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Copper in PDB 7vuw: Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K, PDB code: 7vuw 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) 39.92 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.076, 204.481, 177.68, 90, 90, 90
R / Rfree (%) 15.4 / 17.5

Other elements in 7vuw:

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K also contains other interesting chemical elements:

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

Copper Binding Sites:

The binding sites of Copper atom in the Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K (pdb code 7vuw). 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 Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K, PDB code: 7vuw:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7vuw

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Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized 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 Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:19.7
occ:1.00
 ND1 A:HIS240 2.0 18.4 1.0
NE2 A:HIS291 2.0 18.9 1.0
NE2 A:HIS290 2.0 18.3 1.0
N A:CYN606 2.2 25.3 1.0
C A:CYN606 2.8 14.4 1.0
CE1 A:HIS291 2.9 18.7 1.0
CD2 A:HIS291 3.0 19.2 1.0
CE1 A:HIS240 3.0 20.0 1.0
CE1 A:HIS290 3.0 21.0 1.0
CG A:HIS240 3.0 17.9 1.0
CD2 A:HIS290 3.1 17.8 1.0
CB A:HIS240 3.4 19.1 1.0
CA A:HIS240 3.9 18.3 1.0
ND1 A:HIS291 4.0 17.6 1.0
CG A:HIS291 4.1 17.9 1.0
NE2 A:HIS240 4.1 18.3 1.0
ND1 A:HIS290 4.1 19.3 1.0
CD2 A:HIS240 4.1 19.7 1.0
CG A:HIS290 4.2 19.6 1.0
NA A:HEA602 4.5 18.5 1.0
C1A A:HEA602 4.6 17.5 1.0
C4A A:HEA602 4.7 18.5 1.0
N A:HIS240 4.8 18.9 1.0
CG2 A:VAL243 4.8 20.5 1.0
C2A A:HEA602 4.9 18.4 1.0
FE A:HEA602 4.9 19.1 1.0
C3A A:HEA602 4.9 19.6 1.0

Copper binding site 2 out of 6 in 7vuw

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized 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 Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu303

b:21.7
occ:1.00
 CU1 B:CUA303 0.0 21.7 1.0
ND1 B:HIS161 2.1 21.1 1.0
SG B:CYS196 2.3 22.0 1.0
SG B:CYS200 2.3 22.1 1.0
SD B:MET207 2.4 22.8 1.0
CU2 B:CUA303 2.5 21.6 1.0
CE1 B:HIS161 3.0 24.3 1.0
CG B:HIS161 3.2 21.4 1.0
CE B:MET207 3.2 21.1 1.0
CB B:CYS200 3.2 19.7 1.0
CB B:CYS196 3.4 21.1 1.0
CG B:MET207 3.5 21.4 1.0
CB B:HIS161 3.6 19.2 1.0
O B:GLU198 4.1 20.1 1.0
NE2 B:HIS161 4.1 20.6 1.0
CA B:HIS161 4.2 19.9 1.0
CD2 B:HIS161 4.2 19.9 1.0
ND1 B:HIS204 4.4 20.8 1.0
CA B:HIS204 4.7 19.3 1.0
CA B:CYS200 4.7 22.1 1.0
O B:LEU160 4.7 21.0 1.0
O B:HIS102 4.7 23.2 1.0
CD1 B:TRP104 4.8 23.8 1.0
CA B:CYS196 4.8 21.1 1.0
O B:HIS204 4.9 23.1 1.0
CB B:MET207 4.9 20.5 1.0
N B:CYS200 5.0 22.5 1.0

Copper binding site 3 out of 6 in 7vuw

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized 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 Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu303

b:21.6
occ:1.00
 CU2 B:CUA303 0.0 21.6 1.0
ND1 B:HIS204 2.0 20.8 1.0
SG B:CYS200 2.3 22.1 1.0
SG B:CYS196 2.3 22.0 1.0
CU1 B:CUA303 2.5 21.7 1.0
O B:GLU198 2.5 20.1 1.0
CE1 B:HIS204 2.9 21.0 1.0
CG B:HIS204 3.0 22.0 1.0
CB B:CYS196 3.3 21.1 1.0
CB B:CYS200 3.3 19.7 1.0
CB B:HIS204 3.4 19.6 1.0
C B:GLU198 3.5 19.9 1.0
CA B:HIS204 3.6 19.3 1.0
N B:CYS200 3.7 22.5 1.0
O B:HIS204 3.8 23.1 1.0
NE2 B:HIS204 4.1 21.3 1.0
CA B:CYS200 4.1 22.1 1.0
C B:HIS204 4.1 22.1 1.0
CD2 B:HIS204 4.1 21.8 1.0
N B:GLU198 4.1 21.0 1.0
C B:ILE199 4.2 22.3 1.0
ND1 B:HIS161 4.2 21.1 1.0
C B:CYS196 4.2 21.1 1.0
O B:CYS196 4.2 22.2 1.0
CA B:ILE199 4.2 19.2 1.0
SD B:MET207 4.3 22.8 1.0
N B:ILE199 4.3 21.3 1.0
CA B:CYS196 4.4 21.1 1.0
CA B:GLU198 4.5 21.6 1.0
N B:SER197 4.7 19.4 1.0
CG B:MET207 4.7 21.4 1.0
N B:HIS204 4.8 22.9 1.0
CA B:HIS161 4.9 19.9 1.0
O B:ILE199 5.0 21.4 1.0
C B:CYS200 5.0 22.0 1.0

