Zinc in PDB 6zs1: Chaetomium Thermophilum Cuzn-Superoxide Dismutase

Enzymatic activity of Chaetomium Thermophilum Cuzn-Superoxide Dismutase

All present enzymatic activity of Chaetomium Thermophilum Cuzn-Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of Chaetomium Thermophilum Cuzn-Superoxide Dismutase, PDB code: 6zs1 was solved by A.C.Papageorgiou, I.Mohsin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.59 / 1.56
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 89.11, 89.11, 310.37, 90, 90, 120
R / Rfree (%) 17.3 / 20.4

Other elements in 6zs1:

The structure of Chaetomium Thermophilum Cuzn-Superoxide Dismutase also contains other interesting chemical elements:

Sodium (Na) 15 atoms
Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase (pdb code 6zs1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase, PDB code: 6zs1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6zs1

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Zinc binding site 1 out of 8 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:13.9
occ:1.00
OD1 A:ASP84 2.0 13.3 1.0
ND1 A:HIS64 2.0 13.8 1.0
ND1 A:HIS72 2.0 12.5 1.0
ND1 A:HIS81 2.0 12.1 1.0
CG A:ASP84 2.7 11.1 1.0
OD2 A:ASP84 2.9 11.6 1.0
CE1 A:HIS72 2.9 15.7 1.0
CE1 A:HIS64 2.9 14.8 1.0
CE1 A:HIS81 2.9 12.7 1.0
CG A:HIS64 3.0 15.3 1.0
CG A:HIS81 3.1 13.7 1.0
CG A:HIS72 3.1 14.8 1.0
CB A:HIS64 3.4 17.0 1.0
CB A:HIS81 3.5 12.8 1.0
CB A:HIS72 3.6 11.8 1.0
O A:LYS137 3.8 17.6 1.0
CA A:HIS72 3.8 11.1 1.0
NE2 A:HIS64 4.0 19.9 1.0
NE2 A:HIS72 4.1 13.7 1.0
NE2 A:HIS81 4.1 14.2 1.0
CD2 A:HIS64 4.1 21.0 1.0
CB A:ASP84 4.1 12.4 1.0
CD2 A:HIS81 4.1 11.4 1.0
CD2 A:HIS72 4.2 12.8 1.0
CA A:ASP84 4.6 10.8 1.0
N A:HIS81 4.6 11.8 1.0
O A:HOH699 4.6 21.3 1.0
CA A:HIS81 4.7 13.5 1.0
N A:GLY73 4.7 13.1 1.0
N A:ASP84 4.8 12.3 1.0
C A:LYS137 4.8 16.9 1.0
C A:HIS72 4.8 14.2 1.0
N A:HIS72 4.8 12.6 1.0
CA A:HIS64 4.9 14.3 1.0

Zinc binding site 2 out of 8 in 6zs1

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Zinc binding site 2 out of 8 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:14.0
occ:1.00
OD1 B:ASP84 1.9 13.5 1.0
ND1 B:HIS64 2.0 13.2 1.0
ND1 B:HIS72 2.0 12.1 1.0
ND1 B:HIS81 2.0 14.3 1.0
CG B:ASP84 2.7 13.5 1.0
CE1 B:HIS72 2.9 14.0 1.0
OD2 B:ASP84 2.9 12.1 1.0
CE1 B:HIS64 2.9 15.4 1.0
CE1 B:HIS81 2.9 15.3 1.0
CG B:HIS64 3.0 14.0 1.0
CG B:HIS81 3.1 14.1 1.0
CG B:HIS72 3.1 15.0 1.0
CB B:HIS64 3.3 14.7 1.0
CB B:HIS81 3.5 13.7 1.0
CB B:HIS72 3.5 13.6 1.0
O B:LYS137 3.8 17.5 1.0
CA B:HIS72 3.9 12.3 1.0
NE2 B:HIS64 4.0 19.3 1.0
NE2 B:HIS72 4.0 13.0 1.0
NE2 B:HIS81 4.1 13.7 1.0
CD2 B:HIS64 4.1 19.0 1.0
CB B:ASP84 4.1 14.2 1.0
CD2 B:HIS81 4.2 11.6 1.0
CD2 B:HIS72 4.2 12.5 1.0
CA B:ASP84 4.6 14.1 1.0
N B:HIS81 4.6 14.7 1.0
CA B:HIS81 4.7 13.0 1.0
N B:GLY73 4.7 12.6 1.0
O B:HOH720 4.7 18.2 1.0
N B:ASP84 4.8 12.8 1.0
C B:LYS137 4.8 17.0 1.0
C B:HIS72 4.8 13.5 1.0
N B:HIS72 4.9 13.4 1.0
CA B:HIS64 4.9 13.3 1.0

