SMTL ID : 3hp6.1 (1 other biounit)

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus F710Y mutant bound to G:T mismatch

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

monomer

Ligands

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

DC-DG-DA-DT-DC-DA-DC-DG-DDG.1: 35 residues within 4Å: Chain A: P.235, T.254, K.255, T.256, S.259, T.260, S.261, A.262, 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, E.535 Chain B: G.3, C.4, C.5, G.6, T.7, G.8, A.9, T.10, C.11, G.12 Ligands: D3T.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.418, A:Y.423 Hydrogen bonds: A:N.231, A:S.234, A:Q.237, A:K.286, A:K.286, A:K.286, A:S.289, A:S.289, A:Q.316, A:S.321, A:E.324, A:N.326, A:N.326, A:N.329, A:S.421, A:S.421, A:G.424, A:N.486, A:N.497, A:Q.501, A:R.319, A:R.319, A:R.333 Water bridges: A:K.236, A:Q.316, A:R.319, A:N.326, A:E.362, A:N.428, A:R.475, A:R.493, A:R.493, A:R.333, A:R.333, A:Q.501 Salt bridges: A:R.475, A:R.493, A:R.333

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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.79, A:D.112, A:N.311, A:N.311, A:R.79, A:T.323 Water bridges: A:Y.31, A:D.112, A:Q.312, A:D.112, A:T.323

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

SO4.3: 3 residues within 4Å: Chain A: R.10, T.12, E.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.13 Water bridges: A:E.14 Salt bridges: A:R.10

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

MG.4: 1 residues within 4Å: Ligands: D3T.5 No protein-ligand interaction detected (PLIP)

1 x D3T: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

D3T.5: 10 residues within 4Å: Chain A: R.333, Q.360, H.386, R.406, K.410, Y.414, D.534 Chain B: G.3 Ligands: DC-DG-DA-DT-DC-DA-DC-DG-DDG.1, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.414, A:Y.414 Hydrogen bonds: A:Q.360 Water bridges: A:R.333, A:R.333, A:R.333, A:I.361, A:D.534 Salt bridges: A:H.386, A:H.386, A:R.406, A:K.410, A:K.410, A:K.410

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

2010-06-23

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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