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

Crystal structure of open Bacillus fragment DNA polymerase bound to DNA and dTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x DC- DA- DT- DG- DA- DT- DG- DC- 2DT: Primer DNA(Non-covalent)

DC-DA-DT-DG-DA-DT-DG-DC-2DT.1: 33 residues within 4Å: Chain A: 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, E.535 Chain B: A.6, G.7, C.8, A.9, T.10, C.11, A.12, T.13, G.14 Ligands: TTP.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.319, A:R.319 Water bridges: A:Y.418 Salt bridges: A:R.333

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

GLC-FRU.2: 11 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, T.323 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.79, A:D.112, A:N.311, A:N.311, A:A.313, A:R.79, A:D.112, A:T.323 Water bridges: A:R.79, A:D.112, A:D.112, A:Q.312

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.3: 9 residues within 4Å: Chain A: Q.360, H.386, R.406, K.410, Y.414, Y.418, D.534 Chain B: G.5 Ligands: DC-DA-DT-DG-DA-DT-DG-DC-2DT.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.414 Hydrogen bonds: A:Q.360, A:Y.414, A:Y.418, A:Y.418 Water bridges: A:R.319, A:Q.360, A:Q.360, A:R.406, A:K.410, A:D.534, A:D.534 Salt bridges: A:H.386, A:H.386, A:R.406, A:K.410, A:K.410, A:K.410 pi-Stacking: A:Y.414

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, B.R. et al., The Closing Mechanism of DNA Polymerase I at Atomic Resolution. Structure (2015)

Release Date

2015-07-22

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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