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Copper in PDB 7vvr: Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K

Enzymatic activity of Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K

All present enzymatic activity of Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K:
7.1.1.9;

Protein crystallography data

The structure of Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K, PDB code: 7vvr was solved by A.Shimada, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.95 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.307, 204.706, 177.379, 90, 90, 90
R / Rfree (%) 15.2 / 17.6

Other elements in 7vvr:

The structure of Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Sodium (Na) 2 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K (pdb code 7vvr). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K, PDB code: 7vvr:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7vvr

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Copper binding site 1 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:21.7
occ:1.00
 N A:CYN606 2.0 22.0 1.0
NE2 A:HIS291 2.0 20.9 1.0
ND1 A:HIS240 2.0 19.9 1.0
NE2 A:HIS290 2.1 22.5 1.0
CE1 A:HIS291 2.9 20.2 1.0
CE1 A:HIS240 3.0 20.7 1.0
CD2 A:HIS291 3.0 21.1 1.0
CE1 A:HIS290 3.0 20.2 1.0
CG A:HIS240 3.1 19.6 1.0
C A:CYN606 3.2 21.7 1.0
CD2 A:HIS290 3.2 24.0 1.0
CB A:HIS240 3.5 20.4 1.0
CA A:HIS240 3.9 21.2 1.0
ND1 A:HIS291 4.0 19.5 1.0
CG A:HIS291 4.1 19.7 1.0
NE2 A:HIS240 4.1 19.4 1.0
CD2 A:HIS240 4.2 19.9 1.0
ND1 A:HIS290 4.2 22.2 1.0
CG A:HIS290 4.3 21.6 1.0
CG2 A:VAL243 4.6 21.2 1.0
NA A:HEA602 4.6 23.0 1.0
C1A A:HEA602 4.7 22.3 1.0
N A:HIS240 4.8 20.8 1.0
C4A A:HEA602 4.9 20.7 1.0
FE A:HEA602 5.0 23.1 1.0
C2A A:HEA602 5.0 22.1 1.0
CG1 A:VAL243 5.0 22.1 1.0

Copper binding site 2 out of 6 in 7vvr

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Copper binding site 2 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:24.0
occ:1.00
 CU1 B:CUA302 0.0 24.0 1.0
ND1 B:HIS161 2.1 25.6 1.0
SG B:CYS196 2.3 25.3 1.0
SG B:CYS200 2.4 23.6 1.0
SD B:MET207 2.4 25.6 1.0
CU2 B:CUA302 2.5 23.4 1.0
CE1 B:HIS161 3.0 25.6 1.0
CG B:HIS161 3.2 22.1 1.0
CE B:MET207 3.2 24.0 1.0
CB B:CYS200 3.2 24.1 1.0
CB B:CYS196 3.4 24.7 1.0
CG B:MET207 3.4 23.4 1.0
CB B:HIS161 3.6 21.5 1.0
NE2 B:HIS161 4.2 23.0 1.0
CA B:HIS161 4.2 21.5 1.0
O B:GLU198 4.3 26.1 1.0
CD2 B:HIS161 4.3 22.2 1.0
ND1 B:HIS204 4.4 22.4 1.0
CD1 B:TRP104 4.5 24.9 1.0
CA B:CYS200 4.7 22.5 1.0
O B:HIS102 4.7 26.1 1.0
CA B:HIS204 4.7 23.7 1.0
O B:LEU160 4.8 23.1 1.0
CA B:CYS196 4.8 23.6 1.0
CB B:MET207 4.8 25.5 1.0

Copper binding site 3 out of 6 in 7vvr

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Copper binding site 3 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:23.4
occ:1.00
 CU2 B:CUA302 0.0 23.4 1.0
ND1 B:HIS204 2.0 22.4 1.0
SG B:CYS200 2.2 23.6 1.0
SG B:CYS196 2.3 25.3 1.0
CU1 B:CUA302 2.5 24.0 1.0
O B:GLU198 2.7 26.1 1.0
CE1 B:HIS204 2.9 24.2 1.0
CG B:HIS204 3.1 24.2 1.0
CB B:CYS196 3.3 24.7 1.0
CB B:CYS200 3.3 24.1 1.0
CB B:HIS204 3.5 23.3 1.0
CA B:HIS204 3.5 23.7 1.0
C B:GLU198 3.7 23.1 1.0
N B:CYS200 3.7 23.8 1.0
O B:HIS204 3.8 25.8 1.0
NE2 B:HIS204 4.0 23.9 1.0
CA B:CYS200 4.1 22.5 1.0
CD2 B:HIS204 4.1 22.9 1.0
ND1 B:HIS161 4.2 25.6 1.0
C B:HIS204 4.2 24.7 1.0
C B:CYS196 4.2 23.2 1.0
N B:GLU198 4.2 23.0 1.0
O B:CYS196 4.2 24.2 1.0
CA B:ILE199 4.2 24.1 1.0
C B:ILE199 4.3 23.6 1.0
SD B:MET207 4.3 25.6 1.0
CA B:CYS196 4.4 23.6 1.0
N B:ILE199 4.4 22.2 1.0
CG B:MET207 4.5 23.4 1.0
CA B:GLU198 4.6 24.9 1.0
N B:SER197 4.6 21.9 1.0
N B:HIS204 4.7 25.3 1.0
CA B:HIS161 4.9 21.5 1.0
CB B:HIS161 5.0 21.5 1.0
CG B:HIS161 5.0 22.1 1.0

