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Copper in PDB 1oco: Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State

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

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

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State, PDB code: 1oco 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 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 189.100, 210.500, 178.600, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 25.6

Other elements in 1oco:

The structure of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-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 Carbon Monoxide-Bound State (pdb code 1oco). 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 Carbon Monoxide-Bound State, PDB code: 1oco:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1oco

Go back to Copper Binding Sites List in 1oco
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-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 Carbon Monoxide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:10.1
occ:1.00
 NE2 A:HIS291 2.0 12.7 1.0
NE2 A:HIS290 2.0 7.0 1.0
ND1 A:HIS240 2.2 13.3 1.0
O A:CMO520 2.4 19.1 1.0
CD2 A:HIS291 2.7 20.9 1.0
CE1 A:HIS290 3.0 10.7 1.0
CD2 A:HIS290 3.1 14.5 1.0
CG A:HIS240 3.1 7.5 1.0
CE1 A:HIS291 3.1 17.9 1.0
CE1 A:HIS240 3.2 10.4 1.0
CB A:HIS240 3.4 7.0 1.0
C A:CMO520 3.7 12.2 1.0
CG A:HIS291 3.9 21.0 1.0
CA A:HIS240 4.0 7.0 1.0
ND1 A:HIS291 4.1 21.4 1.0
ND1 A:HIS290 4.2 7.0 1.0
CG A:HIS290 4.2 12.9 1.0
CD2 A:HIS240 4.3 14.2 1.0
NE2 A:HIS240 4.3 20.3 1.0
CG2 A:VAL243 4.8 7.0 1.0
N A:HIS240 4.8 7.0 1.0
O A:TRP288 4.9 18.9 1.0
CA A:TRP288 5.0 7.0 1.0

Copper binding site 2 out of 6 in 1oco

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-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 Carbon Monoxide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:15.2
occ:1.00
 ND1 B:HIS161 1.9 10.8 1.0
SG B:CYS196 2.3 18.5 1.0
SG B:CYS200 2.4 20.9 1.0
CU B:CU229 2.4 19.9 1.0
SD B:MET207 2.7 22.5 1.0
CE1 B:HIS161 2.7 7.0 1.0
CE B:MET207 3.0 10.7 1.0
CG B:HIS161 3.1 7.0 1.0
CB B:CYS200 3.4 17.0 1.0
CB B:CYS196 3.5 18.6 1.0
CB B:HIS161 3.6 7.3 1.0
CG B:MET207 3.8 12.8 1.0
NE2 B:HIS161 3.9 7.0 1.0
O B:GLU198 4.1 26.8 1.0
CA B:HIS161 4.1 9.8 1.0
CD2 B:HIS161 4.1 7.0 1.0
ND1 B:HIS204 4.4 23.3 1.0
O B:LEU160 4.6 17.3 1.0
CD1 B:TRP104 4.7 17.9 1.0
CA B:HIS204 4.8 15.5 1.0
CA B:CYS200 4.8 9.9 1.0
CA B:CYS196 4.9 10.7 1.0
O B:HIS102 4.9 7.0 1.0
O B:HIS204 5.0 19.2 1.0

Copper binding site 3 out of 6 in 1oco

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-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 Carbon Monoxide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu229

b:19.9
occ:1.00
 ND1 B:HIS204 2.1 23.3 1.0
SG B:CYS200 2.2 20.9 1.0
SG B:CYS196 2.2 18.5 1.0
O B:GLU198 2.4 26.8 1.0
CU B:CU228 2.4 15.2 1.0
CE1 B:HIS204 3.0 18.2 1.0
CG B:HIS204 3.0 14.9 1.0
CB B:CYS200 3.3 17.0 1.0
CA B:HIS204 3.3 15.5 1.0
CB B:HIS204 3.4 13.2 1.0
CB B:CYS196 3.5 18.6 1.0
N B:CYS200 3.6 11.3 1.0
C B:GLU198 3.6 14.4 1.0
O B:HIS204 3.7 19.2 1.0
C B:HIS204 4.0 18.2 1.0
CA B:CYS200 4.1 9.9 1.0
NE2 B:HIS204 4.1 13.9 1.0
ND1 B:HIS161 4.1 10.8 1.0
CD2 B:HIS204 4.1 10.4 1.0
C B:ILE199 4.1 13.3 1.0
CA B:ILE199 4.2 11.3 1.0
N B:ILE199 4.3 14.6 1.0
SD B:MET207 4.4 22.5 1.0
N B:GLU198 4.4 12.7 1.0
O B:CYS196 4.5 21.6 1.0
C B:CYS196 4.6 16.0 1.0
N B:HIS204 4.6 18.4 1.0
CA B:GLU198 4.6 8.4 1.0
CA B:CYS196 4.7 10.7 1.0
CG B:MET207 4.7 12.8 1.0
CE1 B:HIS161 4.7 7.0 1.0
O B:ILE199 4.9 10.7 1.0
C B:CYS200 4.9 14.9 1.0

