SMTL ID : 6zs1.1

Chaetomium thermophilum CuZn-superoxide dismutase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-octamer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.67, H.75, H.84, D.87, K.140 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.67, A:H.75, A:H.84, A:D.87, A:D.87 ZN.7: 5 residues within 4Å: Chain B: H.67, H.75, H.84, D.87, K.140 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.67, B:H.75, B:H.84, B:D.87, B:D.87 ZN.12: 5 residues within 4Å: Chain C: H.67, H.75, H.84, D.87, K.140 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.67, C:H.75, C:H.84, C:D.87, C:D.87 ZN.17: 5 residues within 4Å: Chain D: H.67, H.75, H.84, D.87, K.140 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.67, D:H.75, D:H.84, D:D.87, D:D.87 ZN.21: 5 residues within 4Å: Chain E: H.67, H.75, H.84, D.87, K.140 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:H.67, E:H.75, E:H.84, E:D.87, E:D.87 ZN.27: 5 residues within 4Å: Chain F: H.67, H.75, H.84, D.87, K.140 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:H.67, F:H.75, F:H.84, F:D.87, F:D.87 ZN.31: 5 residues within 4Å: Chain G: H.67, H.75, H.84, D.87, K.140 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:H.67, G:H.75, G:H.84, G:D.87, G:D.87 ZN.34: 5 residues within 4Å: Chain H: H.67, H.75, H.84, D.87, K.140 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:H.67, H:H.75, H:H.84, H:D.87, H:D.87

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

PO4.2: 5 residues within 4Å: Chain A: H.124, T.141, G.145, P.146, R.147 8 PLIP interactions: 8 interactions with chain A Water bridges: A:H.124, A:H.124, A:T.141, A:R.147, A:R.147, A:R.147 Salt bridges: A:H.124, A:R.147 PO4.3: 2 residues within 4Å: Chain A: K.73 Chain B: K.73 14 PLIP interactions: 7 interactions with chain A, 7 interactions with chain B Water bridges: A:K.73, A:K.73, A:K.73, A:K.73, A:K.73, A:K.73, B:K.73, B:K.73, B:K.73, B:K.73, B:K.73, B:K.73 Salt bridges: A:K.73, B:K.73 PO4.8: 5 residues within 4Å: Chain B: H.124, T.141, G.145, P.146, R.147 8 PLIP interactions: 8 interactions with chain B Water bridges: B:G.145, B:R.147, B:R.147, B:R.147, B:R.147, B:R.147 Salt bridges: B:H.124, B:R.147 PO4.16: 5 residues within 4Å: Chain C: H.124, T.141, G.145, P.146, R.147 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.145, C:G.145 Water bridges: C:R.147, C:R.147, C:R.147 Salt bridges: C:H.124, C:R.147 PO4.19: 5 residues within 4Å: Chain D: H.124, T.141, G.145, P.146, R.147 8 PLIP interactions: 8 interactions with chain D Water bridges: D:H.124, D:T.141, D:R.147, D:R.147, D:R.147, D:R.147 Salt bridges: D:H.124, D:R.147 PO4.32: 6 residues within 4Å: Chain C: N.96 Chain G: H.124, T.141, G.145, P.146, R.147 8 PLIP interactions: 7 interactions with chain G, 1 interactions with chain C Hydrogen bonds: G:G.145, C:N.96 Water bridges: G:R.147, G:R.147, G:R.147, G:R.147 Salt bridges: G:H.124, G:R.147 PO4.35: 7 residues within 4Å: Chain D: N.96 Chain H: H.124, T.141, G.145, P.146, R.147 Ligands: NA.38 9 PLIP interactions: 7 interactions with chain H, 2 interactions with chain D Hydrogen bonds: H:G.145, D:N.96, D:N.96 Water bridges: H:R.147, H:R.147, H:R.147, H:R.147 Salt bridges: H:H.124, H:R.147

