | Last modified: | 2024-01-31 | Method: | X-RAY DIFFRACTION (1.92 Å) | Cite: | Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase. Chembiochem, 22, 2021
|
|
1HU0
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1hu0 by Molmil](/molmil-images/mine/1hu0) | CRYSTAL STRUCTURE OF AN HOGG1-DNA BOROHYDRIDE TRAPPED INTERMEDIATE COMPLEX | Descriptor: | 5'-D(*GP*CP*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3', 8-OXOGUANINE, ... | Authors: | Fromme, J.C, Bruner, S.D, Yang, W, Karplus, M, Verdine, G.L. | Deposit date: | 2001-01-03 | Release date: | 2003-02-25 | Last modified: | 2023-08-09 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Product-Assisted Catalysis in base-excision DNA Repair Nat.Struct.Biol., 10, 2003
|
|
8TKL
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 8tkl by Molmil](/molmil-images/mine/8tkl) | Murine NF-kappaB p50 Rel Homology Region homodimer in complex with a Test 16-mer kappaB-like DNA | Descriptor: | Nuclear factor NF-kappa-B p50 subunit, Test 17-mer kappaB-like DNA | Authors: | Mitchel, S, Mealka, M, Rogers, W.E, Milani, C, Acuna, L.M, Huxford, T. | Deposit date: | 2023-07-25 | Release date: | 2023-10-18 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | X-ray Crystallographic Study of Preferred Spacing by the NF-kappa B p50 Homodimer on kappa B DNA. Biomolecules, 13, 2023
|
|
1NKE
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1nke by Molmil](/molmil-images/mine/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
|
|
8TKM
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 8tkm by Molmil](/molmil-images/mine/8tkm) | Murine NF-kappaB p50 Rel Homology Region homodimer in complex with 17-mer kappaB DNA from human interleukin-6 (IL-6) promoter | Descriptor: | 17-mer kappaB DNA, Nuclear factor NF-kappa-B p50 subunit | Authors: | Zhu, N, Mealka, M, Mitchel, S, Rogers, W.E, Huxford, T. | Deposit date: | 2023-07-25 | Release date: | 2023-10-11 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | X-ray Crystallographic Study of Preferred Spacing by the NF-kappa B p50 Homodimer on kappa B DNA. Biomolecules, 13, 2023
|
|
3Q05
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3q05 by Molmil](/molmil-images/mine/3q05) | |
6JUQ
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6juq by Molmil](/molmil-images/mine/6juq) | mutant PolIV-DNA incoming nucleotide complex 2 | Descriptor: | 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine, DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3'), DNA (5'-D(P*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3'), ... | Authors: | Nair, D.T, Johnson, M.K. | Deposit date: | 2019-04-15 | Release date: | 2020-02-19 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.74 Å) | Cite: | A polar filter in DNA polymerases prevents ribonucleotide incorporation. Nucleic Acids Res., 47, 2019
|
|
3TFS
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3tfs by Molmil](/molmil-images/mine/3tfs) | Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, b dAMP(CFH)PP in the active site: Stereoselective binding of (S) isomer | Descriptor: | 2'-deoxy-5'-O-[(S)-{(S)-fluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*TP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | Authors: | Chamberlain, B.T, Batra, V.K, Beard, W.A, Kadina, A.P, Shock, D.D, Kashemirov, B.A, McKenna, C.E, Goodman, M.F, Wilson, S.H. | Deposit date: | 2011-08-16 | Release date: | 2012-03-21 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Stereospecific Formation of a Ternary Complex of (S)-alpha, beta-Fluoromethylene-dATP with DNA Pol beta. Chembiochem, 13, 2012
|
|
6JUP
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6jup by Molmil](/molmil-images/mine/6jup) | Mutant PolIV-DNA incoming nucleotide complex | Descriptor: | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*CP*C)-3'), DNA (5'-D(P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3'), ... | Authors: | Nair, D.T, Johnson, M.K. | Deposit date: | 2019-04-15 | Release date: | 2020-02-19 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.44 Å) | Cite: | A polar filter in DNA polymerases prevents ribonucleotide incorporation. Nucleic Acids Res., 47, 2019
|
|
2I5W
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2i5w by Molmil](/molmil-images/mine/2i5w) | |
3IGK
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3igk by Molmil](/molmil-images/mine/3igk) | Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 2) | Descriptor: | Cellular tumor antigen p53, DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3'), ZINC ION | Authors: | Suad, O, Rabinovich, D, Rozenberg, H, Shakked, Z. | Deposit date: | 2009-07-28 | Release date: | 2010-03-31 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs Nat.Struct.Mol.Biol., 17, 2010
|
|
4DTJ
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4dtj by Molmil](/molmil-images/mine/4dtj) | RB69 DNA Polymerase Ternary Complex with dTTP Opposite an Abasic Site and ddT/dA as the Penultimate Base-pair | Descriptor: | CALCIUM ION, DNA polymerase, DNA primer, ... | Authors: | Xia, S, Wang, J, Konigsberg, W.H. | Deposit date: | 2012-02-21 | Release date: | 2012-06-06 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA. Biochemistry, 51, 2012
|
|
4DU3
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4du3 by Molmil](/molmil-images/mine/4du3) | RB69 DNA Polymerase Ternary Complex with dDTP Opposite dT with 3-Deaza-adenine at the N-1 Position of Template Strand | Descriptor: | 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, CALCIUM ION, DNA polymerase, ... | Authors: | Xia, S, Wang, J, Konigsberg, W.H. | Deposit date: | 2012-02-21 | Release date: | 2012-05-23 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (2.02 Å) | Cite: | Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA. Biochemistry, 51, 2012
|
|
4DTO
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4dto by Molmil](/molmil-images/mine/4dto) | RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair | Descriptor: | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, CALCIUM ION, DNA polymerase, ... | Authors: | Xia, S, Wang, J, Konigsberg, W.H. | Deposit date: | 2012-02-21 | Release date: | 2012-06-06 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (2.05 Å) | Cite: | Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA. Biochemistry, 51, 2012
|
|
4DTR
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4dtr by Molmil](/molmil-images/mine/4dtr) | RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddC/dG as the Penultimate Base-pair | Descriptor: | 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, CALCIUM ION, DNA polymerase, ... | Authors: | Xia, S, Wang, J, Konigsberg, W.H. | Deposit date: | 2012-02-21 | Release date: | 2012-06-06 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (2.04 Å) | Cite: | Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA. Biochemistry, 51, 2012
|
|
4DTM
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4dtm by Molmil](/molmil-images/mine/4dtm) | RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddG/dC as the Penultimate Base-pair | Descriptor: | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, CALCIUM ION, DNA polymerase, ... | Authors: | Xia, S, Wang, J, Konigsberg, W.H. | Deposit date: | 2012-02-21 | Release date: | 2012-06-06 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA. Biochemistry, 51, 2012
|
|
4DU4
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4du4 by Molmil](/molmil-images/mine/4du4) | RB69 DNA Polymerase Ternary Complex with dATP Opposite dT with 3-Deaza-adenine at the N-3 Position of Primer Strand | Descriptor: | 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, CALCIUM ION, DNA polymerase, ... | Authors: | Xia, S, Wang, J, Konigsberg, W.H. | Deposit date: | 2012-02-21 | Release date: | 2012-05-23 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (2.28 Å) | Cite: | Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA. Biochemistry, 51, 2012
|
|