SMTL ID : 1q0m.1

Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the state after full x-ray-induced reduction

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-hexamer

Ligands

6 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: H.1, C.2, D.3, C.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.2, A:C.6 NI.3: 4 residues within 4Å: Chain B: H.1, C.2, D.3, C.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.2, B:C.6 NI.5: 4 residues within 4Å: Chain C: H.1, C.2, D.3, C.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.2, C:C.6 NI.9: 4 residues within 4Å: Chain D: H.1, C.2, D.3, C.6 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.2, D:C.6 NI.13: 4 residues within 4Å: Chain E: H.1, C.2, D.3, C.6 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:C.2, E:C.6 NI.15: 4 residues within 4Å: Chain F: H.1, C.2, D.3, C.6 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:C.2, F:C.6

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: P.5, G.7, Y.9, D.61, K.64 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.7 Water bridges: A:C.6, A:G.7, A:K.64 Salt bridges: A:K.64 SO4.4: 5 residues within 4Å: Chain B: P.5, G.7, Y.9, D.61, K.64 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.7, B:Y.9 Water bridges: B:C.6, B:K.64, B:K.64, B:K.64 Salt bridges: B:K.64 SO4.6: 5 residues within 4Å: Chain C: P.5, G.7, Y.9, D.61, K.64 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.7 Water bridges: C:H.1, C:C.6, C:K.64, C:K.64, C:K.64 Salt bridges: C:K.64 SO4.7: 3 residues within 4Å: Chain C: Q.46 Chain E: Q.46 Chain F: Q.46 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C, 1 interactions with chain F Hydrogen bonds: E:Q.46, C:Q.46, F:Q.46 SO4.10: 5 residues within 4Å: Chain D: P.5, G.7, Y.9, D.61, K.64 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.7, D:Y.9 Water bridges: D:C.6, D:K.64 Salt bridges: D:K.64 SO4.11: 3 residues within 4Å: Chain A: Q.46 Chain B: Q.46 Chain D: Q.46 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:Q.46, A:Q.46, D:Q.46 SO4.14: 5 residues within 4Å: Chain E: P.5, G.7, Y.9, D.61, K.64 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.7 Water bridges: E:C.6, E:K.64 Salt bridges: E:K.64 SO4.16: 5 residues within 4Å: Chain F: P.5, G.7, Y.9, D.61, K.64 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:G.7 Water bridges: F:C.6, F:K.64, F:K.64 Salt bridges: F:K.64

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.8: 1 residues within 4Å: Chain C: E.69 No protein-ligand interaction detected (PLIP) ACY.12: 1 residues within 4Å: Chain D: E.69 No protein-ligand interaction detected (PLIP) ACY.17: 1 residues within 4Å: Chain F: E.69 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wuerges, J. et al., Crystal structure of nickel-containing superoxide dismutase reveals another type of active site. Proc.Natl.Acad.Sci.USA (2004)

Release Date

2004-05-18

Peptides

Superoxide dismutase [Ni]: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Superoxide dismutase [Ni]

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