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Copper in PDB 7ypy: Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 7ypy 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) 39.96 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.938, 204.4, 177.896, 90, 90, 90
R / Rfree (%) 15.9 / 17.7

Other elements in 7ypy:

The structure of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution 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 Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution (pdb code 7ypy). 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 Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 7ypy:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7ypy

Go back to Copper Binding Sites List in 7ypy
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution


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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:19.1
occ:1.00
 NE2 A:HIS291 2.0 17.9 1.0
ND1 A:HIS240 2.0 17.8 1.0
NE2 A:HIS290 2.0 17.4 1.0
O2 A:PER606 2.2 23.6 1.0
O1 A:PER606 2.8 16.4 1.0
CE1 A:HIS291 2.9 17.3 1.0
CG A:HIS240 3.0 16.2 1.0
CD2 A:HIS291 3.0 19.4 1.0
CE1 A:HIS240 3.0 19.2 1.0
CE1 A:HIS290 3.0 20.5 1.0
CD2 A:HIS290 3.1 16.6 1.0
CB A:HIS240 3.3 18.6 1.0
CA A:HIS240 3.9 18.0 1.0
ND1 A:HIS291 4.0 18.4 1.0
CG A:HIS291 4.1 18.5 1.0
NE2 A:HIS240 4.1 17.3 1.0
CD2 A:HIS240 4.1 17.0 1.0
ND1 A:HIS290 4.1 19.0 1.0
CG A:HIS290 4.2 18.2 1.0
NA A:HEA602 4.5 17.7 1.0
C1A A:HEA602 4.6 17.2 1.0
C4A A:HEA602 4.6 17.4 1.0
N A:HIS240 4.7 18.2 1.0
C2A A:HEA602 4.8 18.7 1.0
FE A:HEA602 4.8 18.7 1.0
C3A A:HEA602 4.9 18.0 1.0
CG2 A:VAL243 4.9 18.4 1.0
CHA A:HEA602 5.0 19.2 1.0

Copper binding site 2 out of 6 in 7ypy

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution


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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:21.1
occ:1.00
 CU1 B:CUA302 0.0 21.1 1.0
ND1 B:HIS161 2.1 22.5 1.0
SG B:CYS200 2.3 21.2 1.0
SG B:CYS196 2.3 21.1 1.0
SD B:MET207 2.4 21.6 1.0
CU2 B:CUA302 2.5 20.9 1.0
CE1 B:HIS161 3.0 19.7 1.0
CE B:MET207 3.2 21.6 1.0
CG B:HIS161 3.2 21.1 1.0
CB B:CYS200 3.2 21.3 1.0
CB B:CYS196 3.4 21.9 1.0
CG B:MET207 3.5 19.6 1.0
CB B:HIS161 3.6 19.4 1.0
NE2 B:HIS161 4.1 20.0 1.0
O B:GLU198 4.1 19.6 1.0
CA B:HIS161 4.2 18.8 1.0
CD2 B:HIS161 4.3 19.2 1.0
ND1 B:HIS204 4.5 20.8 1.0
CA B:CYS200 4.7 20.1 1.0
O B:HIS102 4.7 22.7 1.0
CA B:HIS204 4.7 18.9 1.0
O B:LEU160 4.7 20.4 1.0
CD1 B:TRP104 4.7 23.5 1.0
CA B:CYS196 4.8 19.7 1.0
O B:HIS204 4.9 22.4 1.0
CB B:MET207 4.9 18.8 1.0

Copper binding site 3 out of 6 in 7ypy

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution


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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:20.9
occ:1.00
 CU2 B:CUA302 0.0 20.9 1.0
ND1 B:HIS204 2.0 20.8 1.0
SG B:CYS200 2.3 21.2 1.0
SG B:CYS196 2.3 21.1 1.0
CU1 B:CUA302 2.5 21.1 1.0
O B:GLU198 2.6 19.6 1.0
CE1 B:HIS204 2.9 20.9 1.0
CG B:HIS204 3.1 20.4 1.0
CB B:CYS196 3.3 21.9 1.0
CB B:CYS200 3.3 21.3 1.0
CB B:HIS204 3.5 20.2 1.0
C B:GLU198 3.6 19.8 1.0
CA B:HIS204 3.6 18.9 1.0
N B:CYS200 3.7 20.9 1.0
O B:HIS204 3.8 22.4 1.0
NE2 B:HIS204 4.1 20.6 1.0
CA B:CYS200 4.1 20.1 1.0
N B:GLU198 4.1 20.5 1.0
C B:HIS204 4.2 21.0 1.0
CD2 B:HIS204 4.2 19.7 1.0
ND1 B:HIS161 4.2 22.5 1.0
C B:ILE199 4.2 19.9 1.0
O B:CYS196 4.2 21.4 1.0
CA B:ILE199 4.2 20.9 1.0
C B:CYS196 4.2 18.4 1.0
SD B:MET207 4.3 21.6 1.0
N B:ILE199 4.3 20.4 1.0
CA B:CYS196 4.4 19.7 1.0
CA B:GLU198 4.5 19.6 1.0
CG B:MET207 4.7 19.6 1.0
N B:SER197 4.7 18.4 1.0
N B:HIS204 4.8 21.1 1.0
CA B:HIS161 4.9 18.8 1.0

