SMTL ID : 8jd8.1

Crystal structure of Citrus limon Cu-Zn superoxide dismutase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-tetramer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.75, H.83, H.92, D.95, T.148 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.75, A:H.83, A:H.92, A:D.95, A:D.95 ZN.3: 4 residues within 4Å: Chain A: M.14, G.165 Chain C: M.14, G.165 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:M.14, C:G.165, A:M.14, H2O.5, H2O.5 ZN.4: 4 residues within 4Å: Chain B: H.75, H.83, H.92, D.95 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.75, B:H.83, B:H.92, B:D.95, B:D.95 ZN.6: 5 residues within 4Å: Chain C: H.75, H.83, H.92, D.95, T.148 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.75, C:H.83, C:H.92, C:D.95, C:D.95 ZN.8: 5 residues within 4Å: Chain D: H.75, H.83, H.92, D.95, T.148 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.75, D:H.83, D:H.92, D:D.95, D:D.95

4 x CU: COPPER (II) ION(Non-covalent)

CU.2: 4 residues within 4Å: Chain A: H.58, H.60, H.75, H.132 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.58, A:H.60, A:H.75, A:H.132, H2O.1 CU.5: 4 residues within 4Å: Chain B: H.58, H.60, H.75, H.132 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.58, B:H.60, B:H.75, B:H.132 CU.7: 4 residues within 4Å: Chain C: H.58, H.60, H.75, H.132 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.58, C:H.60, C:H.75, C:H.132, H2O.5 CU.9: 4 residues within 4Å: Chain D: H.58, H.60, H.75, H.132 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.58, D:H.60, D:H.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Utami, R.A. et al., Direct relationship between dimeric form and activity in the acidic copper-zinc superoxide dismutase from lemon. Acta Crystallogr.,Sect.F (2023)

Release Date

2023-12-27

Peptides

Superoxide dismutase [Cu-Zn]: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Superoxide dismutase [Cu-Zn]