SMTL ID : 1j53.1

Structure of the N-terminal Exonuclease Domain of the Epsilon Subunit of E.coli DNA Polymerase III at pH 8.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: D.12, T.13, E.14, D.167 Ligands: MN.2, TMP.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.12, A:E.14, A:D.167, H2O.1 MN.2: 3 residues within 4Å: Chain A: D.12 Ligands: MN.1, TMP.3 5 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.12, H2O.2, H2O.6, H2O.6, TMP.3

2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.3: 17 residues within 4Å: Chain A: D.12, T.13, E.14, T.15, G.17, M.18, E.61, A.62, V.65, H.66, F.102, R.159, H.162, D.167 Ligands: MN.1, MN.2, TMP.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.62, A:V.65 Hydrogen bonds: A:E.14, A:T.15, A:E.61, A:H.66, A:R.159, A:H.162 Water bridges: A:D.12, A:T.13, A:A.62 TMP.4: 6 residues within 4Å: Chain A: H.98, N.99, F.102, S.144, L.145 Ligands: TMP.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.98, A:N.99, A:L.145 Water bridges: A:R.159

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: N.122, T.123, F.124, C.125, K.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.92, A:T.123 Water bridges: A:G.92 EDO.6: 4 residues within 4Å: Chain A: R.7, Q.8, V.38, V.39 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hamdan, S. et al., Structural Basis for Proofreading during Replication of the Escherichia coli Chromosome. Structure (2002)

Release Date

2002-10-16

Peptides

DNA polymerase III, epsilon chain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase III, epsilon chain

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