SMTL ID : 1k3x.1

Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain C: C.237, C.240, C.257, C.260 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.237, C:C.240, C:C.257, C:C.260

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

SO4.2: 2 residues within 4Å: Chain C: R.8, N.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.12 Water bridges: C:R.8, C:R.8, C:G.213 Salt bridges: C:R.8 SO4.3: 3 residues within 4Å: Chain C: K.140, A.191, D.195 3 PLIP interactions: 3 interactions with chain C Water bridges: C:K.140, C:D.195 Salt bridges: C:K.140 SO4.4: 2 residues within 4Å: Chain C: N.190, A.191 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.191 SO4.5: 2 residues within 4Å: Chain C: P.1, R.212 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.212, C:R.212, C:R.212 Salt bridges: C:R.212 SO4.6: 0 residues within 4Å: (No contacts) 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.151, C:R.151, C:R.151, C:Q.152

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain C: R.147, R.151 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.147, C:R.147 Water bridges: C:R.151, C:R.151, C:R.151, C:R.151 GOL.8: 2 residues within 4Å: Chain C: D.195, H.199 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.195 GOL.9: 1 residues within 4Å: Chain C: E.81 No protein-ligand interaction detected (PLIP) GOL.10: 2 residues within 4Å: Chain C: T.117, T.118 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.117 Water bridges: C:T.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zharkov, D.O. et al., Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate. EMBO J. (2002)

Release Date

2002-10-04

Peptides

Endonuclease VIII: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

Endonuclease VIII

Related Entries With Identical Sequence