SMTL ID : 8iq1.1 (3 other biounits)

Crystal structure of hydrogen sulfide-bound superoxide dismutase in reduced state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x CU: COPPER (II) ION(Non-covalent)

CU.1: 5 residues within 4Å: Chain A: H.44, H.46, H.61, V.116, H.118 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.44, A:H.46, A:H.118 CU.4: 4 residues within 4Å: Chain B: H.44, H.46, H.61, H.118 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.44, B:H.46, B:H.118

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.61, H.69, H.78, D.81, K.134 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.61, A:H.69, A:H.78, A:D.81, A:D.81 ZN.5: 5 residues within 4Å: Chain B: H.61, H.69, H.78, D.81, K.134 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.61, B:H.69, B:H.78, B:D.81, B:D.81

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 2 residues within 4Å: Chain A: S.105, G.106 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.103, A:E.107 EDO.7: 3 residues within 4Å: Chain B: I.94, D.96 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.96 EDO.8: 4 residues within 4Å: Chain B: T.30, V.95, D.96 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.96 Water bridges: B:I.97 EDO.9: 2 residues within 4Å: Chain B: G.106, E.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.107 Water bridges: B:Y.108 EDO.10: 4 residues within 4Å: Chain B: P.72, G.83, N.84, L.124 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.84, B:N.84 Water bridges: B:N.84

1 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.6: 5 residues within 4Å: Chain B: H.46, H.61, H.118, T.135, R.141 No protein-ligand interaction detected (PLIP)

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

SO4.11: 4 residues within 4Å: Chain A: I.149 Chain B: Q.47, F.48, R.113 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.47 Salt bridges: B:R.113

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

CL.12: 3 residues within 4Å: Chain B: P.60, H.61, N.63 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, D.D. et al., Hydrogen sulfide functions as a micro-modulator bound at the copper active site of Cu/Zn-SOD to regulate the catalytic activity of the enzyme. Cell Rep (2023)

Release Date

2023-09-06

Peptides

Superoxide dismutase [Cu-Zn]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Superoxide dismutase [Cu-Zn]

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