SMTL ID : 2ea0.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain B: A.8, A.9 Chain C: L.158 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.158, C:R.252 Water bridges: C:Q.160, C:Q.160, C:Q.160 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: R.149, K.187 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.149, C:K.187 SO4.5: 3 residues within 4Å: Chain C: R.8, N.12, G.213 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.12 Water bridges: C:N.12 Salt bridges: C:R.8 SO4.6: 2 residues within 4Å: Chain C: N.190, A.191 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.191

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 GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain A: G.1 Chain C: R.147 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.147 Water bridges: C:R.151

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 substrate 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

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