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Copper in PDB 1v55: Bovine Heart Cytochrome C Oxidase at the Fully Reduced State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State, PDB code: 1v55 was solved by T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.060, 206.584, 178.298, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 23

Other elements in 1v55:

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Reduced 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 at the Fully Reduced State (pdb code 1v55). 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 at the Fully Reduced State, PDB code: 1v55:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1v55

Go back to Copper Binding Sites List in 1v55
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Reduced 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 at the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:16.4
occ:1.00
 NE2 A:HIS291 2.0 19.9 1.0
ND1 A:HIS240 2.0 21.4 1.0
NE2 A:HIS290 2.0 18.5 1.0
CD2 A:HIS291 2.8 19.3 1.0
CG A:HIS240 3.0 19.0 1.0
CE1 A:HIS240 3.0 20.3 1.0
CE1 A:HIS290 3.0 15.0 1.0
CE1 A:HIS291 3.0 19.4 1.0
CD2 A:HIS290 3.1 17.5 1.0
CB A:HIS240 3.3 15.7 1.0
CA A:HIS240 3.9 15.2 1.0
CG A:HIS291 4.0 18.2 1.0
ND1 A:HIS291 4.1 18.7 1.0
CD2 A:HIS240 4.1 20.1 1.0
NE2 A:HIS240 4.1 22.8 1.0
ND1 A:HIS290 4.2 14.9 1.0
CG A:HIS290 4.2 17.7 1.0
NA A:HEA516 4.6 16.2 1.0
C1A A:HEA516 4.6 14.7 1.0
CG2 A:VAL243 4.7 12.7 1.0
N A:HIS240 4.7 13.9 1.0
C4A A:HEA516 4.8 16.9 1.0
C2A A:HEA516 4.8 16.1 1.0
CHA A:HEA516 4.9 14.9 1.0
C3A A:HEA516 4.9 17.0 1.0

Copper binding site 2 out of 6 in 1v55

Go back to Copper Binding Sites List in 1v55
Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Reduced 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 at the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:18.9
occ:1.00
 CU1 B:CUA228 0.0 18.9 1.0
ND1 B:HIS161 2.0 16.3 1.0
SG B:CYS196 2.3 22.5 1.0
SG B:CYS200 2.4 18.4 1.0
CU2 B:CUA228 2.5 16.0 1.0
SD B:MET207 2.6 19.5 1.0
CE1 B:HIS161 2.8 11.4 1.0
CE B:MET207 3.1 12.3 1.0
CG B:HIS161 3.2 11.9 1.0
CB B:CYS200 3.3 17.5 1.0
CB B:CYS196 3.4 15.7 1.0
CG B:MET207 3.6 18.3 1.0
CB B:HIS161 3.6 12.3 1.0
NE2 B:HIS161 4.1 12.9 1.0
O B:GLU198 4.2 20.2 1.0
CA B:HIS161 4.2 15.2 1.0
CD2 B:HIS161 4.2 13.4 1.0
ND1 B:HIS204 4.4 18.8 1.0
CD1 B:TRP104 4.6 19.8 1.0
CA B:CYS200 4.7 17.9 1.0
O B:LEU160 4.7 18.7 1.0
CA B:CYS196 4.8 17.3 1.0
CA B:HIS204 4.8 17.1 1.0
O B:HIS102 4.8 17.8 1.0
N B:CYS200 4.9 19.2 1.0
CB B:MET207 5.0 16.7 1.0
CZ2 B:TRP106 5.0 20.2 1.0
O B:HIS204 5.0 17.4 1.0

Copper binding site 3 out of 6 in 1v55

Go back to Copper Binding Sites List in 1v55
Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Reduced 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 at the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:16.0
occ:1.00
 CU2 B:CUA228 0.0 16.0 1.0
ND1 B:HIS204 2.0 18.8 1.0
SG B:CYS200 2.2 18.4 1.0
SG B:CYS196 2.3 22.5 1.0
CU1 B:CUA228 2.5 18.9 1.0
O B:GLU198 2.5 20.2 1.0
CE1 B:HIS204 2.9 16.8 1.0
CG B:HIS204 3.1 17.2 1.0
CB B:CYS196 3.3 15.7 1.0
CB B:CYS200 3.5 17.5 1.0
CB B:HIS204 3.5 16.6 1.0
CA B:HIS204 3.5 17.1 1.0
N B:CYS200 3.6 19.2 1.0
C B:GLU198 3.6 19.4 1.0
O B:HIS204 3.8 17.4 1.0
NE2 B:HIS204 4.1 18.0 1.0
C B:HIS204 4.1 18.4 1.0
O B:CYS196 4.1 16.7 1.0
ND1 B:HIS161 4.1 16.3 1.0
CD2 B:HIS204 4.2 16.4 1.0
CA B:CYS200 4.2 17.9 1.0
N B:GLU198 4.2 18.9 1.0
C B:CYS196 4.2 19.2 1.0
C B:ILE199 4.2 18.9 1.0
CA B:ILE199 4.3 17.0 1.0
CA B:CYS196 4.3 17.3 1.0
N B:ILE199 4.4 16.6 1.0
SD B:MET207 4.5 19.5 1.0
CA B:GLU198 4.6 17.6 1.0
CG B:MET207 4.7 18.3 1.0
N B:SER197 4.7 18.8 1.0
N B:HIS204 4.8 22.8 1.0
CA B:HIS161 4.9 15.2 1.0
CE1 B:HIS161 4.9 11.4 1.0

