SMTL ID : 7o8a.1

diFe-sulerythrin reduced with Na-dithionite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.21 Å

Oligo State

homo-hexamer

Ligands

2 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.1: 7 residues within 4Å: Chain A: E.36 Chain B: G.59, D.62, F.63 Chain C: E.114, W.118 Chain D: R.65 11 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: A:E.36, B:D.62, C:E.114, D:R.65 Water bridges: A:R.33, A:R.33, A:E.36, C:E.114, D:D.62, D:R.65 Salt bridges: A:E.36 BTB.11: 7 residues within 4Å: Chain A: R.65 Chain D: E.36 Chain E: G.59, D.62, F.63 Chain F: E.114, W.118 10 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A, 1 interactions with chain F, 2 interactions with chain E Water bridges: D:R.33, D:R.33, D:E.36, A:D.62, A:R.65, F:E.114 Salt bridges: D:E.36 Hydrogen bonds: A:R.65, E:D.62, E:D.62

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

FE.2: 5 residues within 4Å: Chain A: E.20, E.53, H.56 Chain D: E.126 Ligands: FE.13 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:E.20, A:E.53, A:H.56, D:E.126, H2O.1 FE.3: 5 residues within 4Å: Chain A: E.92, E.126, H.129 Chain D: E.53 Ligands: FE.12 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:E.92, A:E.126, A:H.129, D:E.53, H2O.2 FE.5: 5 residues within 4Å: Chain B: E.92, E.126, H.129 Chain C: E.53 Ligands: FE.9 5 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:E.53, B:E.92, B:E.126, B:H.129, H2O.9 FE.7: 5 residues within 4Å: Chain B: E.20, E.53, H.56 Chain C: E.126 Ligands: FE.8 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:E.20, B:E.53, B:H.56, C:E.126, H2O.9 FE.8: 5 residues within 4Å: Chain B: E.53 Chain C: E.92, E.126, H.129 Ligands: FE.7 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:E.53, C:E.92, C:E.126, C:H.129, H2O.17 FE.9: 5 residues within 4Å: Chain B: E.126 Chain C: E.20, E.53, H.56 Ligands: FE.5 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:E.20, C:E.53, C:H.56, B:E.126, H2O.19 FE.12: 5 residues within 4Å: Chain A: E.126 Chain D: E.20, E.53, H.56 Ligands: FE.3 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:E.20, D:E.53, D:H.56, A:E.126, H2O.24 FE.13: 5 residues within 4Å: Chain A: E.53 Chain D: E.92, E.126, H.129 Ligands: FE.2 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:E.92, D:E.126, D:H.129, A:E.53, H2O.24 FE.15: 5 residues within 4Å: Chain E: E.92, E.126, H.129 Chain F: E.53 Ligands: FE.19 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: E:E.92, E:E.126, E:H.129, F:E.53, H2O.31 FE.17: 5 residues within 4Å: Chain E: E.20, E.53, H.56 Chain F: E.126 Ligands: FE.18 5 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: F:E.126, E:E.20, E:E.53, E:H.56, H2O.32 FE.18: 5 residues within 4Å: Chain E: E.53 Chain F: E.92, E.126, H.129 Ligands: FE.17 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: F:E.92, F:E.126, F:H.129, E:E.53, H2O.39 FE.19: 5 residues within 4Å: Chain E: E.126 Chain F: E.20, E.53, H.56 Ligands: FE.15 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: F:E.20, F:E.53, F:H.56, E:E.126, H2O.41

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

CL.4: 5 residues within 4Å: Chain A: Y.39, P.40, E.41, I.42 Chain C: K.132 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain B: Y.39, P.40, E.41, I.42 Chain C: Q.139 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: K.132 Chain C: Y.39, P.40, E.41, I.42 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain D: Y.39, P.40, E.41, I.42 Chain F: K.132 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain E: Y.39, P.40, E.41, I.42 Chain F: Q.139 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain D: K.132 Chain F: Y.39, P.40, E.41, I.42 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeoung, J.H. et al., Bimetallic Mn, Fe, Co, and Ni Sites in a Four-Helix Bundle Protein: Metal Binding, Structure, and Peroxide Activation. Inorg.Chem. (2021)

Release Date

2021-12-01

Peptides

Sulerythrin: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Sulerythrin

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