Copper binding site 4 out of 6 in 7vvr

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Copper binding site 4 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:23.5
occ:1.00
 ND1 N:HIS240 2.0 20.1 1.0
N N:CYN606 2.0 26.4 1.0
NE2 N:HIS291 2.0 24.3 1.0
NE2 N:HIS290 2.1 25.8 1.0
CE1 N:HIS240 2.9 22.8 1.0
CE1 N:HIS291 2.9 21.5 1.0
CD2 N:HIS291 3.0 26.3 1.0
CG N:HIS240 3.1 19.6 1.0
CE1 N:HIS290 3.1 25.3 1.0
C N:CYN606 3.1 25.5 1.0
CD2 N:HIS290 3.1 23.4 1.0
CB N:HIS240 3.4 21.6 1.0
CA N:HIS240 3.9 21.1 1.0
ND1 N:HIS291 4.0 20.9 1.0
NE2 N:HIS240 4.1 21.5 1.0
CG N:HIS291 4.1 22.8 1.0
CD2 N:HIS240 4.2 20.6 1.0
ND1 N:HIS290 4.2 23.4 1.0
CG N:HIS290 4.3 23.3 1.0
CG2 N:VAL243 4.6 23.7 1.0
NA N:HEA602 4.6 25.8 1.0
C1A N:HEA602 4.8 25.7 1.0
N N:HIS240 4.8 22.0 1.0
C4A N:HEA602 4.8 22.1 1.0
FE N:HEA602 5.0 24.9 1.0
CG1 N:VAL243 5.0 24.7 1.0

Copper binding site 5 out of 6 in 7vvr

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Copper binding site 5 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu302

b:28.4
occ:1.00
 CU1 O:CUA302 0.0 28.4 1.0
ND1 O:HIS161 2.1 27.9 1.0
SD O:MET207 2.3 30.6 1.0
SG O:CYS196 2.3 28.8 1.0
SG O:CYS200 2.4 29.4 1.0
CU2 O:CUA302 2.5 27.9 1.0
CE1 O:HIS161 2.9 27.4 1.0
CE O:MET207 3.1 29.8 1.0
CG O:HIS161 3.2 25.6 1.0
CB O:CYS200 3.3 26.3 1.0
CB O:CYS196 3.4 30.9 1.0
CG O:MET207 3.4 26.9 1.0
CB O:HIS161 3.6 26.2 1.0
NE2 O:HIS161 4.1 27.6 1.0
CA O:HIS161 4.2 27.1 1.0
O O:GLU198 4.2 27.9 1.0
CD2 O:HIS161 4.2 28.1 1.0
CD1 O:TRP104 4.4 32.3 1.0
ND1 O:HIS204 4.4 28.9 1.0
O O:HIS102 4.7 31.1 1.0
CA O:CYS200 4.7 28.1 1.0
O O:LEU160 4.7 27.4 1.0
CA O:HIS204 4.7 30.2 1.0
CA O:CYS196 4.8 25.8 1.0
CB O:MET207 4.8 29.7 1.0
N O:CYS200 5.0 27.4 1.0

Copper binding site 6 out of 6 in 7vvr

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Copper binding site 6 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu302

b:27.9
occ:1.00
 CU2 O:CUA302 0.0 27.9 1.0
ND1 O:HIS204 2.0 28.9 1.0
SG O:CYS200 2.3 29.4 1.0
SG O:CYS196 2.3 28.8 1.0
CU1 O:CUA302 2.5 28.4 1.0
O O:GLU198 2.7 27.9 1.0
CE1 O:HIS204 2.9 26.1 1.0
CG O:HIS204 3.1 28.4 1.0
CB O:CYS196 3.2 30.9 1.0
CB O:CYS200 3.4 26.3 1.0
CA O:HIS204 3.5 30.2 1.0
CB O:HIS204 3.6 27.0 1.0
N O:CYS200 3.7 27.4 1.0
C O:GLU198 3.7 26.4 1.0
O O:HIS204 3.8 29.9 1.0
NE2 O:HIS204 4.0 26.7 1.0
ND1 O:HIS161 4.1 27.9 1.0
CA O:CYS200 4.2 28.1 1.0
C O:HIS204 4.2 29.2 1.0
CD2 O:HIS204 4.2 26.3 1.0
C O:CYS196 4.2 28.6 1.0
N O:GLU198 4.2 27.2 1.0
O O:CYS196 4.2 28.4 1.0
CA O:ILE199 4.3 27.5 1.0
C O:ILE199 4.3 27.2 1.0
SD O:MET207 4.3 30.6 1.0
CA O:CYS196 4.3 25.8 1.0
N O:ILE199 4.4 25.7 1.0
CG O:MET207 4.5 26.9 1.0
N O:SER197 4.6 27.5 1.0
CA O:GLU198 4.6 29.0 1.0
N O:HIS204 4.7 29.5 1.0
CA O:HIS161 4.9 27.1 1.0
CB O:HIS161 5.0 26.2 1.0

Reference:

A.Shimada, T.Tsukihara. Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K To Be Published.
Page generated: Wed Jul 31 09:18:09 2024

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