SMTL ID : 6ueu.2 (1 other biounit)

Crystal structure of BF DNA polymerase F710Y mutant bound to tetrahydrofuran and dATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x DC- DG- DA- DT- DC- DA- DC- DG- 2DT: DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(2DT))-3')(Non-covalent)

DC-DG-DA-DT-DC-DA-DC-DG-2DT.1: 33 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, V.532, H.533, D.534 Chain B: A.4, C.5, G.6, T.7, G.8, A.9, T.10, C.11, G.12 Ligands: DTP.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:R.319, A:R.319, A:N.231, A:S.234, A:Q.237, A:K.286, A:K.286, A:K.286, A:S.289, A:L.314, A:Q.316, A:R.319, A:S.321, A:E.324, A:N.326, A:N.329, A:Q.501 Water bridges: A:R.333, A:R.341, A:Q.316, A:N.326, A:R.475, A:N.497 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 1 PLIP interactions: 1 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

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.3: 14 residues within 4Å: Chain A: R.319, Y.358, S.359, Q.360, E.362, H.386, R.406, K.410, Y.414, Y.418, D.534 Chain B: N.3, A.4 Ligands: DC-DG-DA-DT-DC-DA-DC-DG-2DT.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.414 Hydrogen bonds: A:R.319, A:Q.360, A:Q.360, A:Y.414 Water bridges: A:R.319, A:D.357, A:D.357, A:E.362, A:E.362, A:R.406, A:R.407, A:K.410, A:N.497, A:D.534 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)

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

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 3 residues within 4Å: Chain A: L.56, K.87, I.89 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walsh, A.R. et al., Structural basis for blockage of DNA synthesis by a thymine dimer lesion in a high-fidelity DNA polymerase. To Be Published

Release Date

2020-09-30

Peptides

DNA polymerase I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

DNA polymerase I

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