SMTL ID : 8rly.2 (4 other biounits)

E. coli endonuclease IV complexed with sulfate, catalytic Fe2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 9 residues within 4Å: Chain A: H.69, Y.72, N.107, H.109, E.145, H.182, H.216 Ligands: FE2.2, SO4.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.69, A:H.109, A:E.145, H2O.1 ZN.3: 4 residues within 4Å: Chain A: H.182, D.229, H.231 Ligands: SO4.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.182, A:D.229, A:D.229, A:H.231

1 x FE2: FE (II) ION(Non-covalent)

FE2.2: 9 residues within 4Å: Chain A: E.145, D.179, H.182, H.216, N.218, H.231, E.261 Ligands: ZN.1, SO4.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.145, A:D.179, A:H.216, A:E.261, H2O.1

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

SO4.4: 12 residues within 4Å: Chain A: H.69, Y.72, H.109, E.145, D.179, H.182, D.229, H.231, E.261 Ligands: ZN.1, FE2.2, ZN.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.261 Water bridges: A:Y.72 Salt bridges: A:H.109, A:H.182, A:H.231

2 x NI: NICKEL (II) ION(Non-covalent)

NI.5: 2 residues within 4Å: Chain A: K.58, H.60 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.60, H2O.1, H2O.4, H2O.4 NI.6: 2 residues within 4Å: Chain A: G.235, H.241 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.241, H2O.4, H2O.7

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

CL.7: 5 residues within 4Å: Chain A: T.147, A.148, G.149, Q.150, N.153 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirillov, S. et al., Octahedral Iron in Catalytic Sites of Endonuclease IV from Staphylococcus aureus and Escherichia coli . Biochemistry (2025)

Release Date

2024-12-11

Peptides

Endonuclease 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Endonuclease 4

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