Zinc binding site 3 out of 8 in 6zs1

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Zinc binding site 3 out of 8 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:16.7
occ:1.00
OD1 C:ASP84 2.0 14.4 1.0
ND1 C:HIS64 2.0 18.4 1.0
ND1 C:HIS81 2.0 15.3 1.0
ND1 C:HIS72 2.1 16.6 1.0
CG C:ASP84 2.7 15.9 1.0
CE1 C:HIS81 2.9 17.6 1.0
OD2 C:ASP84 2.9 16.1 1.0
CE1 C:HIS72 2.9 14.5 1.0
CG C:HIS64 3.0 18.3 1.0
CE1 C:HIS64 3.0 20.2 1.0
CG C:HIS81 3.1 15.3 1.0
CG C:HIS72 3.2 18.4 1.0
CB C:HIS64 3.3 18.8 1.0
CB C:HIS81 3.5 13.6 1.0
CB C:HIS72 3.6 15.6 1.0
O C:LYS137 3.8 23.0 1.0
CA C:HIS72 3.9 12.9 1.0
NE2 C:HIS81 4.0 15.4 1.0
NE2 C:HIS64 4.1 21.3 1.0
NE2 C:HIS72 4.1 19.7 1.0
CD2 C:HIS64 4.1 17.4 1.0
CD2 C:HIS81 4.1 20.9 1.0
CB C:ASP84 4.1 14.5 1.0
CD2 C:HIS72 4.2 18.4 1.0
CA C:ASP84 4.6 12.9 1.0
N C:HIS81 4.7 18.1 1.0
N C:GLY73 4.8 16.6 1.0
CA C:HIS81 4.8 14.1 1.0
O C:HOH677 4.8 22.0 1.0
C C:LYS137 4.8 21.7 1.0
CA C:HIS64 4.8 15.4 1.0
C C:HIS72 4.9 19.6 1.0
N C:HIS72 4.9 14.7 1.0
N C:ASP84 4.9 12.6 1.0
CD2 C:HIS47 4.9 20.1 1.0

Zinc binding site 4 out of 8 in 6zs1

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Zinc binding site 4 out of 8 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:16.9
occ:1.00
ND1 D:HIS64 1.9 16.3 1.0
OD1 D:ASP84 2.0 15.2 1.0
ND1 D:HIS81 2.0 15.1 1.0
ND1 D:HIS72 2.1 15.7 1.0
CG D:ASP84 2.7 15.3 1.0
OD2 D:ASP84 2.9 15.0 1.0
CE1 D:HIS81 2.9 15.7 1.0
CE1 D:HIS64 2.9 22.0 1.0
CG D:HIS64 2.9 18.3 1.0
CE1 D:HIS72 3.0 14.8 1.0
CG D:HIS81 3.1 15.8 1.0
CG D:HIS72 3.2 19.2 1.0
CB D:HIS64 3.3 20.1 1.0
CB D:HIS81 3.5 13.8 1.0
CB D:HIS72 3.6 14.9 1.0
O D:LYS137 3.8 21.4 1.0
CA D:HIS72 3.9 13.9 1.0
NE2 D:HIS81 4.0 16.7 1.0
NE2 D:HIS64 4.0 21.1 1.0
CD2 D:HIS64 4.1 16.9 1.0
CD2 D:HIS81 4.1 21.5 1.0
NE2 D:HIS72 4.1 18.2 1.0
CB D:ASP84 4.1 14.0 1.0
CD2 D:HIS72 4.3 18.9 1.0
CA D:ASP84 4.6 12.2 1.0
N D:HIS81 4.7 17.3 1.0
CA D:HIS81 4.7 15.4 1.0
O D:HOH668 4.7 23.3 1.0
N D:GLY73 4.7 17.7 1.0
C D:LYS137 4.8 20.1 1.0
CA D:HIS64 4.8 17.9 1.0
C D:HIS72 4.8 19.8 1.0
N D:HIS72 4.9 16.8 1.0
N D:ASP84 4.9 14.2 1.0
CD2 D:HIS47 4.9 21.2 1.0

