SMTL ID : 1qyb.2 (1 other biounit)

X-ray crystal structure of Desulfovibrio vulgaris rubrerythrin with zinc substituted into the [Fe(SCys)4] site and alternative diiron site structures

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: E.53, E.94, E.128, H.131 Ligands: FE.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.53, A:E.94, A:E.128, A:H.131, H2O.4 FE.2: 5 residues within 4Å: Chain A: E.20, E.53, E.97, E.128 Ligands: FE.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.20, A:E.20, A:E.97, A:E.128, H2O.4 FE.5: 5 residues within 4Å: Chain B: E.53, E.94, E.128, H.131 Ligands: FE.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.53, B:E.94, B:E.128, B:H.131, H2O.13 FE.6: 5 residues within 4Å: Chain B: E.20, E.53, E.97, E.128 Ligands: FE.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.20, B:E.20, B:E.97, B:E.128, H2O.13 FE.9: 5 residues within 4Å: Chain C: E.53, E.94, E.128, H.131 Ligands: FE.10 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.53, C:E.94, C:E.128, C:H.131, H2O.23 FE.10: 5 residues within 4Å: Chain C: E.20, E.53, E.97, E.128 Ligands: FE.9 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.20, C:E.20, C:E.97, C:E.128, H2O.23 FE.13: 5 residues within 4Å: Chain D: E.53, E.94, E.128, H.131 Ligands: FE.14 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.53, D:E.94, D:E.128, D:H.131, H2O.32 FE.14: 5 residues within 4Å: Chain D: E.20, E.53, E.97, E.128 Ligands: FE.13 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.20, D:E.20, D:E.97, D:E.128, H2O.32

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.158, C.161, C.174, C.177 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.158, A:C.161, A:C.174, A:C.177 ZN.7: 4 residues within 4Å: Chain B: C.158, C.161, C.174, C.177 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.158, B:C.161, B:C.174, B:C.177 ZN.11: 4 residues within 4Å: Chain C: C.158, C.161, C.174, C.177 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.158, C:C.161, C:C.174, C:C.177 ZN.15: 4 residues within 4Å: Chain D: C.158, C.161, C.174, C.177 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.158, D:C.161, D:C.174, D:C.177

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

SO4.4: 4 residues within 4Å: Chain A: R.146, R.150, E.151, Q.152 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.151, A:Q.152, A:Q.152 Water bridges: A:R.146, A:R.146, A:Q.152 Salt bridges: A:R.146 SO4.8: 4 residues within 4Å: Chain B: R.146, R.150, E.151, Q.152 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.151, B:Q.152, B:Q.152 Water bridges: B:R.146, B:R.146, B:Q.152 Salt bridges: B:R.146 SO4.12: 4 residues within 4Å: Chain C: R.146, R.150, E.151, Q.152 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.151, C:Q.152, C:Q.152 Water bridges: C:R.146, C:R.146, C:Q.152 Salt bridges: C:R.146 SO4.16: 4 residues within 4Å: Chain D: R.146, R.150, E.151, Q.152 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.151, D:Q.152, D:Q.152 Water bridges: D:R.146, D:R.146, D:Q.152 Salt bridges: D:R.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, S. et al., X-ray Crystal Structure of Desulfovibrio vulgaris Rubrerythrin with Zinc Substituted into the [Fe(SCys)(4)] Site and Alternative Diiron Site Structures. Biochemistry (2004)

Release Date

2004-03-30

Peptides

Rubrerythrin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Rubrerythrin

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