SMTL ID : 3ht3.1 (1 other biounit)

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus V713P mutant bound to G:dCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

DC-DG-DA-DT-DC-DA-DC-DG-DOC.1: 32 residues within 4Å: Chain A: P.234, T.253, K.254, T.255, S.258, T.259, S.260, A.261, R.281, Q.282, K.285, Y.290, R.318, Q.327, N.328, I.329, P.330, I.331, R.332, V.531, H.532, D.533 Chain B: G.4, C.5, G.6, T.7, G.8, A.9, T.10, C.11, G.12 Ligands: DCP.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.417 Hydrogen bonds: A:N.230, A:S.233, A:S.233, A:K.235, A:Q.236, A:K.285, A:K.285, A:K.285, A:S.288, A:Q.315, A:R.318, A:R.318, A:S.320, A:E.323, A:N.325, A:N.325, A:N.328, A:G.423, A:N.485, A:Q.500, A:R.318, A:R.318 Water bridges: A:T.289, A:T.289, A:Q.315, A:N.325, A:E.361, A:E.361, A:E.361, A:R.474, A:R.474, A:R.474, A:R.492, A:R.492, A:N.496, A:R.332, A:R.332 Salt bridges: A:R.474, A:R.492, A:R.332 pi-Stacking: A:Y.422

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

GLC-FRU.2: 11 residues within 4Å: Chain A: E.28, N.29, Y.30, D.75, R.78, L.98, D.111, I.308, N.310, A.312, T.322 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.78, A:D.111, A:N.310, A:N.310, A:R.78, A:T.322 Water bridges: A:R.78, A:Q.311, A:T.322

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 1 residues within 4Å: Ligands: DCP.4 No protein-ligand interaction detected (PLIP)

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

DCP.4: 10 residues within 4Å: Chain A: R.332, Q.359, H.385, R.405, K.409, F.413 Chain B: G.3, G.4 Ligands: DC-DG-DA-DT-DC-DA-DC-DG-DOC.1, MG.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.413 Hydrogen bonds: A:Q.359 Water bridges: A:R.332, A:R.332, A:R.332, A:Q.359, A:I.360, A:E.361 Salt bridges: A:R.332, A:H.385, A:H.385, A:R.405, A:K.409, A:K.409, A:K.409 pi-Stacking: A:F.413 DCP.5: 7 residues within 4Å: Chain A: E.172, Q.173, D.174, R.175, L.176, L.470, H.471 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.174, A:D.174, A:R.175, A:L.176 Salt bridges: A:R.175, A:H.471 pi-Cation interactions: A:R.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, E.Y. et al., The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism. J.Biol.Chem. (2011)

Release Date

2010-07-14

Peptides

DNA polymerase I, large fragment: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, large fragment

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