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Zinc in PDB 1srd: Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution

Enzymatic activity of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution

All present enzymatic activity of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution:
1.15.1.1;

Protein crystallography data

The structure of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution, PDB code: 1srd was solved by Y.Kitagawa, Y.Katsube, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 5.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.270, 45.970, 85.680, 90.00, 99.38, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1srd:

The structure of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution (pdb code 1srd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution, PDB code: 1srd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1srd

Go back to Zinc Binding Sites List in 1srd
Zinc binding site 1 out of 4 in the Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn156

b:9.0
occ:1.00
 OD1 A:ASP83 2.0 8.6 1.0
ND1 A:HIS63 2.1 8.4 1.0
ND1 A:HIS80 2.1 8.7 1.0
ND1 A:HIS71 2.2 8.1 1.0
CE1 A:HIS71 3.1 8.1 1.0
CE1 A:HIS80 3.2 8.5 1.0
CG A:HIS63 3.2 8.2 1.0
CE1 A:HIS63 3.2 8.7 1.0
CG A:ASP83 3.2 8.9 1.0
CG A:HIS80 3.2 8.7 1.0
CG A:HIS71 3.3 8.2 1.0
CB A:HIS80 3.5 9.1 1.0
CB A:HIS63 3.6 8.1 1.0
CB A:HIS71 3.7 8.4 1.0
OD2 A:ASP83 3.7 8.8 1.0
O A:THR136 3.9 9.3 1.0
CA A:HIS71 3.9 8.4 1.0
CD2 A:HIS63 4.2 8.4 1.0
NE2 A:HIS80 4.2 8.6 1.0
NE2 A:HIS71 4.3 8.0 1.0
CD2 A:HIS80 4.3 8.5 1.0
NE2 A:HIS63 4.3 9.0 1.0
CD2 A:HIS71 4.3 8.0 1.0
CB A:ASP83 4.4 8.8 1.0
O A:HOH171 4.4 11.7 1.0
C A:THR136 4.7 9.4 1.0
CA A:HIS80 4.8 9.5 1.0
CA A:ASP83 4.8 9.0 1.0
N A:HIS71 4.8 8.3 1.0
N A:GLY72 4.8 8.6 1.0
C A:HIS71 4.9 8.6 1.0
N A:ASP83 5.0 8.7 1.0
O A:THR137 5.0 9.6 1.0

Zinc binding site 2 out of 4 in 1srd

Go back to Zinc Binding Sites List in 1srd
Zinc binding site 2 out of 4 in the Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn156

b:9.4
occ:1.00
 OD1 B:ASP83 2.0 8.6 1.0
ND1 B:HIS80 2.1 8.6 1.0
ND1 B:HIS63 2.1 8.4 1.0
ND1 B:HIS71 2.2 8.2 1.0
CE1 B:HIS80 3.1 8.6 1.0
CG B:ASP83 3.1 8.9 1.0
CE1 B:HIS71 3.1 8.1 1.0
CE1 B:HIS63 3.2 8.7 1.0
CG B:HIS80 3.2 8.7 1.0
CG B:HIS63 3.2 8.2 1.0
CG B:HIS71 3.2 8.1 1.0
OD2 B:ASP83 3.5 8.8 1.0
CB B:HIS63 3.5 8.1 1.0
CB B:HIS80 3.6 9.1 1.0
O B:THR136 3.6 9.3 1.0
CB B:HIS71 3.7 8.4 1.0
NE2 B:HIS80 4.2 8.7 1.0
O B:HOH173 4.2 11.5 1.0
CD2 B:HIS80 4.2 8.5 1.0
CD2 B:HIS63 4.2 8.4 1.0
CA B:HIS71 4.2 8.4 1.0
NE2 B:HIS71 4.2 8.1 1.0
NE2 B:HIS63 4.2 9.0 1.0
CB B:ASP83 4.3 8.8 1.0
CD2 B:HIS71 4.3 8.1 1.0
N B:ASP83 4.7 8.8 1.0
C B:THR136 4.7 9.5 1.0
CA B:ASP83 4.7 9.0 1.0
CA B:HIS80 4.8 9.5 1.0
CD2 B:HIS46 5.0 8.9 1.0

