SMTL ID : 2opf.1

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (R252A) in complex with AP-site containing DNA substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: C.6, A.7 Chain B: G.3, G.4, A.5 No protein-ligand interaction detected (PLIP) GOL.4: 6 residues within 4Å: Chain C: Q.177, V.178, A.196, H.199, A.200, E.203 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.177, C:Q.177, C:A.200, C:E.203 GOL.5: 5 residues within 4Å: Chain C: A.9, N.12, N.68, V.73, W.74 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.12, C:N.68, C:W.74 Water bridges: C:A.9 GOL.6: 4 residues within 4Å: Chain C: D.24, V.25, W.26, Q.36 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.24, C:Q.36 GOL.7: 3 residues within 4Å: Chain C: R.75, P.83, Q.84 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.75, C:R.75, C:Q.84, C:Q.84

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 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

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

SO4.3: 4 residues within 4Å: Chain C: R.8, N.12, G.213, Q.214 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.12 Salt bridges: C:R.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Golan, G. et al., Active site plasticity of endonuclease VIII: Conformational changes compensating for different substrates and mutations of critical residues. To be Published

Release Date

2008-02-26

Peptides

Endonuclease VIII: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

Endonuclease VIII

Related Entries With Identical Sequence