15 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: L.88, N.90, M.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.88, A:N.90 NA.5: 2 residues within 4Å: Chain A: I.33 Chain D: T.102 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:T.102 Water bridges: D:T.102, A:T.102 NA.6: 4 residues within 4Å: Chain A: K.6, A.7, T.22, A.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.6, A:A.7 Water bridges: A:K.6 NA.9: 8 residues within 4Å: Chain B: S.30, P.31, T.32, D.105, H.106, L.107, V.108, K.109 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.30, B:T.32, B:K.109 NA.10: 4 residues within 4Å: Chain B: K.6, A.7, T.22, A.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.7, B:A.7 NA.11: 1 residues within 4Å: Chain B: V.5 No protein-ligand interaction detected (PLIP) NA.14: 3 residues within 4Å: Chain C: R.12, G.13, S.15 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.12 Water bridges: C:G.13, C:S.15 NA.20: 1 residues within 4Å: Chain D: T.104 5 PLIP interactions: 5 interactions with chain D Water bridges: D:P.78, D:P.78, D:T.104, D:T.104, D:D.105 NA.23: 7 residues within 4Å: Chain E: E.28, K.109, I.111, G.112, P.113, E.114, S.115 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.28, E:I.111, E:E.114 NA.24: 3 residues within 4Å: Chain E: T.104, D.105, H.106 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.104 Water bridges: E:T.104, E:D.105, E:H.106 NA.25: 5 residues within 4Å: Chain E: H.124, T.141, A.144, G.145 Ligands: GOL.26 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:H.124, E:A.144, E:G.145 NA.30: 1 residues within 4Å: Chain F: L.130 1 PLIP interactions: 1 interactions with chain F Water bridges: F:N.90 NA.33: 3 residues within 4Å: Chain G: H.71, L.107, K.109 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:L.107 NA.36: 3 residues within 4Å: Chain H: R.12, G.13, S.15 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:R.12, H:S.15, H:S.15 Water bridges: H:G.13 NA.38: 4 residues within 4Å: Chain A: S.29 Chain H: P.66, R.147 Ligands: PO4.35 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain A Hydrogen bonds: H:R.147, A:S.29, A:S.29

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

CU.13: 4 residues within 4Å: Chain C: H.50, H.52, H.67, H.124 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.50, C:H.52, C:H.67, C:H.124, H2O.30 CU.18: 4 residues within 4Å: Chain D: H.50, H.52, H.67, H.124 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.50, D:H.52, D:H.67, D:H.124, H2O.42 CU.22: 4 residues within 4Å: Chain E: H.50, H.52, H.67, H.124 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.50, E:H.52, E:H.67, E:H.124, H2O.53 CU.28: 5 residues within 4Å: Chain F: H.50, H.52, H.67, H.124 Ligands: GOL.29 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.50, F:H.52, F:H.67, F:H.124, H2O.64

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 3 residues within 4Å: Chain C: S.27, E.28, S.29 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.29, C:S.29 Water bridges: C:S.27, C:S.27, C:E.28 GOL.26: 5 residues within 4Å: Chain E: H.124, T.141, G.145, R.147 Ligands: NA.25 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.147, E:R.147 GOL.29: 7 residues within 4Å: Chain F: H.52, H.67, H.124, T.141, G.145, R.147 Ligands: CU.28 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:H.67, F:G.145, F:R.147 Water bridges: F:T.141, F:G.145 GOL.37: 5 residues within 4Å: Chain C: G.133, G.134, N.135 Chain H: R.47, T.127 6 PLIP interactions: 5 interactions with chain H, 1 interactions with chain C Hydrogen bonds: H:R.47, H:R.47, H:T.127, C:N.135 Water bridges: H:T.127, H:T.127

Links

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Citation

Mohsin, I. et al., Crystal Structure of a Cu,Zn Superoxide Dismutase From the Thermophilic Fungus Chaetomium thermophilum. Protein Pept.Lett. (2021)

Release Date

2021-04-07

Peptides

Superoxide dismutase [Cu-Zn]: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Superoxide dismutase [Cu-Zn]