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Copper in PDB 3kbf: C. Elegans Cu,Zn Superoxide Dismutase

Enzymatic activity of C. Elegans Cu,Zn Superoxide Dismutase

All present enzymatic activity of C. Elegans Cu,Zn Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of C. Elegans Cu,Zn Superoxide Dismutase, PDB code: 3kbf was solved by O.N.Pakhomova, A.B.Taylor, J.P.Schuermann, V.L.Culotta, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.93 / 1.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 39.204, 68.986, 110.488, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 15.9

Copper Binding Sites:

The binding sites of Copper atom in the C. Elegans Cu,Zn Superoxide Dismutase (pdb code 3kbf). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the C. Elegans Cu,Zn Superoxide Dismutase, PDB code: 3kbf:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 3kbf

Go back to Copper Binding Sites List in 3kbf
Copper binding site 1 out of 2 in the C. Elegans Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of C. Elegans Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu158

b:8.9
occ:0.58
CU A:CU158 0.0 8.9 0.6
CU A:CU158 1.0 12.5 0.2
NE2 A:HIS47 2.0 11.9 1.0
ND1 A:HIS45 2.1 13.1 1.0
NE2 A:HIS119 2.1 12.5 1.0
CD2 A:HIS119 3.0 10.5 1.0
CG A:HIS45 3.0 11.1 1.0
CD2 A:HIS47 3.0 11.3 1.0
CE1 A:HIS47 3.0 12.0 1.0
CE1 A:HIS45 3.1 13.0 1.0
CE1 A:HIS119 3.2 11.9 1.0
O3 A:SO4160 3.2 19.7 0.5
CB A:HIS45 3.3 11.4 1.0
NE2 A:HIS62 3.6 13.7 1.0
O A:HOH304 3.8 16.8 0.5
CD2 A:HIS62 3.8 15.4 1.0
CB A:VAL117 3.9 10.3 1.0
CG1 A:VAL117 4.1 11.9 1.0
O A:VAL117 4.1 10.3 1.0
N A:HIS45 4.1 8.5 1.0
ND1 A:HIS47 4.1 12.0 1.0
CG A:HIS119 4.2 9.6 1.0
NE2 A:HIS45 4.2 11.3 1.0
CD2 A:HIS45 4.2 11.2 1.0
CG A:HIS47 4.2 10.1 1.0
CA A:HIS45 4.2 8.8 1.0
ND1 A:HIS119 4.2 11.6 1.0
S A:SO4160 4.4 21.9 0.5
O4 A:SO4160 4.5 23.8 0.5
CE1 A:HIS62 4.5 12.2 1.0
O A:HIS45 4.6 9.8 1.0
C A:VAL117 4.7 8.4 1.0
C A:HIS45 4.7 8.7 1.0
CG2 A:VAL117 4.8 12.4 1.0
CG A:HIS62 4.9 12.6 1.0
CA A:VAL117 4.9 9.2 1.0
C A:PHE44 5.0 7.9 1.0
O2 A:SO4160 5.0 25.5 0.5

Copper binding site 2 out of 2 in 3kbf

Go back to Copper Binding Sites List in 3kbf
Copper binding site 2 out of 2 in the C. Elegans Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of C. Elegans Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu158

b:12.5
occ:0.22
CU A:CU158 0.0 12.5 0.2
CU A:CU158 1.0 8.9 0.6
NE2 A:HIS119 2.0 12.5 1.0
NE2 A:HIS47 2.2 11.9 1.0
O3 A:SO4160 2.2 19.7 0.5
ND1 A:HIS45 2.4 13.1 1.0
CE1 A:HIS119 2.7 11.9 1.0
CE1 A:HIS47 2.7 12.0 1.0
NE2 A:HIS62 2.9 13.7 1.0
O A:HOH304 3.0 16.8 0.5
CE1 A:HIS45 3.1 13.0 1.0
CD2 A:HIS119 3.2 10.5 1.0
CD2 A:HIS62 3.4 15.4 1.0
S A:SO4160 3.4 21.9 0.5
CD2 A:HIS47 3.4 11.3 1.0
CG A:HIS45 3.5 11.1 1.0
O4 A:SO4160 3.6 23.8 0.5
ND1 A:HIS119 3.9 11.6 1.0
CB A:HIS45 4.0 11.4 1.0
ND1 A:HIS47 4.0 12.0 1.0
CE1 A:HIS62 4.0 12.2 1.0
O2 A:SO4160 4.0 25.5 0.5
CG A:HIS119 4.1 9.6 1.0
NE2 A:HIS45 4.3 11.3 1.0
CG A:HIS47 4.3 10.1 1.0
O1 A:SO4160 4.5 27.0 0.5
CD2 A:HIS45 4.5 11.2 1.0
CG A:HIS62 4.5 12.6 1.0
CG1 A:VAL117 4.5 11.9 1.0
CB A:VAL117 4.6 10.3 1.0
O A:HOH324 4.8 24.4 1.0
ND1 A:HIS62 4.8 11.2 1.0

Reference:

O.N.Pakhomova, A.B.Taylor, J.P.Schuermann, V.L.Culotta, P.J.Hart. X-Ray Crystal Structure of C. Elegans Cu,Zn Superoxide Dismutase To Be Published.
Page generated: Fri Sep 4 08:06:59 2020
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