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Copper in PDB 5b3s: Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K):
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K), PDB code: 5b3s was solved by J.Baba, A.Shimada, E.Yamashita, K.Shinzawa-Ito, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.491, 203.303, 177.484, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 17.4

Other elements in 5b3s:

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) 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 the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) (pdb code 5b3s). 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 Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K), PDB code: 5b3s:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5b3s

Go back to Copper Binding Sites List in 5b3s
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (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 Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:23.2
occ:1.00
 NE2 A:HIS291 2.0 19.6 1.0
NE2 A:HIS290 2.0 23.3 1.0
ND1 A:HIS240 2.1 20.7 1.0
C A:CMO606 2.3 29.8 1.0
O A:CMO606 2.7 30.7 1.0
CE1 A:HIS291 2.9 17.9 1.0
CE1 A:HIS240 3.0 20.6 1.0
CE1 A:HIS290 3.0 23.6 1.0
CD2 A:HIS291 3.1 19.0 1.0
CD2 A:HIS290 3.1 22.6 1.0
CG A:HIS240 3.2 20.0 1.0
CB A:HIS240 3.6 17.7 1.0
ND1 A:HIS291 4.0 20.4 1.0
CG A:HIS291 4.1 20.0 1.0
CA A:HIS240 4.2 18.0 1.0
ND1 A:HIS290 4.2 20.9 1.0
NE2 A:HIS240 4.2 21.6 1.0
CG A:HIS290 4.2 19.4 1.0
C1A A:HEA602 4.3 19.0 1.0
CD2 A:HIS240 4.3 21.4 1.0
C4A A:HEA602 4.3 19.9 1.0
NA A:HEA602 4.5 24.3 1.0
C2A A:HEA602 4.5 20.7 1.0
C3A A:HEA602 4.6 22.3 1.0
CG2 A:VAL243 4.8 21.7 1.0
CHA A:HEA602 4.9 21.6 1.0
FE A:HEA602 4.9 22.5 1.0

Copper binding site 2 out of 6 in 5b3s

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (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 Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:25.4
occ:1.00
 CU1 B:CUA302 0.0 25.4 1.0
ND1 B:HIS161 2.1 24.3 1.0
SG B:CYS196 2.3 24.3 1.0
SG B:CYS200 2.4 23.4 1.0
SD B:MET207 2.4 25.6 1.0
CU2 B:CUA302 2.5 24.7 1.0
CE1 B:HIS161 3.0 25.9 1.0
CE B:MET207 3.2 23.6 1.0
CG B:HIS161 3.2 23.6 1.0
CB B:CYS200 3.3 21.5 1.0
CB B:CYS196 3.4 23.7 1.0
CG B:MET207 3.5 23.1 1.0
CB B:HIS161 3.6 19.8 1.0
O B:GLU198 4.0 25.9 1.0
CA B:HIS161 4.2 19.7 1.0
NE2 B:HIS161 4.2 23.5 1.0
CD2 B:HIS161 4.3 22.2 1.0
ND1 B:HIS204 4.4 24.4 1.0
CA B:HIS204 4.6 21.3 1.0
O B:HIS102 4.7 26.4 1.0
O B:LEU160 4.7 22.6 1.0
CA B:CYS200 4.7 23.4 1.0
CD1 B:TRP104 4.7 23.8 1.0
CA B:CYS196 4.7 22.5 1.0
CB B:MET207 4.9 23.6 1.0
O B:HIS204 4.9 26.1 1.0

Copper binding site 3 out of 6 in 5b3s

Go back to Copper Binding Sites List in 5b3s
Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (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 Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:24.7
occ:1.00
 CU2 B:CUA302 0.0 24.7 1.0
ND1 B:HIS204 2.0 24.4 1.0
SG B:CYS200 2.3 23.4 1.0
O B:GLU198 2.3 25.9 1.0
SG B:CYS196 2.3 24.3 1.0
CU1 B:CUA302 2.5 25.4 1.0
CE1 B:HIS204 3.0 23.9 1.0
CG B:HIS204 3.1 21.9 1.0
CB B:CYS196 3.3 23.7 1.0
CB B:CYS200 3.4 21.5 1.0
C B:GLU198 3.5 21.0 1.0
CB B:HIS204 3.5 22.9 1.0
CA B:HIS204 3.5 21.3 1.0
N B:CYS200 3.7 24.6 1.0
O B:HIS204 3.8 26.1 1.0
N B:GLU198 4.1 22.7 1.0
NE2 B:HIS204 4.1 23.6 1.0
C B:HIS204 4.1 23.7 1.0
C B:ILE199 4.1 24.9 1.0
CA B:CYS200 4.1 23.4 1.0
ND1 B:HIS161 4.2 24.3 1.0
CD2 B:HIS204 4.2 23.2 1.0
C B:CYS196 4.2 20.8 1.0
O B:CYS196 4.2 23.3 1.0
CA B:ILE199 4.3 25.7 1.0
N B:ILE199 4.3 23.2 1.0
SD B:MET207 4.3 25.6 1.0
CA B:CYS196 4.4 22.5 1.0
CA B:GLU198 4.5 20.9 1.0
N B:SER197 4.6 22.2 1.0
CG B:MET207 4.6 23.1 1.0
N B:HIS204 4.8 23.1 1.0
CA B:HIS161 4.9 19.7 1.0

