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Copper in PDB 1ocz: Bovine Heart Cytochrome C Oxidase in Azide-Bound State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in Azide-Bound State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Azide-Bound State:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in Azide-Bound State, PDB code: 1ocz was solved by T.Tsukihara, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 189.200, 210.600, 178.500, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 25.5

Other elements in 1ocz:

The structure of Bovine Heart Cytochrome C Oxidase in Azide-Bound State also contains other interesting chemical elements:

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

Copper Binding Sites:

The binding sites of Copper atom in the Bovine Heart Cytochrome C Oxidase in Azide-Bound State (pdb code 1ocz). 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 Azide-Bound State, PDB code: 1ocz:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1ocz

Go back to Copper Binding Sites List in 1ocz
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in Azide-Bound State


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 Azide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:26.4
occ:1.00
 N3 A:AZI520 1.9 28.8 1.0
NE2 A:HIS291 1.9 25.8 1.0
NE2 A:HIS290 2.0 12.3 1.0
ND1 A:HIS240 2.2 21.8 1.0
N2 A:AZI520 2.5 33.2 1.0
CD2 A:HIS291 2.8 27.7 1.0
CE1 A:HIS290 3.0 14.3 1.0
CE1 A:HIS291 3.1 30.3 1.0
CD2 A:HIS290 3.1 17.9 1.0
CG A:HIS240 3.1 18.8 1.0
CE1 A:HIS240 3.3 22.3 1.0
CB A:HIS240 3.3 10.0 1.0
N1 A:AZI520 3.4 21.1 1.0
CA A:HIS240 3.9 14.8 1.0
CG A:HIS291 4.0 23.2 1.0
ND1 A:HIS291 4.1 23.4 1.0
ND1 A:HIS290 4.2 18.8 1.0
CG A:HIS290 4.3 20.5 1.0
CD2 A:HIS240 4.3 26.7 1.0
NE2 A:HIS240 4.4 27.3 1.0
N A:HIS240 4.7 7.0 1.0
C1A A:HEA516 4.7 7.0 1.0
NA A:HEA516 4.8 10.3 1.0
CG2 A:VAL243 4.9 9.4 1.0
C2A A:HEA516 4.9 12.2 1.0
C4A A:HEA516 4.9 12.8 1.0
C A:HIS240 5.0 23.5 1.0
C3A A:HEA516 5.0 7.6 1.0

Copper binding site 2 out of 6 in 1ocz

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in Azide-Bound State


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 Azide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:24.7
occ:1.00
 ND1 B:HIS161 1.9 11.3 1.0
CE1 B:HIS161 2.1 11.0 1.0
SG B:CYS196 2.2 16.8 1.0
SG B:CYS200 2.3 7.0 1.0
CU B:CU229 2.5 24.1 1.0
SD B:MET207 2.7 32.9 1.0
CE B:MET207 2.9 20.4 1.0
CG B:HIS161 3.2 13.4 1.0
CB B:CYS200 3.5 22.5 1.0
NE2 B:HIS161 3.5 7.0 1.0
CB B:CYS196 3.5 11.6 1.0
CG B:MET207 3.7 31.4 1.0
CD2 B:HIS161 4.0 7.0 1.0
O B:GLU198 4.0 27.2 1.0
CB B:HIS161 4.1 14.3 1.0
ND1 B:HIS204 4.4 33.9 1.0
CA B:HIS161 4.4 7.0 1.0
O B:HIS204 4.7 25.9 1.0
CD1 B:TRP104 4.7 25.1 1.0
O B:LEU160 4.7 18.5 1.0
CA B:CYS200 4.8 21.8 1.0
CA B:HIS204 4.9 25.8 1.0
CA B:CYS196 4.9 7.9 1.0
O B:HIS102 4.9 18.4 1.0
CB B:MET207 5.0 31.9 1.0

Copper binding site 3 out of 6 in 1ocz

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in Azide-Bound State


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 Azide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu229

b:24.1
occ:1.00
 ND1 B:HIS204 2.0 33.9 1.0
SG B:CYS200 2.3 7.0 1.0
SG B:CYS196 2.3 16.8 1.0
O B:GLU198 2.4 27.2 1.0
CU B:CU228 2.5 24.7 1.0
CE1 B:HIS204 2.7 31.0 1.0
CG B:HIS204 3.2 29.5 1.0
O B:HIS204 3.4 25.9 1.0
CB B:CYS196 3.4 11.6 1.0
C B:GLU198 3.4 14.9 1.0
CB B:CYS200 3.6 22.5 1.0
O B:CYS196 3.6 24.8 1.0
CA B:HIS204 3.7 25.8 1.0
CB B:HIS204 3.8 27.0 1.0
N B:CYS200 3.9 27.2 1.0
NE2 B:HIS204 4.0 25.1 1.0
C B:HIS204 4.0 25.4 1.0
ND1 B:HIS161 4.0 11.3 1.0
CD2 B:HIS204 4.2 29.4 1.0
N B:GLU198 4.2 17.8 1.0
C B:CYS196 4.2 15.2 1.0
C B:ILE199 4.2 24.4 1.0
N B:ILE199 4.2 21.2 1.0
CA B:ILE199 4.3 20.8 1.0
CA B:GLU198 4.4 17.6 1.0
CA B:CYS200 4.4 21.8 1.0
CE1 B:HIS161 4.4 11.0 1.0
CA B:CYS196 4.4 7.9 1.0
SD B:MET207 4.6 32.9 1.0
CG B:MET207 4.7 31.4 1.0
O B:ILE199 5.0 27.1 1.0

