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Copper 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:

Zinc (Zn) 4 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 4 binding sites of Copper where determined in the Three-Dimensional Structure of Cu,Zn-Superoxide Dismutase From Spinach at 2.0 Angstroms Resolution, PDB code: 1srd:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 1srd

Go back to Copper Binding Sites List in 1srd
Copper 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 Copper with other atoms in the Cu 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:Cu155

b:13.0
occ:1.00
ND1 A:HIS46 2.0 9.3 1.0
NE2 A:HIS48 2.1 10.0 1.0
NE2 A:HIS120 2.1 9.8 1.0
NE2 A:HIS63 2.1 9.0 1.0
CE1 A:HIS120 2.3 9.8 1.0
CE1 A:HIS48 2.8 9.6 1.0
CD2 A:HIS63 2.8 8.4 1.0
CG A:HIS46 3.0 8.9 1.0
CE1 A:HIS46 3.0 8.9 1.0
CE1 A:HIS63 3.2 8.7 1.0
CD2 A:HIS48 3.2 9.4 1.0
CD2 A:HIS120 3.3 9.5 1.0
CB A:HIS46 3.3 8.6 1.0
ND1 A:HIS120 3.4 9.7 1.0
NE2 A:HIS46 4.0 9.0 1.0
ND1 A:HIS48 4.0 9.3 1.0
CG A:HIS120 4.0 9.4 1.0
CG A:HIS63 4.0 8.2 1.0
CD2 A:HIS46 4.1 8.9 1.0
CG A:HIS48 4.2 9.3 1.0
ND1 A:HIS63 4.2 8.4 1.0
CA A:HIS46 4.6 8.4 1.0
N A:HIS46 4.7 8.4 1.0
CG2 A:THR137 4.8 10.1 1.0

Copper binding site 2 out of 4 in 1srd

Go back to Copper Binding Sites List in 1srd
Copper 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 Copper with other atoms in the Cu 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:Cu155

b:13.1
occ:1.00
NE2 B:HIS63 2.0 9.0 1.0
NE2 B:HIS120 2.1 9.8 1.0
ND1 B:HIS46 2.1 9.3 1.0
NE2 B:HIS48 2.1 10.0 1.0
CE1 B:HIS120 2.1 9.8 1.0
CD2 B:HIS63 2.7 8.4 1.0
CE1 B:HIS48 2.9 9.6 1.0
CG B:HIS46 3.0 8.9 1.0
CE1 B:HIS46 3.1 9.1 1.0
CE1 B:HIS63 3.2 8.7 1.0
CD2 B:HIS48 3.3 9.4 1.0
ND1 B:HIS120 3.3 9.8 1.0
CB B:HIS46 3.3 8.6 1.0
CD2 B:HIS120 3.3 9.5 1.0
CG B:HIS120 3.9 9.4 1.0
CG B:HIS63 3.9 8.2 1.0
ND1 B:HIS48 4.1 9.4 1.0
CD2 B:HIS46 4.1 8.9 1.0
NE2 B:HIS46 4.1 9.0 1.0
ND1 B:HIS63 4.2 8.4 1.0
CG B:HIS48 4.3 9.3 1.0
CA B:HIS46 4.5 8.4 1.0
CG2 B:THR137 4.5 10.1 1.0
N B:HIS46 4.7 8.4 1.0
O B:VAL118 4.8 7.7 1.0
O B:HOH178 4.8 19.0 1.0
CG1 B:VAL118 4.9 7.5 1.0
CB B:VAL118 5.0 7.3 1.0

Copper binding site 3 out of 4 in 1srd

Go back to Copper Binding Sites List in 1srd
Copper 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 Copper with other atoms in the Cu 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:Cu155

b:13.5
occ:1.00
NE2 C:HIS63 2.0 9.1 1.0
NE2 C:HIS120 2.1 9.8 1.0
NE2 C:HIS48 2.2 10.0 1.0
ND1 C:HIS46 2.3 9.2 1.0
CE1 C:HIS120 2.3 9.8 1.0
CD2 C:HIS63 2.9 8.4 1.0
CE1 C:HIS48 2.9 9.6 1.0
CG C:HIS46 3.1 8.8 1.0
CE1 C:HIS63 3.1 8.7 1.0
CD2 C:HIS120 3.2 9.6 1.0
CE1 C:HIS46 3.2 9.0 1.0
CB C:HIS46 3.3 8.6 1.0
CD2 C:HIS48 3.4 9.4 1.0
ND1 C:HIS120 3.4 9.7 1.0
CG C:HIS120 3.9 9.4 1.0
CG C:HIS63 4.0 8.2 1.0
ND1 C:HIS48 4.1 9.4 1.0
CD2 C:HIS46 4.2 8.9 1.0
ND1 C:HIS63 4.2 8.4 1.0
CG2 C:THR137 4.2 10.2 1.0
NE2 C:HIS46 4.2 8.9 1.0
CG C:HIS48 4.3 9.3 1.0
CA C:HIS46 4.8 8.4 1.0
O C:HOH175 4.8 19.0 1.0
O C:THR137 4.9 9.5 1.0

Copper binding site 4 out of 4 in 1srd

Go back to Copper Binding Sites List in 1srd
Copper 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 Copper with other atoms in the Cu 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:Cu155

b:13.4
occ:1.00
NE2 D:HIS120 2.0 9.8 1.0
NE2 D:HIS48 2.0 9.9 1.0
ND1 D:HIS46 2.0 9.3 1.0
NE2 D:HIS63 2.1 9.1 1.0
CE1 D:HIS120 2.5 9.9 1.0
CE1 D:HIS48 2.8 9.6 1.0
CG D:HIS46 2.8 8.8 1.0
CD2 D:HIS63 2.9 8.4 1.0
CD2 D:HIS120 3.0 9.6 1.0
CB D:HIS46 3.1 8.6 1.0
CE1 D:HIS63 3.1 8.7 1.0
CD2 D:HIS48 3.1 9.4 1.0
CE1 D:HIS46 3.1 9.0 1.0
ND1 D:HIS120 3.6 9.7 1.0
ND1 D:HIS48 3.9 9.4 1.0
CG D:HIS120 4.0 9.4 1.0
CD2 D:HIS46 4.0 8.9 1.0
CG D:HIS63 4.0 8.2 1.0
NE2 D:HIS46 4.1 9.0 1.0
ND1 D:HIS63 4.1 8.3 1.0
CG D:HIS48 4.1 9.3 1.0
CA D:HIS46 4.4 8.3 1.0
N D:HIS46 4.5 8.5 1.0
CB D:VAL118 5.0 7.3 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: Sun Dec 13 11:02:04 2020

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