SMTL ID : 3ak2.1

Superoxide dismutase from Aeropyrum pernix K1, Mn-bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: H.31, H.79, D.165, H.169 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.31, A:H.79, A:D.165, A:H.169, H2O.1 MN.7: 4 residues within 4Å: Chain B: H.31, H.79, D.165, H.169 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.31, B:H.79, B:D.165, B:H.169, H2O.7 MN.12: 4 residues within 4Å: Chain C: H.31, H.79, D.165, H.169 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.31, C:H.79, C:D.165, C:H.169, H2O.15 MN.17: 4 residues within 4Å: Chain D: H.31, H.79, D.165, H.169 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.31, D:H.79, D:D.165, D:H.169, H2O.22

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

EDO.2: 5 residues within 4Å: Chain A: E.148, K.149 Chain C: E.148, K.149 Ligands: EDO.4 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: P.11, L.12, Y.14, N.15, Y.16, H.32 Ligands: EDO.6 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain C: V.152 Chain D: V.152 Ligands: EDO.2, EDO.10, EDO.15, EDO.22 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: K.34, H.35, T.38 Chain C: N.177 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: L.9, P.10, P.11, H.32 Ligands: EDO.3 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain B: P.21, Y.22, Q.174, Y.175, N.185 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain B: P.11, L.12, Y.14, Y.16, H.32 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain B: E.148, K.149, V.152 Chain D: E.148, K.149, V.152 Ligands: EDO.4, EDO.15 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain B: H.35, Y.39, W.167, H.169 Chain D: E.168, R.179 Ligands: EDO.20 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain C: P.11, L.12, Y.16, H.32 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain C: Q.107, F.108, L.142, R.143 Chain D: F.4, L.47 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain B: R.67, K.149 Chain C: R.67 Chain D: E.148, L.153 Ligands: EDO.4, EDO.10 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: W.167 Chain C: V.125, G.127, E.168, R.179 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain D: P.96, G.97, G.98, W.192, D.193, E.196 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain C: T.124 Chain D: D.61, V.62, R.63 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: Y.39, F.71, W.167 Chain D: V.125, E.126, G.127 Ligands: EDO.11 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain D: P.11, L.12, Y.14, Y.16, H.32 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: R.67, K.149 Chain C: E.148, L.153 Chain D: R.67 Ligands: EDO.4 Ligand excluded by PLIP

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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