SMTL ID : 8edd.1

Staphylococcus aureus endonuclease IV Y33F mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 9 residues within 4Å: Chain A: H.68, Y.71, V.107, H.109, E.144, H.181, H.213 Ligands: FE.2, PO4.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.68, A:H.109, A:E.144, H2O.1 FE.2: 9 residues within 4Å: Chain A: E.144, D.178, H.181, H.213, N.215, H.228, E.258 Ligands: FE.1, PO4.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.144, A:D.178, A:H.213, A:E.258, H2O.1

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.181, D.226, H.228 Ligands: PO4.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.181, A:D.226, A:D.226, A:H.228

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 12 residues within 4Å: Chain A: H.68, Y.71, H.109, E.144, D.178, H.181, D.226, H.228, E.258 Ligands: FE.1, FE.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.258 Salt bridges: A:H.109, A:H.181, A:H.228 PO4.5: 5 residues within 4Å: Chain A: R.155, S.156, A.185, G.186, Y.187 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.187

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 6 residues within 4Å: Chain A: M.1, L.2, K.251, D.252, I.253, K.255 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: H.183, D.220, R.221, Y.235 Ligand excluded by PLIP CL.8: 7 residues within 4Å: Chain A: I.95, L.133, T.134, N.135, D.136, N.137, R.172 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirillov, S. et al., Octahedrally coordinated iron in the catalytic site of endonuclease IV from Staphylococcus aureus. To Be Published

Release Date

2023-09-06

Peptides

Probable endonuclease 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Probable endonuclease 4