SMTL ID : 4dqi.2 (1 other biounit)

Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and dCTP (paired with dG of template)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

monomer

Ligands

1 x DC- DC- DT- DG- DA- DC- DT- DC- DOC: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')(Non-covalent)

DC-DC-DT-DG-DA-DC-DT-DC-DOC.1: 36 residues within 4Å: Chain A: P.247, T.266, K.267, T.268, S.271, T.272, S.273, A.274, L.291, R.294, Q.295, K.298, L.299, Y.303, R.331, Q.340, N.341, I.342, P.343, I.344, R.345, R.353, R.419, V.544, H.545, D.546 Chain B: G.5, G.6, A.7, G.8, T.9, C.10, A.11, G.12, G.13 Ligands: DCP.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.331, A:R.331 Water bridges: A:R.419

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.369, Y.370, S.371, Q.372, D.546 Ligands: DCP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.370, A:D.546, H2O.29

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.3: 19 residues within 4Å: Chain A: R.331, D.369, Y.370, S.371, Q.372, I.373, E.374, L.375, H.398, R.418, K.422, A.423, F.426, Y.430, D.546 Chain B: G.4, G.5 Ligands: DC-DC-DT-DG-DA-DC-DT-DC-DOC.1, MG.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:E.374, A:F.426 Hydrogen bonds: A:R.331, A:D.369, A:Q.372, A:I.373, A:E.374, A:D.546 Water bridges: A:R.331, A:R.418, A:K.422, A:K.422, A:K.422, A:A.423 Salt bridges: A:H.398, A:R.418, A:K.422, A:K.422, A:K.422 pi-Stacking: A:F.426

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

SO4.4: 4 residues within 4Å: Chain A: K.14, M.15, A.16, R.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.16 Salt bridges: A:R.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. J.Biol.Chem. (2012)

Release Date

2012-06-06

Peptides

DNA polymerase I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

DNA polymerase I

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