SMTL ID : 4dqp.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 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: 37 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, L.346, R.353, V.544, H.545, D.546, E.547 Chain B: G.5, G.6, A.7, G.8, T.9, C.10, A.11, G.12, G.13 Ligands: DCT.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.331, A:R.331

2 x DCT: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE(Non-covalent)

DCT.2: 13 residues within 4Å: Chain A: R.331, Q.372, E.374, H.398, R.418, K.422, A.423, F.426, D.546 Chain B: G.4, G.5 Ligands: DC-DC-DT-DG-DA-DC-DT-DC-DOC.1, MG.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:E.374, A:F.426 Hydrogen bonds: A:R.331, A:Q.372, A:Q.372, A:D.546 Water bridges: A:R.331, A:I.373, A:E.374 Salt bridges: A:H.398, A:H.398, A:R.418, A:K.422, A:K.422, A:K.422 pi-Stacking: A:F.426 DCT.3: 9 residues within 4Å: Chain A: R.182, E.185, Q.186, D.187, R.188, L.189, L.482, L.483, H.484 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.483 Hydrogen bonds: A:D.187, A:D.187, A:R.188, A:R.188, A:L.189 Salt bridges: A:H.484, A:H.484 pi-Cation interactions: A:R.188

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: D.369, Y.370, S.371, Q.372, D.546 Ligands: DCT.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.546

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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