SMTL ID : 8axy.1

Staphylococcus aureus endonuclease IV orthorhombic crystal form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

monomer

Ligands

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

FE.1: 7 residues within 4Å: Chain A: H.68, H.109, E.144, H.181, H.213 Ligands: FE.2, SO4.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.68, A:H.109, A:E.144, H2O.2, H2O.4 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, SO4.4 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.2

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.181, D.226, H.228 Ligands: SO4.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.181, A:D.226, A:D.226, A:H.228, H2O.4

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

SO4.4: 12 residues within 4Å: Chain A: H.109, E.144, M.146, D.178, H.181, N.215, D.226, H.228, E.258 Ligands: FE.1, FE.2, ZN.3 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.109, A:H.181, A:H.228 SO4.5: 3 residues within 4Å: Chain A: K.104, R.140, K.210 9 PLIP interactions: 9 interactions with chain A Water bridges: A:K.104, A:R.140, A:R.140, A:K.210, A:D.252, A:D.252 Salt bridges: A:K.104, A:R.140, A:K.210 SO4.6: 5 residues within 4Å: Chain A: S.10, G.11, K.12, K.13, M.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.12, A:K.13 Water bridges: A:K.13, A:M.14, A:M.14 SO4.7: 3 residues within 4Å: Chain A: S.8, M.9, S.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.9, A:S.10 SO4.8: 3 residues within 4Å: Chain A: M.57, S.63, N.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.64 Water bridges: A:L.62, A:I.65 SO4.9: 3 residues within 4Å: Chain A: G.117, V.118, D.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.118, A:D.119 Water bridges: A:A.116, A:A.120 SO4.10: 6 residues within 4Å: Chain A: A.112, V.114, K.149, G.150, T.151, E.152 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.151, A:T.151, A:E.152 SO4.11: 2 residues within 4Å: Chain A: E.171, R.208 5 PLIP interactions: 5 interactions with chain A Water bridges: A:E.171, A:R.208, A:R.208, A:R.208 Salt bridges: A:R.208 SO4.12: 3 residues within 4Å: Chain A: M.1, H.246, Q.283 6 PLIP interactions: 6 interactions with chain A Water bridges: A:M.1, A:H.246, A:H.246, A:Q.283, A:Q.283 Salt bridges: A:H.246 SO4.13: 3 residues within 4Å: Chain A: I.50, T.51, H.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.51 Water bridges: A:T.51, A:T.51 Salt bridges: A:H.54 SO4.14: 2 residues within 4Å: Chain A: S.44, I.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.45 Water bridges: A:E.46 SO4.15: 2 residues within 4Å: Chain A: R.155, Q.224 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.224 Water bridges: A:R.155, A:R.155 Salt bridges: A:R.155

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

2023-09-13

Peptides

Probable endonuclease 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Probable endonuclease 4