Copper binding site 4 out of 6 in 7ypy

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution


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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:21.6
occ:1.00
 NE2 N:HIS291 1.9 21.1 1.0
ND1 N:HIS240 2.0 19.3 1.0
NE2 N:HIS290 2.0 20.8 1.0
O1 N:PER606 2.2 26.8 1.0
O2 N:PER606 2.7 19.8 1.0
CE1 N:HIS291 2.9 21.6 1.0
CG N:HIS240 3.0 17.6 1.0
CD2 N:HIS291 3.0 24.3 1.0
CE1 N:HIS290 3.0 23.8 1.0
CE1 N:HIS240 3.0 20.8 1.0
CD2 N:HIS290 3.1 19.6 1.0
CB N:HIS240 3.3 20.5 1.0
CA N:HIS240 3.9 19.6 1.0
ND1 N:HIS291 4.0 21.4 1.0
CG N:HIS291 4.1 21.1 1.0
NE2 N:HIS240 4.1 19.9 1.0
CD2 N:HIS240 4.1 18.7 1.0
ND1 N:HIS290 4.1 21.2 1.0
CG N:HIS290 4.2 18.6 1.0
NA N:HEA602 4.5 19.8 1.0
C1A N:HEA602 4.6 21.1 1.0
C4A N:HEA602 4.6 19.2 1.0
N N:HIS240 4.8 20.1 1.0
FE N:HEA602 4.8 21.4 1.0
C2A N:HEA602 4.8 21.0 1.0
C3A N:HEA602 4.9 20.3 1.0
CG2 N:VAL243 4.9 20.5 1.0
CHA N:HEA602 5.0 21.2 1.0

Copper binding site 5 out of 6 in 7ypy

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution


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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu302

b:26.6
occ:1.00
 CU1 O:CUA302 0.0 26.6 1.0
ND1 O:HIS161 2.1 26.9 1.0
SG O:CYS196 2.4 27.5 1.0
SG O:CYS200 2.4 28.2 1.0
SD O:MET207 2.4 28.8 1.0
CU2 O:CUA302 2.5 26.3 1.0
CE1 O:HIS161 2.9 25.2 1.0
CE O:MET207 3.1 28.4 1.0
CG O:HIS161 3.2 25.6 1.0
CB O:CYS200 3.3 26.6 1.0
CB O:CYS196 3.4 27.9 1.0
CG O:MET207 3.5 27.1 1.0
CB O:HIS161 3.6 24.5 1.0
NE2 O:HIS161 4.1 27.0 1.0
O O:GLU198 4.2 25.4 1.0
CA O:HIS161 4.2 24.4 1.0
CD2 O:HIS161 4.2 27.1 1.0
ND1 O:HIS204 4.5 26.9 1.0
CD1 O:TRP104 4.6 30.1 1.0
O O:HIS102 4.6 29.9 1.0
O O:LEU160 4.7 26.2 1.0
CA O:CYS200 4.7 27.5 1.0
CA O:HIS204 4.7 25.3 1.0
CA O:CYS196 4.8 25.6 1.0
CB O:MET207 4.9 26.1 1.0
O O:HIS204 5.0 27.5 1.0

Copper binding site 6 out of 6 in 7ypy

Go back to Copper Binding Sites List in 7ypy
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution


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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu302

b:26.3
occ:1.00
 CU2 O:CUA302 0.0 26.3 1.0
ND1 O:HIS204 2.0 26.9 1.0
SG O:CYS200 2.3 28.2 1.0
SG O:CYS196 2.3 27.5 1.0
CU1 O:CUA302 2.5 26.6 1.0
O O:GLU198 2.6 25.4 1.0
CE1 O:HIS204 3.0 26.4 1.0
CG O:HIS204 3.1 25.6 1.0
CB O:CYS196 3.3 27.9 1.0
CB O:CYS200 3.3 26.6 1.0
C O:GLU198 3.5 25.5 1.0
CB O:HIS204 3.6 26.4 1.0
CA O:HIS204 3.6 25.3 1.0
N O:CYS200 3.7 27.9 1.0
O O:HIS204 3.8 27.5 1.0
NE2 O:HIS204 4.1 26.1 1.0
N O:GLU198 4.1 25.6 1.0
CA O:CYS200 4.2 27.5 1.0
C O:HIS204 4.2 26.6 1.0
CD2 O:HIS204 4.2 26.1 1.0
ND1 O:HIS161 4.2 26.9 1.0
C O:CYS196 4.2 27.3 1.0
C O:ILE199 4.2 25.9 1.0
CA O:ILE199 4.3 25.5 1.0
O O:CYS196 4.3 28.0 1.0
N O:ILE199 4.3 25.3 1.0
SD O:MET207 4.3 28.8 1.0
CA O:CYS196 4.4 25.6 1.0
CA O:GLU198 4.5 24.6 1.0
N O:SER197 4.7 24.7 1.0
CG O:MET207 4.7 27.1 1.0
N O:HIS204 4.9 27.9 1.0
CA O:HIS161 4.9 24.4 1.0

Reference:

N.Yano, K.Muramoto, A.Shimada, K.Shinzawa-Itoh, T.Tsukihara, S.Yoshikawa. The MG2+-Containing Water Cluster of Mammalian Cytochrome C Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle. J. Biol. Chem. V. 291 23882 2016.
ISSN: ESSN 1083-351X
PubMed: 27605664
DOI: 10.1074/JBC.M115.711770
Page generated: Tue Apr 4 23:33:30 2023

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