SMTL ID : 6fbu.1

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.8, N.12, G.213 Ligands: ACT.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.12 Water bridges: A:N.12, A:G.213 Salt bridges: A:R.8 SO4.2: 5 residues within 4Å: Chain A: P.1, E.5, Y.169, R.212 Chain C: X.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.5 Water bridges: A:R.212, A:R.212 Salt bridges: A:R.212 SO4.3: 2 residues within 4Å: Chain A: R.149, K.187 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.149, A:K.187

1 x ZN: ZINC ION(Non-covalent)

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

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 3 residues within 4Å: Chain A: E.5, N.12 Ligands: SO4.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.12 Salt bridges: A:R.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pomyalov, S. et al., Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate. To Be Published

Release Date

2019-01-30

Peptides

Endonuclease 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endonuclease 8

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