Copper binding site 4 out of 6 in 5b3s

Go back to Copper Binding Sites List in 5b3s
Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (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 Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:24.7
occ:1.00
 NE2 N:HIS291 2.0 20.4 1.0
NE2 N:HIS290 2.0 26.3 1.0
ND1 N:HIS240 2.1 21.6 1.0
C N:CMO606 2.3 29.7 1.0
O N:CMO606 2.8 31.4 1.0
CE1 N:HIS291 2.9 20.0 1.0
CE1 N:HIS240 3.0 22.7 1.0
CE1 N:HIS290 3.0 24.4 1.0
CD2 N:HIS291 3.0 22.4 1.0
CD2 N:HIS290 3.1 21.7 1.0
CG N:HIS240 3.2 21.0 1.0
CB N:HIS240 3.5 17.8 1.0
ND1 N:HIS291 4.0 23.5 1.0
CA N:HIS240 4.1 21.5 1.0
CG N:HIS291 4.1 23.8 1.0
ND1 N:HIS290 4.2 24.5 1.0
NE2 N:HIS240 4.2 21.9 1.0
CG N:HIS290 4.2 22.5 1.0
CD2 N:HIS240 4.3 20.6 1.0
C1A N:HEA602 4.3 23.0 1.0
C4A N:HEA602 4.4 21.6 1.0
NA N:HEA602 4.5 25.8 1.0
C2A N:HEA602 4.6 21.4 1.0
C3A N:HEA602 4.6 22.5 1.0
CG2 N:VAL243 4.8 23.0 1.0
CHA N:HEA602 4.9 22.5 1.0
FE N:HEA602 4.9 24.2 1.0
CHB N:HEA602 5.0 20.5 1.0

Copper binding site 5 out of 6 in 5b3s

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (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 Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:29.2
occ:1.00
 CU1 O:CUA301 0.0 29.2 1.0
ND1 O:HIS161 2.1 29.9 1.0
SG O:CYS196 2.3 28.0 1.0
SG O:CYS200 2.3 28.1 1.0
SD O:MET207 2.4 29.6 1.0
CU2 O:CUA301 2.5 28.7 1.0
CE1 O:HIS161 3.0 30.5 1.0
CG O:HIS161 3.1 26.7 1.0
CE O:MET207 3.2 27.7 1.0
CB O:CYS200 3.3 28.9 1.0
CB O:CYS196 3.3 25.6 1.0
CB O:HIS161 3.6 27.5 1.0
CG O:MET207 3.6 28.8 1.0
O O:GLU198 3.9 28.1 1.0
CA O:HIS161 4.1 25.4 1.0
NE2 O:HIS161 4.2 27.0 1.0
CD2 O:HIS161 4.3 26.7 1.0
ND1 O:HIS204 4.4 28.6 1.0
CA O:HIS204 4.6 25.4 1.0
CD1 O:TRP104 4.7 29.6 1.0
O O:HIS102 4.7 29.2 1.0
O O:LEU160 4.7 26.7 1.0
CA O:CYS200 4.7 27.2 1.0
CA O:CYS196 4.8 25.1 1.0
O O:HIS204 4.9 29.8 1.0
CB O:MET207 5.0 28.8 1.0

Copper binding site 6 out of 6 in 5b3s

Go back to Copper Binding Sites List in 5b3s
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (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 Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:28.7
occ:1.00
 CU2 O:CUA301 0.0 28.7 1.0
ND1 O:HIS204 2.0 28.6 1.0
O O:GLU198 2.3 28.1 1.0
SG O:CYS200 2.3 28.1 1.0
SG O:CYS196 2.3 28.0 1.0
CU1 O:CUA301 2.5 29.2 1.0
CE1 O:HIS204 3.0 27.3 1.0
CG O:HIS204 3.1 27.4 1.0
CB O:CYS196 3.3 25.6 1.0
CB O:CYS200 3.4 28.9 1.0
C O:GLU198 3.4 23.1 1.0
CB O:HIS204 3.5 29.9 1.0
CA O:HIS204 3.5 25.4 1.0
N O:CYS200 3.7 26.8 1.0
O O:HIS204 3.8 29.8 1.0
N O:GLU198 4.1 26.4 1.0
NE2 O:HIS204 4.1 27.1 1.0
C O:HIS204 4.1 27.5 1.0
C O:ILE199 4.2 26.0 1.0
ND1 O:HIS161 4.2 29.9 1.0
CA O:CYS200 4.2 27.2 1.0
CD2 O:HIS204 4.2 26.2 1.0
CA O:ILE199 4.2 22.7 1.0
C O:CYS196 4.2 25.4 1.0
O O:CYS196 4.3 26.5 1.0
N O:ILE199 4.3 26.1 1.0
SD O:MET207 4.4 29.6 1.0
CA O:CYS196 4.4 25.1 1.0
CA O:GLU198 4.5 24.3 1.0
N O:SER197 4.6 27.0 1.0
CG O:MET207 4.8 28.8 1.0
N O:HIS204 4.8 28.6 1.0
CA O:HIS161 4.9 25.4 1.0

Reference:

A.Shimada, J.Baba, E.Yamashita, K.Shinzawa-Ito, S.Yoshikawa, T.Tsukihara. Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed-Valence State at 1.68 Angstrom Resolution (50 K) To Be Published.
Page generated: Wed Jul 31 03:52:21 2024

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