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Copper in PDB 8h8r: Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State, PDB code: 8h8r was solved by K.Muramoto, K.Shinzawa-Itoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.8, 205.7, 177.9, 90, 90, 90
R / Rfree (%) 12.2 / 15.3

Other elements in 8h8r:

The structure of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms
Zinc (Zn) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State (pdb code 8h8r). 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 Calcium-Bound Fully Oxidized State, PDB code: 8h8r:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 8h8r

Go back to Copper Binding Sites List in 8h8r
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized 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 the Calcium-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:28.6
occ:1.00
 NE2 A:HIS291 2.0 27.0 1.0
ND1 A:HIS240 2.0 27.6 1.0
NE2 A:HIS290 2.1 28.8 1.0
O2 A:PER606 2.2 35.0 1.0
O1 A:PER606 2.8 29.8 1.0
CE1 A:HIS291 2.9 26.9 1.0
CE1 A:HIS240 3.0 29.0 1.0
CG A:HIS240 3.0 26.9 1.0
CD2 A:HIS291 3.0 27.5 1.0
CE1 A:HIS290 3.0 31.9 1.0
CD2 A:HIS290 3.1 27.5 1.0
CB A:HIS240 3.3 26.2 1.0
CA A:HIS240 3.8 26.6 1.0
ND1 A:HIS291 4.0 27.2 1.0
NE2 A:HIS240 4.1 29.0 1.0
CD2 A:HIS240 4.1 26.2 1.0
CG A:HIS291 4.1 27.4 1.0
ND1 A:HIS290 4.1 28.8 1.0
CG A:HIS290 4.2 28.0 1.0
C1A A:HEA602 4.6 27.7 1.0
NA A:HEA602 4.6 26.2 1.0
N A:HIS240 4.7 27.0 1.0
C4A A:HEA602 4.7 25.8 1.0
CG2 A:VAL243 4.9 28.2 1.0
C2A A:HEA602 4.9 24.9 1.0
FE A:HEA602 4.9 27.9 1.0
C A:HIS240 5.0 28.7 1.0
C3A A:HEA602 5.0 26.4 1.0

Copper binding site 2 out of 6 in 8h8r

Go back to Copper Binding Sites List in 8h8r
Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized 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 the Calcium-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:30.4
occ:1.00
 CU1 B:CUA301 0.0 30.4 1.0
ND1 B:HIS161 2.1 30.9 1.0
SG B:CYS196 2.3 29.6 1.0
SD B:MET207 2.4 30.1 1.0
SG B:CYS200 2.4 29.2 1.0
CU2 B:CUA301 2.5 29.8 1.0
CE1 B:HIS161 3.0 30.1 1.0
CE B:MET207 3.2 32.8 1.0
CG B:HIS161 3.2 29.8 1.0
CB B:CYS200 3.3 28.3 1.0
CB B:CYS196 3.3 30.1 1.0
CG B:MET207 3.5 31.6 1.0
CB B:HIS161 3.6 29.0 1.0
O B:GLU198 4.1 31.3 1.0
NE2 B:HIS161 4.2 27.9 1.0
CA B:HIS161 4.3 27.4 1.0
CD2 B:HIS161 4.3 28.5 1.0
ND1 B:HIS204 4.5 31.7 1.0
CA B:CYS200 4.7 29.4 1.0
O B:HIS102 4.7 30.6 1.0
CA B:CYS196 4.7 28.0 1.0
CA B:HIS204 4.7 29.8 1.0
O B:LEU160 4.7 29.9 1.0
CD1 B:TRP104 4.8 30.3 1.0
CB B:MET207 4.9 32.4 1.0
O B:HIS204 4.9 30.8 1.0

Copper binding site 3 out of 6 in 8h8r

Go back to Copper Binding Sites List in 8h8r
Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized 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 the Calcium-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:29.8
occ:1.00
 CU2 B:CUA301 0.0 29.8 1.0
ND1 B:HIS204 2.0 31.7 1.0
SG B:CYS200 2.3 29.2 1.0
SG B:CYS196 2.3 29.6 1.0
O B:GLU198 2.4 31.3 1.0
CU1 B:CUA301 2.5 30.4 1.0
CE1 B:HIS204 2.9 28.8 1.0
CG B:HIS204 3.1 28.4 1.0
CB B:CYS196 3.3 30.1 1.0
CB B:CYS200 3.3 28.3 1.0
C B:GLU198 3.5 28.0 1.0
CB B:HIS204 3.5 29.3 1.0
CA B:HIS204 3.6 29.8 1.0
N B:CYS200 3.7 30.0 1.0
O B:HIS204 3.8 30.8 1.0
NE2 B:HIS204 4.1 28.7 1.0
CA B:CYS200 4.1 29.4 1.0
CD2 B:HIS204 4.2 30.8 1.0
N B:GLU198 4.2 29.8 1.0
C B:HIS204 4.2 31.9 1.0
C B:ILE199 4.2 29.5 1.0
ND1 B:HIS161 4.2 30.9 1.0
C B:CYS196 4.2 29.0 1.0
O B:CYS196 4.3 29.3 1.0
CA B:ILE199 4.3 27.7 1.0
N B:ILE199 4.3 29.1 1.0
SD B:MET207 4.3 30.1 1.0
CA B:CYS196 4.3 28.0 1.0
CA B:GLU198 4.5 27.0 1.0
N B:SER197 4.7 29.5 1.0
CG B:MET207 4.7 31.6 1.0
N B:HIS204 4.8 29.1 1.0
CA B:HIS161 5.0 27.4 1.0