Copper binding site 4 out of 6 in 1ocz

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in Azide-Bound State


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 Azide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:28.1
occ:1.00
 N3 N:AZI520 1.9 37.3 1.0
NE2 N:HIS291 1.9 27.8 1.0
NE2 N:HIS290 1.9 21.3 1.0
N2 N:AZI520 2.2 48.5 1.0
ND1 N:HIS240 2.3 21.1 1.0
CD2 N:HIS291 2.8 31.9 1.0
CE1 N:HIS290 2.9 26.9 1.0
CD2 N:HIS290 3.0 27.3 1.0
N1 N:AZI520 3.0 34.3 1.0
CE1 N:HIS291 3.1 32.2 1.0
CG N:HIS240 3.2 27.2 1.0
CE1 N:HIS240 3.3 22.9 1.0
CB N:HIS240 3.5 25.3 1.0
CG N:HIS291 4.0 27.8 1.0
CA N:HIS240 4.0 28.2 1.0
ND1 N:HIS290 4.0 19.7 1.0
ND1 N:HIS291 4.1 32.1 1.0
CG N:HIS290 4.1 19.1 1.0
CD2 N:HIS240 4.4 35.6 1.0
NE2 N:HIS240 4.4 29.9 1.0
C1A N:HEA516 4.7 10.7 1.0
C2A N:HEA516 4.7 19.6 1.0
C4A N:HEA516 4.7 16.6 1.0
NA N:HEA516 4.8 8.4 1.0
C3A N:HEA516 4.8 19.1 1.0
N N:HIS240 4.9 24.3 1.0

Copper binding site 5 out of 6 in 1ocz

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in Azide-Bound State


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 Azide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:38.5
occ:1.00
 ND1 O:HIS161 1.9 28.4 1.0
CU O:CU229 2.2 36.7 1.0
CE1 O:HIS161 2.2 28.8 1.0
SG O:CYS196 2.3 37.2 1.0
SG O:CYS200 2.3 22.1 1.0
SD O:MET207 2.7 42.5 1.0
CE O:MET207 3.0 26.0 1.0
CG O:HIS161 3.3 35.2 1.0
CB O:CYS200 3.4 36.5 1.0
CB O:CYS196 3.5 35.8 1.0
NE2 O:HIS161 3.5 33.5 1.0
CG O:MET207 3.7 41.6 1.0
O O:GLU198 3.8 47.1 1.0
CD2 O:HIS161 4.0 28.1 1.0
CB O:HIS161 4.1 37.7 1.0
ND1 O:HIS204 4.2 39.7 1.0
CA O:HIS161 4.4 35.4 1.0
O O:HIS204 4.6 45.9 1.0
O O:LEU160 4.7 32.4 1.0
CD1 O:TRP104 4.7 34.9 1.0
CA O:HIS204 4.7 40.6 1.0
CA O:CYS200 4.7 37.8 1.0
CA O:CYS196 4.9 34.2 1.0
N O:CYS200 5.0 37.2 1.0

Copper binding site 6 out of 6 in 1ocz

Go back to Copper Binding Sites List in 1ocz
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in Azide-Bound State


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 Azide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu229

b:36.7
occ:1.00
 ND1 O:HIS204 2.1 39.7 1.0
CU O:CU228 2.2 38.5 1.0
SG O:CYS200 2.2 22.1 1.0
SG O:CYS196 2.3 37.2 1.0
O O:GLU198 2.4 47.1 1.0
CE1 O:HIS204 2.9 34.9 1.0
CG O:HIS204 3.3 40.8 1.0
CB O:CYS200 3.4 36.5 1.0
CB O:CYS196 3.4 35.8 1.0
O O:HIS204 3.5 45.9 1.0
C O:GLU198 3.5 35.7 1.0
O O:CYS196 3.6 28.7 1.0
CA O:HIS204 3.7 40.6 1.0
CB O:HIS204 3.8 40.3 1.0
N O:CYS200 3.8 37.2 1.0
ND1 O:HIS161 3.9 28.4 1.0
C O:HIS204 4.0 41.1 1.0
NE2 O:HIS204 4.1 31.1 1.0
C O:ILE199 4.2 32.6 1.0
CE1 O:HIS161 4.2 28.8 1.0
C O:CYS196 4.3 33.2 1.0
CA O:CYS200 4.3 37.8 1.0
CD2 O:HIS204 4.3 32.3 1.0
N O:ILE199 4.3 32.4 1.0
CA O:ILE199 4.3 27.1 1.0
N O:GLU198 4.3 36.9 1.0
SD O:MET207 4.4 42.5 1.0
CA O:GLU198 4.5 33.7 1.0
CA O:CYS196 4.5 34.2 1.0
CG O:MET207 4.7 41.6 1.0
O O:ILE199 4.9 38.2 1.0
CE O:MET207 4.9 26.0 1.0
N O:HIS204 5.0 46.1 1.0

Reference:

S.Yoshikawa, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, E.Yamashita, N.Inoue, M.Yao, M.J.Fei, C.P.Libeu, T.Mizushima, H.Yamaguchi, T.Tomizaki, T.Tsukihara. Redox-Coupled Crystal Structural Changes in Bovine Heart Cytochrome C Oxidase. Science V. 280 1723 1998.
ISSN: ISSN 0036-8075
PubMed: 9624044
DOI: 10.1126/SCIENCE.280.5370.1723
Page generated: Mon Jul 14 00:13:17 2025

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