Zinc binding site 3 out of 4 in 1srd

Go back to Zinc Binding Sites List in 1srd
Zinc binding site 3 out of 4 in the Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn156

b:9.2
occ:1.00
 OD1 C:ASP83 2.0 8.7 1.0
ND1 C:HIS63 2.1 8.4 1.0
ND1 C:HIS80 2.2 8.6 1.0
ND1 C:HIS71 2.2 8.2 1.0
CE1 C:HIS63 3.1 8.7 1.0
CG C:ASP83 3.1 8.9 1.0
CE1 C:HIS71 3.1 8.2 1.0
CE1 C:HIS80 3.2 8.6 1.0
CG C:HIS80 3.2 8.7 1.0
CG C:HIS63 3.2 8.2 1.0
CG C:HIS71 3.3 8.1 1.0
CB C:HIS80 3.5 9.1 1.0
O C:THR136 3.5 9.3 1.0
OD2 C:ASP83 3.5 8.9 1.0
CB C:HIS63 3.6 8.1 1.0
CA C:HIS71 3.7 8.4 1.0
CB C:HIS71 3.8 8.3 1.0
NE2 C:HIS63 4.2 9.1 1.0
CD2 C:HIS63 4.2 8.4 1.0
CD2 C:HIS80 4.3 8.5 1.0
NE2 C:HIS80 4.3 8.7 1.0
CB C:ASP83 4.3 8.8 1.0
NE2 C:HIS71 4.3 8.1 1.0
CD2 C:HIS71 4.4 8.0 1.0
C C:THR136 4.6 9.5 1.0
O C:HOH171 4.6 11.6 1.0
N C:HIS71 4.7 8.4 1.0
N C:GLY72 4.7 8.7 1.0
CA C:HIS80 4.7 9.5 1.0
C C:HIS71 4.8 8.7 1.0
CA C:ASP83 4.9 9.0 1.0
N C:HIS80 4.9 9.6 1.0
CD2 C:HIS46 4.9 8.9 1.0
N C:ASP83 5.0 8.7 1.0

Zinc binding site 4 out of 4 in 1srd

Go back to Zinc Binding Sites List in 1srd
Zinc binding site 4 out of 4 in the Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn156

b:9.1
occ:1.00
 OD1 D:ASP83 2.1 8.7 1.0
ND1 D:HIS71 2.1 8.1 1.0
ND1 D:HIS80 2.1 8.6 1.0
ND1 D:HIS63 2.2 8.3 1.0
CE1 D:HIS71 3.1 8.0 1.0
CE1 D:HIS80 3.1 8.5 1.0
CG D:ASP83 3.1 8.9 1.0
CG D:HIS63 3.1 8.2 1.0
CG D:HIS80 3.2 8.7 1.0
CE1 D:HIS63 3.2 8.7 1.0
CG D:HIS71 3.2 8.1 1.0
OD2 D:ASP83 3.3 8.8 1.0
CB D:HIS63 3.4 8.1 1.0
CB D:HIS80 3.5 9.1 1.0
CB D:HIS71 3.8 8.4 1.0
O D:THR136 3.9 9.3 1.0
CA D:HIS71 4.1 8.4 1.0
NE2 D:HIS80 4.2 8.7 1.0
NE2 D:HIS71 4.2 8.0 1.0
CD2 D:HIS80 4.2 8.5 1.0
CD2 D:HIS63 4.2 8.4 1.0
NE2 D:HIS63 4.3 9.1 1.0
CD2 D:HIS71 4.3 8.1 1.0
CB D:ASP83 4.4 8.8 1.0
O D:HOH173 4.5 11.6 1.0
CA D:HIS80 4.6 9.5 1.0
N D:HIS80 4.6 9.6 1.0
C D:THR136 4.7 9.5 1.0
CA D:ASP83 4.8 9.0 1.0
N D:ASP83 4.9 8.8 1.0
CA D:HIS63 4.9 7.9 1.0
N D:GLY72 5.0 8.5 1.0
CD2 D:HIS46 5.0 8.9 1.0

Reference:

Y.Kitagawa, N.Tanaka, Y.Hata, M.Kusunoki, G.P.Lee, Y.Katsube, K.Asada, S.Aibara, Y.Morita. Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 A Resolution. J.Biochem.(Tokyo) V. 109 477 1991.
ISSN: ISSN 0021-924X
PubMed: 1880134
Page generated: Wed Oct 16 18:54:23 2024

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