SMTL ID : 3ak3.1

Superoxide dismutase from Aeropyrum pernix K1, Fe-bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-tetramer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: H.31, H.79, D.165, H.169 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.31, A:H.79, A:D.165, H2O.1, H2O.3 FE.3: 4 residues within 4Å: Chain B: H.31, H.79, D.165, H.169 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.31, B:H.79, B:D.165, B:H.169, H2O.5, H2O.6 FE.9: 4 residues within 4Å: Chain C: H.31, H.79, D.165, H.169 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.31, C:H.79, C:D.165, H2O.10, H2O.11 FE.11: 4 residues within 4Å: Chain D: H.31, H.79, D.165, H.169 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.31, D:H.79, D:D.165, D:H.169, H2O.13, H2O.15

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

EDO.2: 6 residues within 4Å: Chain A: E.148, K.149, V.152 Chain C: E.148, K.149, V.152 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.148, A:E.148, C:E.148 EDO.4: 4 residues within 4Å: Chain B: P.21, Y.22, Y.175, N.185 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.185 Water bridges: B:Q.174 EDO.5: 4 residues within 4Å: Chain B: K.49, I.60, D.61, V.65 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.61 Water bridges: B:K.49 EDO.6: 7 residues within 4Å: Chain A: L.153 Chain B: R.67, K.149, N.151, V.152 Chain C: R.67 Chain D: E.126 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: B:R.67, B:K.149, B:N.151, D:E.126 Water bridges: C:R.67 EDO.7: 2 residues within 4Å: Chain B: E.20, E.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.20 EDO.8: 6 residues within 4Å: Chain B: A.64, R.67, D.68 Chain C: A.64, R.67, D.68 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.67, B:D.68, C:R.67, C:D.68 Water bridges: B:R.67, C:R.67 EDO.10: 6 residues within 4Å: Chain C: L.142, R.143 Chain D: F.4, L.47, I.50, E.51 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.142, C:R.143 EDO.12: 6 residues within 4Å: Chain A: R.67 Chain B: E.126 Chain C: E.148, L.153 Chain D: R.67, K.149 6 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: D:R.67, D:K.149, B:E.126, C:E.148 Water bridges: D:N.151, A:R.67 EDO.13: 4 residues within 4Å: Chain B: N.177 Chain D: K.34, H.35, T.38 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:H.35, B:N.177 EDO.14: 5 residues within 4Å: Chain C: R.63 Chain D: K.123, T.124, V.125, E.126 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:V.125, C:R.63 Water bridges: D:G.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, T. et al., Crystal structure of the cambialistic superoxide dismutase from Aeropyrum pernix K1 - insights into the enzyme mechanism and stability. Febs J. (2011)

Release Date

2011-02-02

Peptides

Superoxide dismutase [Mn/Fe]: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Superoxide dismutase [Mn/Fe]

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