SMTL ID : 3eyz.1

Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA (open form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

GLC-FRU.1: 11 residues within 4Å: Chain A: E.29, N.30, Y.31, D.76, R.79, L.99, D.112, I.309, N.311, T.323, E.324 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.135 Hydrogen bonds: A:R.79, A:D.112, A:N.311, A:N.311, A:A.313, A:R.79, A:E.324, A:E.324 Water bridges: A:D.76, A:R.79, A:Q.312

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

SO4.2: 4 residues within 4Å: Chain A: Q.360, H.386, K.410, Y.414 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.360, A:Q.360, A:Y.414 Water bridges: A:R.406 Salt bridges: A:H.386, A:K.410 SO4.3: 1 residues within 4Å: Chain A: R.523 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.523, A:R.523 Salt bridges: A:R.523 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Golosov, A.A. et al., The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis. Structure (2010)

Release Date

2009-11-10

Peptides

DNA polymerase I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I