SMTL ID : 8vj5.1

Peroxide-Soaked MnSOD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-tetramer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: H.27, H.75, D.160, H.164 Ligands: PEO.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.27, A:H.75, A:D.160, A:H.164 MN.4: 5 residues within 4Å: Chain B: H.27, H.75, D.160, H.164 Ligands: PEO.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.27, B:H.75, B:D.160, B:H.164 MN.7: 5 residues within 4Å: Chain C: H.27, H.75, D.160, H.164 Ligands: PEO.8 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.27, C:H.75, C:D.160, C:H.164 MN.10: 5 residues within 4Å: Chain D: H.27, H.75, D.160, H.164 Ligands: PEO.11 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.27, D:H.75, D:D.160, D:H.164

4 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.2: 8 residues within 4Å: Chain A: Y.35, H.75, W.124, Q.144, D.160, W.162, H.164 Ligands: MN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.144, A:W.162 PEO.5: 8 residues within 4Å: Chain B: Y.35, H.75, W.124, Q.144, D.160, W.162, H.164 Ligands: MN.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.35, B:Q.144, B:W.162 PEO.8: 8 residues within 4Å: Chain C: Y.35, H.75, W.124, Q.144, D.160, W.162, H.164 Ligands: MN.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.35, C:Q.144, C:W.162 PEO.11: 8 residues within 4Å: Chain D: Y.35, H.75, W.124, Q.144, D.160, W.162, H.164 Ligands: MN.10 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.144, D:W.162

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: K.2, H.3, S.4, H.72 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.4 Water bridges: A:H.3, A:S.4, A:H.72, B:G.53 Salt bridges: A:H.3, A:H.72 PO4.6: 3 residues within 4Å: Chain B: H.3, S.4, H.72 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.4 Water bridges: B:H.3, B:S.4, B:H.72, B:S.76 Salt bridges: B:H.3, B:H.72 PO4.9: 4 residues within 4Å: Chain C: K.2, H.3, S.4, H.72 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.4 Water bridges: C:S.4, C:H.72, D:G.53 Salt bridges: C:H.3, C:H.72 PO4.12: 3 residues within 4Å: Chain D: H.3, S.4, H.72 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.4 Water bridges: D:H.3, D:H.3, D:S.4, D:S.76 Salt bridges: D:H.3, D:H.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Azadmanesh, J. et al., Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition. Nat Commun (2024)

Release Date

2024-07-31

Peptides

Superoxide dismutase [Mn], mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Superoxide dismutase [Mn], mitochondrial

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