Zinc binding site 5 out of 8 in 6zs1

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Zinc binding site 5 out of 8 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:17.9
occ:1.00
OD1 E:ASP84 1.9 16.5 1.0
ND1 E:HIS64 1.9 16.8 1.0
ND1 E:HIS81 2.0 17.0 1.0
ND1 E:HIS72 2.1 19.0 1.0
CG E:ASP84 2.7 18.7 1.0
OD2 E:ASP84 2.8 17.7 1.0
CE1 E:HIS64 2.9 21.7 1.0
CE1 E:HIS81 2.9 17.1 1.0
CE1 E:HIS72 2.9 18.1 1.0
CG E:HIS64 3.0 21.6 1.0
CG E:HIS81 3.0 17.5 1.0
CG E:HIS72 3.2 21.0 1.0
CB E:HIS64 3.4 16.9 1.0
CB E:HIS81 3.5 15.9 1.0
CB E:HIS72 3.6 15.9 1.0
O E:LYS137 3.7 23.7 1.0
CA E:HIS72 3.9 19.2 1.0
NE2 E:HIS81 4.0 16.8 1.0
NE2 E:HIS64 4.0 20.2 1.0
CD2 E:HIS64 4.1 19.0 1.0
CD2 E:HIS81 4.1 20.0 1.0
CB E:ASP84 4.1 17.2 1.0
NE2 E:HIS72 4.1 18.7 1.0
CD2 E:HIS72 4.3 19.5 1.0
CA E:ASP84 4.6 14.8 1.0
N E:HIS81 4.6 15.6 1.0
CA E:HIS81 4.7 18.8 1.0
C E:LYS137 4.7 20.1 1.0
N E:GLY73 4.7 20.7 1.0
N E:ASP84 4.8 15.9 1.0
O E:HOH675 4.8 24.1 1.0
C E:HIS72 4.8 23.1 1.0
N E:HIS72 4.9 17.1 1.0
CA E:HIS64 4.9 15.5 1.0
CD2 E:HIS47 5.0 20.9 1.0
CA E:THR138 5.0 19.5 1.0

Zinc binding site 6 out of 8 in 6zs1

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Zinc binding site 6 out of 8 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:18.4
occ:1.00
OD1 F:ASP84 1.9 19.0 1.0
ND1 F:HIS64 2.0 17.0 1.0
ND1 F:HIS81 2.0 16.0 1.0
ND1 F:HIS72 2.1 18.6 1.0
CG F:ASP84 2.7 17.4 1.0
CE1 F:HIS81 2.8 16.9 1.0
OD2 F:ASP84 2.8 17.5 1.0
CE1 F:HIS72 2.9 18.3 1.0
CE1 F:HIS64 2.9 22.2 1.0
CG F:HIS64 3.0 19.9 1.0
CG F:HIS81 3.0 17.1 1.0
CG F:HIS72 3.2 22.7 1.0
CB F:HIS64 3.4 16.2 1.0
CB F:HIS81 3.5 15.0 1.0
CB F:HIS72 3.7 19.0 1.0
O F:LYS137 3.8 24.3 1.0
CA F:HIS72 3.9 17.8 1.0
NE2 F:HIS81 4.0 18.0 1.0
NE2 F:HIS64 4.0 21.0 1.0
NE2 F:HIS72 4.1 19.5 1.0
CD2 F:HIS81 4.1 19.8 1.0
CD2 F:HIS64 4.1 19.6 1.0
CB F:ASP84 4.1 15.6 1.0
CD2 F:HIS72 4.2 21.1 1.0
CA F:ASP84 4.6 17.5 1.0
N F:HIS81 4.7 15.1 1.0
CA F:HIS81 4.7 18.7 1.0
N F:GLY73 4.7 18.5 1.0
C F:LYS137 4.7 22.3 1.0
N F:ASP84 4.8 17.3 1.0
C F:HIS72 4.8 20.0 1.0
CA F:HIS64 4.9 17.9 1.0
N F:HIS72 4.9 17.5 1.0
CD2 F:HIS47 4.9 24.8 1.0
O F:HOH700 4.9 27.4 1.0
CA F:THR138 5.0 19.8 1.0

