SMTL ID : 2gui.1

Structure and Function of Cyclized Versions of the Proofreading Exonuclease Subunit of E. coli DNA Polymerase III

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.15 Ligands: MN.2, U5P.3 5 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.15, H2O.1, H2O.1, H2O.1, U5P.3 MN.2: 7 residues within 4Å: Chain A: D.15, T.16, E.17, G.166, D.170 Ligands: MN.1, U5P.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.15, A:E.17, A:D.170, H2O.4

2 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.3: 16 residues within 4Å: Chain A: D.15, T.16, E.17, T.18, G.20, M.21, E.64, A.65, V.68, H.69, F.105, H.165, D.170 Ligands: MN.1, MN.2, U5P.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.68 Hydrogen bonds: A:T.18, A:T.18, A:H.69, A:R.162 Water bridges: A:T.16, A:T.16, A:A.65, A:H.165, A:H.165, A:H.165, A:H.165 Salt bridges: A:H.165 U5P.4: 9 residues within 4Å: Chain A: M.21, H.101, N.102, F.105, S.147, L.148, R.162, H.165 Ligands: U5P.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.102, A:L.148 Water bridges: A:R.162, A:R.162, A:H.165 Salt bridges: A:R.162, A:H.165

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

EDO.5: 5 residues within 4Å: Chain A: G.95, T.126, F.127, C.128, K.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.95, A:T.126 EDO.6: 3 residues within 4Å: Chain A: I.107, N.125, V.130 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.130

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 5 residues within 4Å: Chain A: H.69, G.70, I.71, F.75, L.164 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, A.Y. et al., Structure and Function of Cyclized Versions of the Proofreading Exonuclease Subunit E. coli DNA Polymerase III. To be Published

Release Date

2007-03-13

Peptides

DNA polymerase III epsilon subunit: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase III epsilon subunit