SMTL ID : 3ez5.2 (1 other biounit)

Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA , dCTP, and zinc (closed form).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x DC- DC- DT- DG- DA- DC- DT- DC- DG: 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DG)-3'(Non-covalent)

DC-DC-DT-DG-DA-DC-DT-DC-DG.1: 35 residues within 4Å: Chain A: P.235, T.254, K.255, T.256, S.259, T.260, S.261, A.262, L.279, R.282, Q.283, K.286, Y.291, R.319, Q.328, N.329, I.330, P.331, I.332, R.333, Q.501, V.532, H.533, D.534 Chain B: C.4, G.5, A.6, G.7, T.8, C.9, A.10, G.11, G.12 Ligands: ZN.4, DAD.6 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:Y.423 Hydrogen bonds: A:N.231, A:S.234, A:Q.237, A:K.286, A:K.286, A:Q.316, A:R.319, A:S.321, A:E.324, A:N.326, A:N.329, A:S.421, A:S.421, A:S.421, A:G.424, A:Q.501 Water bridges: A:K.297, A:L.314, A:Q.316, A:R.475, A:N.497, A:H.533, A:H.533 Salt bridges: A:R.475, A:R.493 pi-Stacking: A:Y.423

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.2: 10 residues within 4Å: Chain A: E.29, N.30, Y.31, D.76, R.79, L.99, D.112, I.309, N.311, A.313 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.79, A:D.112, A:N.311, A:N.311, A:A.313, A:R.79 Water bridges: A:R.79, A:Q.312, A:E.324

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: D.357, Y.358, D.534 Ligands: ZN.4, DAD.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.357, A:Y.358, A:D.534 ZN.4: 5 residues within 4Å: Chain A: D.357, D.534 Ligands: DC-DC-DT-DG-DA-DC-DT-DC-DG.1, ZN.3, DAD.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.357, A:D.357, A:D.534, H2O.9, H2O.12 ZN.5: 2 residues within 4Å: Chain A: D.569, H.571 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.569, A:D.569, A:H.571

1 x DAD: 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

DAD.6: 18 residues within 4Å: Chain A: R.319, D.357, Y.358, S.359, Q.360, I.361, E.362, H.386, R.406, K.410, A.411, Y.414, D.534 Chain B: T.3, C.4 Ligands: DC-DC-DT-DG-DA-DC-DT-DC-DG.1, ZN.3, ZN.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:E.362, A:Y.414 Hydrogen bonds: A:R.319, A:S.359, A:Q.360, A:I.361, A:Y.414 Water bridges: A:R.333, A:R.333, A:R.406, A:Y.418 Salt bridges: A:H.386, A:R.406, A:K.410, A:K.410, A:K.410 pi-Stacking: A:Y.414

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 4 residues within 4Å: Chain A: K.2, M.3, A.4, R.47 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.4 Water bridges: A:R.47, A:R.47 Salt bridges: A:R.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Golosov, A.A. et al., The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis. Structure (2010)

Release Date

2009-11-10

Peptides

DNA polymerase I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

DNA polymerase I

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