Copper binding site 4 out of 6 in 7vuw

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized 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 Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:21.7
occ:1.00
 ND1 N:HIS240 2.0 19.2 1.0
NE2 N:HIS291 2.0 22.4 1.0
NE2 N:HIS290 2.0 22.4 1.0
N N:CYN606 2.2 29.1 1.0
C N:CYN606 2.8 18.0 1.0
CE1 N:HIS291 3.0 21.8 1.0
CE1 N:HIS240 3.0 21.9 1.0
CD2 N:HIS291 3.0 24.7 1.0
CG N:HIS240 3.0 19.4 1.0
CE1 N:HIS290 3.0 25.1 1.0
CD2 N:HIS290 3.1 21.3 1.0
CB N:HIS240 3.4 19.6 1.0
CA N:HIS240 3.9 20.0 1.0
ND1 N:HIS291 4.0 20.7 1.0
NE2 N:HIS240 4.1 20.5 1.0
CG N:HIS291 4.1 21.1 1.0
CD2 N:HIS240 4.1 22.7 1.0
ND1 N:HIS290 4.1 20.3 1.0
CG N:HIS290 4.2 19.9 1.0
NA N:HEA602 4.5 20.8 1.0
C1A N:HEA602 4.6 21.5 1.0
C4A N:HEA602 4.7 19.6 1.0
N N:HIS240 4.8 20.8 1.0
CG2 N:VAL243 4.9 22.1 1.0
FE N:HEA602 4.9 21.8 1.0
C2A N:HEA602 4.9 21.2 1.0
C3A N:HEA602 4.9 20.7 1.0
C N:HIS240 5.0 21.3 1.0

Copper binding site 5 out of 6 in 7vuw

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized 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 Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:26.6
occ:1.00
 CU1 O:CUA301 0.0 26.6 1.0
ND1 O:HIS161 2.1 27.6 1.0
SG O:CYS200 2.3 29.2 1.0
SG O:CYS196 2.3 28.2 1.0
SD O:MET207 2.4 30.4 1.0
CU2 O:CUA301 2.5 26.2 1.0
CE1 O:HIS161 2.9 26.0 1.0
CE O:MET207 3.2 29.2 1.0
CG O:HIS161 3.2 24.9 1.0
CB O:CYS200 3.3 26.8 1.0
CB O:CYS196 3.4 28.4 1.0
CG O:MET207 3.5 26.7 1.0
CB O:HIS161 3.7 25.8 1.0
NE2 O:HIS161 4.1 27.2 1.0
O O:GLU198 4.1 26.3 1.0
CA O:HIS161 4.2 27.4 1.0
CD2 O:HIS161 4.3 27.6 1.0
ND1 O:HIS204 4.4 27.3 1.0
CD1 O:TRP104 4.6 30.8 1.0
CA O:HIS204 4.7 26.6 1.0
O O:HIS102 4.7 29.4 1.0
O O:LEU160 4.7 27.0 1.0
CA O:CYS200 4.7 26.2 1.0
CA O:CYS196 4.8 26.8 1.0
O O:HIS204 4.9 29.8 1.0
CB O:MET207 4.9 24.8 1.0
N O:CYS200 5.0 27.7 1.0

Copper binding site 6 out of 6 in 7vuw

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Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized 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 Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:26.2
occ:1.00
 CU2 O:CUA301 0.0 26.2 1.0
ND1 O:HIS204 2.0 27.3 1.0
SG O:CYS196 2.3 28.2 1.0
SG O:CYS200 2.3 29.2 1.0
CU1 O:CUA301 2.5 26.6 1.0
O O:GLU198 2.5 26.3 1.0
CE1 O:HIS204 2.9 25.8 1.0
CG O:HIS204 3.1 26.6 1.0
CB O:CYS196 3.3 28.4 1.0
CB O:CYS200 3.4 26.8 1.0
CB O:HIS204 3.5 28.2 1.0
C O:GLU198 3.6 24.4 1.0
CA O:HIS204 3.6 26.6 1.0
N O:CYS200 3.7 27.7 1.0
O O:HIS204 3.8 29.8 1.0
NE2 O:HIS204 4.0 26.0 1.0
N O:GLU198 4.1 26.9 1.0
C O:HIS204 4.1 28.6 1.0
CD2 O:HIS204 4.1 27.2 1.0
CA O:CYS200 4.2 26.2 1.0
ND1 O:HIS161 4.2 27.6 1.0
C O:ILE199 4.2 26.5 1.0
O O:CYS196 4.2 28.4 1.0
C O:CYS196 4.2 28.6 1.0
CA O:ILE199 4.3 23.9 1.0
SD O:MET207 4.3 30.4 1.0
N O:ILE199 4.3 25.9 1.0
CA O:CYS196 4.4 26.8 1.0
CA O:GLU198 4.5 26.8 1.0
N O:SER197 4.7 26.1 1.0
CG O:MET207 4.7 26.7 1.0
N O:HIS204 4.8 28.4 1.0
CA O:HIS161 4.9 27.4 1.0
CE1 O:HIS161 5.0 26.0 1.0

Reference:

A.Shimada, T.Tsukihara. Bovine Cytochrome C Oxidese in Cn-Bound Fully Oxidized State at 50 K To Be Published.
Page generated: Wed Jul 31 09:18:08 2024

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