Copper binding site 4 out of 6 in 1oco

Go back to Copper Binding Sites List in 1oco
Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-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 Carbon Monoxide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:21.6
occ:1.00
 NE2 N:HIS291 2.0 26.4 1.0
NE2 N:HIS290 2.1 9.5 1.0
ND1 N:HIS240 2.1 18.9 1.0
O N:CMO520 2.6 22.4 1.0
CD2 N:HIS291 2.8 26.9 1.0
CE1 N:HIS290 3.0 11.4 1.0
CE1 N:HIS240 3.1 8.8 1.0
CE1 N:HIS291 3.1 26.9 1.0
CD2 N:HIS290 3.2 13.6 1.0
CG N:HIS240 3.2 16.1 1.0
C N:CMO520 3.4 11.7 1.0
CB N:HIS240 3.5 16.3 1.0
CA N:HIS240 4.0 16.8 1.0
CG N:HIS291 4.0 23.4 1.0
ND1 N:HIS291 4.2 24.9 1.0
ND1 N:HIS290 4.2 11.4 1.0
NE2 N:HIS240 4.2 17.7 1.0
CG N:HIS290 4.3 13.2 1.0
CD2 N:HIS240 4.3 21.2 1.0
CG2 N:VAL243 4.7 24.2 1.0
N N:HIS240 4.8 9.7 1.0
NA N:HEA516 4.9 12.5 1.0

Copper binding site 5 out of 6 in 1oco

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-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 Carbon Monoxide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:31.1
occ:1.00
 ND1 O:HIS161 2.0 16.9 1.0
SG O:CYS196 2.2 17.3 1.0
CU O:CU229 2.3 26.9 1.0
SG O:CYS200 2.4 19.4 1.0
SD O:MET207 2.7 32.6 1.0
CE1 O:HIS161 2.8 22.7 1.0
CE O:MET207 3.0 17.2 1.0
CG O:HIS161 3.2 19.3 1.0
CB O:CYS196 3.4 29.4 1.0
CB O:CYS200 3.5 24.4 1.0
CB O:HIS161 3.7 26.8 1.0
CG O:MET207 3.8 22.9 1.0
O O:GLU198 3.9 29.4 1.0
NE2 O:HIS161 4.1 21.2 1.0
CA O:HIS161 4.1 27.6 1.0
ND1 O:HIS204 4.2 29.8 1.0
CD2 O:HIS161 4.3 17.2 1.0
O O:LEU160 4.6 32.2 1.0
CA O:CYS196 4.7 26.6 1.0
CA O:HIS204 4.7 27.8 1.0
CA O:CYS200 4.8 27.5 1.0
O O:HIS204 4.8 29.2 1.0
CD1 O:TRP104 4.8 25.7 1.0
N O:CYS200 5.0 27.3 1.0

Copper binding site 6 out of 6 in 1oco

Go back to Copper Binding Sites List in 1oco
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-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 Carbon Monoxide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu229

b:26.9
occ:1.00
 ND1 O:HIS204 2.0 29.8 1.0
SG O:CYS200 2.1 19.4 1.0
CU O:CU228 2.3 31.1 1.0
SG O:CYS196 2.4 17.3 1.0
O O:GLU198 2.4 29.4 1.0
CG O:HIS204 2.9 23.5 1.0
CE1 O:HIS204 3.1 26.9 1.0
CB O:CYS200 3.2 24.4 1.0
CB O:HIS204 3.3 24.9 1.0
CA O:HIS204 3.3 27.8 1.0
N O:CYS200 3.4 27.3 1.0
C O:GLU198 3.6 21.9 1.0
CB O:CYS196 3.6 29.4 1.0
O O:HIS204 3.7 29.2 1.0
CA O:CYS200 3.9 27.5 1.0
C O:HIS204 4.0 25.4 1.0
C O:ILE199 4.0 24.3 1.0
CD2 O:HIS204 4.1 17.1 1.0
ND1 O:HIS161 4.1 16.9 1.0
NE2 O:HIS204 4.1 25.3 1.0
CA O:ILE199 4.2 18.1 1.0
N O:ILE199 4.3 21.8 1.0
SD O:MET207 4.4 32.6 1.0
N O:HIS204 4.5 33.8 1.0
N O:GLU198 4.5 23.2 1.0
O O:CYS196 4.6 29.4 1.0
CE1 O:HIS161 4.7 22.7 1.0
CA O:GLU198 4.7 18.2 1.0
C O:CYS196 4.8 29.1 1.0
CG O:MET207 4.8 22.9 1.0
C O:CYS200 4.8 30.3 1.0
O O:ILE199 4.8 26.7 1.0
CA O:CYS196 4.8 26.6 1.0
O O:LEU160 5.0 32.2 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: Sun Dec 13 11:01:04 2020

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