Copper binding site 4 out of 6 in 1v55

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Reduced 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 at the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:19.7
occ:1.00
 NE2 N:HIS291 2.0 22.7 1.0
ND1 N:HIS240 2.0 20.8 1.0
NE2 N:HIS290 2.0 16.1 1.0
CD2 N:HIS291 2.9 25.1 1.0
CE1 N:HIS290 2.9 18.4 1.0
CG N:HIS240 3.0 23.2 1.0
CE1 N:HIS240 3.0 22.4 1.0
CE1 N:HIS291 3.0 22.8 1.0
CD2 N:HIS290 3.1 16.2 1.0
CB N:HIS240 3.3 18.1 1.0
CA N:HIS240 3.9 19.6 1.0
CG N:HIS291 4.1 23.6 1.0
CD2 N:HIS240 4.1 23.7 1.0
ND1 N:HIS290 4.1 15.8 1.0
NE2 N:HIS240 4.1 26.0 1.0
ND1 N:HIS291 4.1 24.7 1.0
CG N:HIS290 4.2 17.6 1.0
NA N:HEA516 4.6 19.1 1.0
C1A N:HEA516 4.6 19.3 1.0
N N:HIS240 4.7 18.3 1.0
CG2 N:VAL243 4.8 18.4 1.0
C4A N:HEA516 4.8 18.9 1.0
C2A N:HEA516 4.9 18.8 1.0
CHA N:HEA516 4.9 18.2 1.0
C3A N:HEA516 4.9 17.9 1.0

Copper binding site 5 out of 6 in 1v55

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

b:24.1
occ:1.00
 CU1 O:CUA228 0.0 24.1 1.0
ND1 O:HIS161 2.0 25.4 1.0
SG O:CYS196 2.3 21.9 1.0
SG O:CYS200 2.3 23.8 1.0
CU2 O:CUA228 2.4 27.4 1.0
SD O:MET207 2.7 27.9 1.0
CE1 O:HIS161 2.8 23.4 1.0
CE O:MET207 3.2 19.8 1.0
CG O:HIS161 3.2 20.9 1.0
CB O:CYS200 3.3 26.5 1.0
CB O:CYS196 3.4 25.4 1.0
CG O:MET207 3.6 25.7 1.0
CB O:HIS161 3.7 20.9 1.0
NE2 O:HIS161 4.0 21.3 1.0
O O:GLU198 4.1 24.8 1.0
CA O:HIS161 4.2 20.4 1.0
CD2 O:HIS161 4.2 20.6 1.0
ND1 O:HIS204 4.3 27.2 1.0
CA O:CYS200 4.7 25.2 1.0
O O:LEU160 4.7 20.7 1.0
CD1 O:TRP104 4.7 24.1 1.0
CA O:CYS196 4.7 23.6 1.0
CA O:HIS204 4.7 23.4 1.0
O O:HIS102 4.9 21.3 1.0
N O:CYS200 4.9 27.4 1.0
O O:HIS204 4.9 24.5 1.0
CB O:MET207 5.0 25.1 1.0

Copper binding site 6 out of 6 in 1v55

Go back to Copper Binding Sites List in 1v55
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Reduced 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 at the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:27.4
occ:1.00
 CU2 O:CUA228 0.0 27.4 1.0
ND1 O:HIS204 2.1 27.2 1.0
SG O:CYS200 2.3 23.8 1.0
SG O:CYS196 2.3 21.9 1.0
CU1 O:CUA228 2.4 24.1 1.0
O O:GLU198 2.5 24.8 1.0
CE1 O:HIS204 2.9 23.7 1.0
CG O:HIS204 3.1 25.9 1.0
CB O:CYS196 3.3 25.4 1.0
CB O:CYS200 3.4 26.5 1.0
N O:CYS200 3.6 27.4 1.0
CA O:HIS204 3.6 23.4 1.0
C O:GLU198 3.6 21.7 1.0
CB O:HIS204 3.6 23.7 1.0
O O:HIS204 3.8 24.5 1.0
ND1 O:HIS161 4.0 25.4 1.0
NE2 O:HIS204 4.1 24.9 1.0
CA O:CYS200 4.1 25.2 1.0
O O:CYS196 4.1 25.4 1.0
C O:HIS204 4.2 23.3 1.0
N O:GLU198 4.2 20.1 1.0
CD2 O:HIS204 4.2 22.8 1.0
C O:ILE199 4.2 25.8 1.0
C O:CYS196 4.3 26.5 1.0
CA O:ILE199 4.3 22.6 1.0
N O:ILE199 4.4 20.4 1.0
CA O:CYS196 4.4 23.6 1.0
SD O:MET207 4.5 27.9 1.0
CA O:GLU198 4.6 21.3 1.0
CG O:MET207 4.7 25.7 1.0
CE1 O:HIS161 4.7 23.4 1.0
N O:SER197 4.8 26.5 1.0
N O:HIS204 4.8 23.8 1.0
CA O:HIS161 4.9 20.4 1.0
CG O:HIS161 5.0 20.9 1.0

Reference:

T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa. The Low-Spin Heme of Cytochrome C Oxidase As the Driving Element of the Proton-Pumping Process. Proc.Natl.Acad.Sci.Usa V. 100 15304 2003.
ISSN: ISSN 0027-8424
PubMed: 14673090
DOI: 10.1073/PNAS.2635097100
Page generated: Tue Jul 30 22:53:38 2024

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