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

Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-tetramer

Ligands

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

FE2.1: 5 residues within 4Å: Chain A: E.53, E.94, E.128, H.131 Ligands: FE2.2 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.1 FE2.2: 5 residues within 4Å: Chain A: E.20, E.53, H.56, E.128 Ligands: FE2.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.20, A:E.53, A:H.56, A:E.128, H2O.6 FE2.3: 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 FE2.4: 5 residues within 4Å: Chain B: E.53, E.94, E.128, H.131 Ligands: FE2.5 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.12 FE2.5: 5 residues within 4Å: Chain B: E.20, E.53, H.56, E.128 Ligands: FE2.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.20, B:E.53, B:H.56, B:E.128, H2O.17 FE2.6: 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 FE2.7: 5 residues within 4Å: Chain C: E.53, E.94, E.128, H.131 Ligands: FE2.8 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.22 FE2.8: 5 residues within 4Å: Chain C: E.20, E.53, H.56, E.128 Ligands: FE2.7 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.20, C:E.53, C:H.56, C:E.128, H2O.27 FE2.9: 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 FE2.10: 5 residues within 4Å: Chain D: E.53, E.94, E.128, H.131 Ligands: FE2.11 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.33 FE2.11: 5 residues within 4Å: Chain D: E.20, E.53, H.56, E.128 Ligands: FE2.10 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.20, D:E.53, D:H.56, D:E.128, H2O.38 FE2.12: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, S. et al., X-ray Crystal Structures of Reduced Rubrerythrin and its Azide Adduct: A Structure-Based Mechanism for a Non-Heme DiIron Peroxidase. J.Am.Chem.Soc. (2002)

Release Date

2002-09-18

Peptides

Rubrerythrin all-iron(II) form: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Rubrerythrin all-iron(II) form

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