SMTL ID : 5cfe.1

Bacillus subtilis AP endonuclease ExoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: N.9, E.36 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.36, H2O.1, H2O.3, H2O.5, H2O.7 CA.5: 1 residues within 4Å: Chain A: E.98 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.98, A:E.98, H2O.6 CA.6: 1 residues within 4Å: Chain A: E.195 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.195, A:E.195, H2O.6, H2O.7, H2O.7

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

PEG.2: 4 residues within 4Å: Chain A: E.133, L.134, K.137 Ligands: PEG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.137 PEG.3: 6 residues within 4Å: Chain A: I.78, Y.79, G.80, I.81, G.82 Ligands: PEG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.79 Water bridges: A:Q.76 PEG.4: 5 residues within 4Å: Chain A: A.165, G.166, W.200, W.214, I.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.165 Water bridges: A:N.109, A:N.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Redrejo-Rodriguez, M. et al., Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA. Biochimie (2016)

Release Date

2016-07-06

Peptides

Exodeoxyribonuclease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Exodeoxyribonuclease