Zinc binding site 7 out of 8 in 6zs1

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Zinc binding site 7 out of 8 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn501

b:13.9
occ:1.00
OD1 G:ASP84 1.9 13.4 1.0
ND1 G:HIS81 2.0 13.3 1.0
ND1 G:HIS64 2.0 16.0 1.0
ND1 G:HIS72 2.0 13.0 1.0
CG G:ASP84 2.7 13.0 1.0
OD2 G:ASP84 2.9 12.7 1.0
CE1 G:HIS72 2.9 12.8 1.0
CE1 G:HIS81 2.9 12.6 1.0
CE1 G:HIS64 3.0 16.4 1.0
CG G:HIS64 3.0 14.8 1.0
CG G:HIS81 3.1 11.7 1.0
CG G:HIS72 3.1 12.8 1.0
CB G:HIS64 3.4 14.6 1.0
CB G:HIS81 3.5 13.0 1.0
CB G:HIS72 3.6 11.8 1.0
O G:LYS137 3.8 16.1 1.0
CA G:HIS72 3.9 12.4 1.0
NE2 G:HIS81 4.0 12.6 1.0
NE2 G:HIS72 4.1 14.8 1.0
NE2 G:HIS64 4.1 20.6 1.0
CD2 G:HIS81 4.1 13.4 1.0
CB G:ASP84 4.1 12.2 1.0
CD2 G:HIS64 4.2 19.3 1.0
CD2 G:HIS72 4.2 15.0 1.0
CA G:ASP84 4.6 15.4 1.0
N G:HIS81 4.6 14.4 1.0
CA G:HIS81 4.7 13.9 1.0
N G:GLY73 4.7 13.8 1.0
N G:ASP84 4.8 13.0 1.0
C G:LYS137 4.8 14.3 1.0
C G:HIS72 4.8 15.6 1.0
O G:HOH711 4.8 21.2 1.0
N G:HIS72 4.9 13.2 1.0
CA G:HIS64 4.9 13.2 1.0

Zinc binding site 8 out of 8 in 6zs1

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Zinc binding site 8 out of 8 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn501

b:13.7
occ:1.00
OD1 H:ASP84 2.0 13.8 1.0
ND1 H:HIS64 2.0 15.9 1.0
ND1 H:HIS81 2.0 13.5 1.0
ND1 H:HIS72 2.0 12.1 1.0
CG H:ASP84 2.7 13.1 1.0
OD2 H:ASP84 2.9 13.1 1.0
CE1 H:HIS72 2.9 12.9 1.0
CE1 H:HIS81 2.9 13.3 1.0
CE1 H:HIS64 2.9 15.2 1.0
CG H:HIS64 3.0 13.7 1.0
CG H:HIS81 3.1 11.7 1.0
CG H:HIS72 3.1 12.5 1.0
CB H:HIS64 3.4 13.3 1.0
CB H:HIS81 3.5 12.1 1.0
CB H:HIS72 3.6 11.1 1.0
O H:LYS137 3.8 16.9 1.0
CA H:HIS72 3.8 11.2 1.0
NE2 H:HIS81 4.0 14.0 1.0
NE2 H:HIS72 4.1 15.8 1.0
NE2 H:HIS64 4.1 19.2 1.0
CD2 H:HIS64 4.1 17.0 1.0
CD2 H:HIS81 4.1 13.1 1.0
CB H:ASP84 4.1 13.0 1.0
CD2 H:HIS72 4.2 13.7 1.0
CA H:ASP84 4.6 14.4 1.0
N H:HIS81 4.6 14.2 1.0
N H:GLY73 4.6 12.9 1.0
CA H:HIS81 4.7 12.1 1.0
C H:HIS72 4.8 16.2 1.0
C H:LYS137 4.8 17.6 1.0
O H:HOH692 4.8 20.0 1.0
N H:ASP84 4.8 14.3 1.0
N H:HIS72 4.9 12.8 1.0
CA H:HIS64 4.9 13.9 1.0

Reference:

I.Mohsin, L.Q.Zhang, D.C.Li, A.C.Papageorgiou. Crystal Structure of A Cu,Zn Superoxide Dismutase From the Thermophilic Fungus Chaetomium Thermophilum. Protein Pept.Lett. 2021.
ISSN: ISSN 0929-8665
PubMed: 33726638
DOI: 10.2174/0929866528666210316104919
Page generated: Sat Apr 17 17:45:50 2021

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