SMTL ID : 9nr0.1

Finding the exit route of hydrogen peroxide from the manganese superoxide dismutase (MnSOD) active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

3 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: P.17, H.18, Q.169, Y.170, A.180 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.170, H2O.11, H2O.13 K.10: 1 residues within 4Å: Chain B: P.17 No protein-ligand interaction detected (PLIP) K.11: 3 residues within 4Å: Chain B: G.86, G.87, N.183 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.86, B:N.183, H2O.22

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

PO4.2: 5 residues within 4Å: Chain A: G.53, D.54, V.55, T.56 Chain B: I.73 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.54, A:V.55, A:T.56, A:T.56 Water bridges: A:G.53, A:A.57 PO4.4: 5 residues within 4Å: Chain A: H.3, S.4, H.72 Chain B: G.53 Ligands: PO4.14 5 PLIP interactions: 5 interactions with chain A Water bridges: A:H.3, A:H.3, A:H.3 Salt bridges: A:H.3, A:H.72 PO4.5: 1 residues within 4Å: Chain A: K.171 4 PLIP interactions: 4 interactions with chain A Water bridges: A:L.168, A:K.171, A:K.171 Salt bridges: A:K.171 PO4.6: 1 residues within 4Å: Chain B: K.171 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.171 PO4.7: 3 residues within 4Å: Chain B: S.104, D.106, K.107 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.104, B:S.104, B:S.104, B:D.106 Water bridges: B:D.106 PO4.9: 2 residues within 4Å: Chain B: K.66, N.143 6 PLIP interactions: 6 interactions with chain B Water bridges: B:K.66, B:K.66, B:N.143, B:N.143, B:D.145 Salt bridges: B:K.66 PO4.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PO4.13: 3 residues within 4Å: Chain B: H.3, S.4, H.72 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.4, B:S.4 Salt bridges: B:H.3, B:H.72 PO4.14: 6 residues within 4Å: Chain A: I.73 Chain B: G.53, D.54, V.55, T.56 Ligands: PO4.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.54, B:D.54, B:D.54, B:V.55, B:T.56, B:T.56 PO4.15: 1 residues within 4Å: Chain B: K.30 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.30, B:K.30, B:K.30 Salt bridges: B:K.30 PO4.16: 1 residues within 4Å: Chain B: K.45 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.45, B:K.45, B:K.45 Salt bridges: B:K.45

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

MN.3: 6 residues within 4Å: Chain A: H.27, H.75, W.124, D.160, W.162, H.164 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.27, A:H.75, A:D.160, H2O.1, H2O.5 MN.8: 7 residues within 4Å: Chain B: H.27, Y.35, H.75, W.124, D.160, W.162, H.164 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.27, B:H.75, B:D.160, H2O.15, H2O.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dasgupta, M. et al., Mapping the Exit Route of Hydrogen Peroxide From the Manganese Superoxide Dismutase (MnSOD) Active Site. Biorxiv (2025)

Release Date

2025-08-27

Peptides

Superoxide dismutase [Mn], mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Superoxide dismutase [Mn], mitochondrial

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