Copper binding site 4 out of 6 in 8h8r

Go back to Copper Binding Sites List in 8h8r
Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized 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 the Calcium-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu605

b:32.8
occ:1.00
 ND1 N:HIS240 2.0 30.5 1.0
NE2 N:HIS291 2.0 31.6 1.0
NE2 N:HIS290 2.1 32.7 1.0
O2 N:PER608 2.3 40.8 1.0
O1 N:PER608 2.8 33.9 1.0
CE1 N:HIS240 3.0 32.3 1.0
CG N:HIS240 3.0 31.1 1.0
CE1 N:HIS291 3.0 33.5 1.0
CD2 N:HIS291 3.0 32.4 1.0
CE1 N:HIS290 3.0 36.4 1.0
CD2 N:HIS290 3.1 32.7 1.0
CB N:HIS240 3.3 29.7 1.0
CA N:HIS240 3.8 29.9 1.0
ND1 N:HIS291 4.1 31.3 1.0
NE2 N:HIS240 4.1 31.0 1.0
CD2 N:HIS240 4.1 31.9 1.0
CG N:HIS291 4.1 32.1 1.0
ND1 N:HIS290 4.2 31.9 1.0
CG N:HIS290 4.2 32.1 1.0
C1A N:HEA604 4.6 32.3 1.0
NA N:HEA604 4.6 32.9 1.0
C4A N:HEA604 4.7 28.4 1.0
N N:HIS240 4.7 29.8 1.0
C2A N:HEA604 4.9 31.7 1.0
CG2 N:VAL243 4.9 34.5 1.0
FE N:HEA604 4.9 32.0 1.0
C3A N:HEA604 4.9 29.8 1.0
C N:HIS240 5.0 30.7 1.0

Copper binding site 5 out of 6 in 8h8r

Go back to Copper Binding Sites List in 8h8r
Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized 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 the Calcium-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu305

b:40.2
occ:1.00
 CU1 O:CUA305 0.0 40.2 1.0
ND1 O:HIS161 2.1 42.3 1.0
SG O:CYS196 2.3 39.7 1.0
SG O:CYS200 2.3 39.3 1.0
SD O:MET207 2.4 40.4 1.0
CU2 O:CUA305 2.5 39.5 1.0
CE1 O:HIS161 2.9 41.9 1.0
CE O:MET207 3.1 40.0 1.0
CG O:HIS161 3.2 37.6 1.0
CB O:CYS200 3.3 37.8 1.0
CB O:CYS196 3.4 40.9 1.0
CG O:MET207 3.5 41.7 1.0
CB O:HIS161 3.6 37.4 1.0
O O:GLU198 4.0 40.1 1.0
NE2 O:HIS161 4.1 38.2 1.0
CD2 O:HIS161 4.2 37.3 1.0
CA O:HIS161 4.2 40.1 1.0
ND1 O:HIS204 4.5 38.3 1.0
CA O:CYS200 4.7 39.9 1.0
CD1 O:TRP104 4.7 40.6 1.0
CA O:HIS204 4.7 40.7 1.0
O O:HIS102 4.7 42.4 1.0
O O:LEU160 4.7 38.5 1.0
CA O:CYS196 4.8 41.7 1.0
CB O:MET207 4.9 43.9 1.0
O O:HIS204 5.0 40.1 1.0

Copper binding site 6 out of 6 in 8h8r

Go back to Copper Binding Sites List in 8h8r
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized 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 the Calcium-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu305

b:39.5
occ:1.00
 CU2 O:CUA305 0.0 39.5 1.0
ND1 O:HIS204 2.0 38.3 1.0
SG O:CYS196 2.3 39.7 1.0
O O:GLU198 2.3 40.1 1.0
SG O:CYS200 2.3 39.3 1.0
CU1 O:CUA305 2.5 40.2 1.0
CE1 O:HIS204 3.0 40.7 1.0
CG O:HIS204 3.1 36.2 1.0
CB O:CYS196 3.3 40.9 1.0
CB O:CYS200 3.3 37.8 1.0
C O:GLU198 3.4 35.0 1.0
CB O:HIS204 3.5 37.2 1.0
CA O:HIS204 3.6 40.7 1.0
N O:CYS200 3.7 39.6 1.0
O O:HIS204 3.9 40.1 1.0
NE2 O:HIS204 4.1 39.7 1.0
CA O:CYS200 4.1 39.9 1.0
N O:GLU198 4.2 36.9 1.0
CD2 O:HIS204 4.2 39.9 1.0
C O:HIS204 4.2 42.0 1.0
C O:ILE199 4.2 38.1 1.0
ND1 O:HIS161 4.2 42.3 1.0
C O:CYS196 4.2 39.6 1.0
O O:CYS196 4.2 39.1 1.0
N O:ILE199 4.2 37.7 1.0
CA O:ILE199 4.3 36.6 1.0
CA O:CYS196 4.4 41.7 1.0
SD O:MET207 4.4 40.4 1.0
CA O:GLU198 4.4 37.1 1.0
N O:SER197 4.7 39.2 1.0
CG O:MET207 4.7 41.7 1.0
N O:HIS204 4.8 39.2 1.0
CA O:HIS161 4.9 40.1 1.0

Reference:

K.Muramoto, K.Shinzawa-Itoh. Calcium-Bound Structure of Bovine Cytochrome C Oxidase. Biochim Biophys Acta 48956 2023BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 36708913
DOI: 10.1016/J.BBABIO.2023.148956
Page generated: Wed Jul 31 09:44:36 2024

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