SMTL ID : 5t30.1

Human MnSOD-azide complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 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: AZI.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.27, A:H.75, A:D.160, A:H.164, H2O.1 MN.6: 4 residues within 4Å: Chain B: H.27, H.75, D.160, H.164 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.27, B:H.75, B:D.160, B:H.164, H2O.7 MN.8: 5 residues within 4Å: Chain C: H.27, H.75, D.160, H.164 Ligands: AZI.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.27, C:H.75, C:D.160, C:H.164, H2O.14 MN.13: 4 residues within 4Å: Chain D: H.27, H.75, D.160, H.164 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.27, D:H.75, D:D.160, D:H.164, H2O.21

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

PO4.2: 3 residues within 4Å: Chain A: H.3, H.72 Chain B: G.53 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.72, A:S.76 Salt bridges: A:H.3, A:H.72 PO4.7: 3 residues within 4Å: Chain A: G.53 Chain B: H.3, H.72 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Water bridges: B:H.3, B:S.4, B:H.72, B:S.76, B:S.76 Salt bridges: B:H.3, B:H.72 Hydrogen bonds: A:G.53 PO4.9: 3 residues within 4Å: Chain C: H.3, H.72 Chain D: G.53 4 PLIP interactions: 4 interactions with chain C Water bridges: C:H.72, C:S.76 Salt bridges: C:H.3, C:H.72 PO4.14: 3 residues within 4Å: Chain C: G.53 Chain D: H.3, H.72 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:G.53 Water bridges: D:H.3, D:S.4, D:H.72, D:S.76, D:S.76 Salt bridges: D:H.3, D:H.72

4 x K: POTASSIUM ION(Non-covalent)

K.3: 1 residues within 4Å: Chain A: G.13 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.13, H2O.3 K.4: 3 residues within 4Å: Chain A: P.17, Q.169, Y.170 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:P.17, A:Y.170, H2O.6 K.10: 1 residues within 4Å: Chain C: G.13 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:G.13, H2O.16 K.11: 3 residues within 4Å: Chain C: P.17, Q.169, Y.170 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:P.17, C:Y.170, H2O.20

2 x AZI: AZIDE ION(Non-covalent)

AZI.5: 8 residues within 4Å: Chain A: H.27, H.31, H.32, Y.35, H.75, D.160, H.164 Ligands: MN.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.31 Water bridges: A:H.31, A:H.31, A:Q.144, A:Q.144 AZI.12: 8 residues within 4Å: Chain C: H.27, H.31, H.32, Y.35, H.75, D.160, H.164 Ligands: MN.8 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.27 Water bridges: C:Q.144, C:Q.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Azadmanesh, J. et al., Substrate-analog binding and electrostatic surfaces of human manganese superoxide dismutase. J. Struct. Biol. (2017)

Release Date

2017-05-17

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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