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Copper in PDB 3x2q: X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution

Enzymatic activity of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution

All present enzymatic activity of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution, PDB code: 3x2q was solved by N.Yano, K.Muramoto, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, 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 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.678, 206.675, 178.201, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.4

Other elements in 3x2q:

The structure of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution 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 X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution (pdb code 3x2q). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution, PDB code: 3x2q:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3x2q

Go back to Copper Binding Sites List in 3x2q
Copper binding site 1 out of 6 in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:25.7
occ:1.00
 N A:CYN601 2.0 24.8 1.0
ND1 A:HIS240 2.0 25.5 1.0
NE2 A:HIS290 2.0 24.8 1.0
NE2 A:HIS291 2.0 27.7 1.0
CE1 A:HIS240 2.9 23.6 1.0
CD2 A:HIS291 2.9 22.0 1.0
C A:CYN601 2.9 20.9 1.0
CE1 A:HIS291 3.0 20.8 1.0
CE1 A:HIS290 3.0 24.1 1.0
CD2 A:HIS290 3.0 23.2 1.0
CG A:HIS240 3.1 25.1 1.0
CB A:HIS240 3.4 20.9 1.0
CA A:HIS240 4.0 22.1 1.0
ND1 A:HIS291 4.0 22.3 1.0
CG A:HIS291 4.0 20.0 1.0
NE2 A:HIS240 4.1 25.6 1.0
ND1 A:HIS290 4.1 22.6 1.0
CD2 A:HIS240 4.1 23.2 1.0
CG A:HIS290 4.2 19.6 1.0
NA A:HEA603 4.7 24.2 1.0
CG2 A:VAL243 4.7 24.0 1.0
C1A A:HEA603 4.7 23.9 1.0
C4A A:HEA603 4.7 20.6 1.0
N A:HIS240 4.8 21.6 1.0
FE A:HEA603 4.9 24.0 1.0
C2A A:HEA603 5.0 23.9 1.0

Copper binding site 2 out of 6 in 3x2q

Go back to Copper Binding Sites List in 3x2q
Copper binding site 2 out of 6 in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:27.9
occ:1.00
 CU1 B:CUA301 0.0 27.9 1.0
ND1 B:HIS161 2.1 22.8 1.0
SG B:CYS196 2.3 26.7 1.0
SD B:MET207 2.4 26.8 1.0
SG B:CYS200 2.4 25.2 1.0
CU2 B:CUA301 2.5 26.4 1.0
CE1 B:HIS161 2.9 19.5 1.0
CE B:MET207 3.2 23.3 1.0
CG B:HIS161 3.2 23.9 1.0
CB B:CYS200 3.4 23.8 1.0
CB B:CYS196 3.4 23.6 1.0
CG B:MET207 3.4 27.4 1.0
CB B:HIS161 3.6 23.9 1.0
O B:GLU198 4.0 25.9 1.0
NE2 B:HIS161 4.1 24.8 1.0
CA B:HIS161 4.2 24.0 1.0
CD2 B:HIS161 4.3 24.0 1.0
ND1 B:HIS204 4.5 27.2 1.0
CD1 B:TRP104 4.7 25.1 1.0
CA B:HIS204 4.7 26.6 1.0
O B:LEU160 4.7 24.5 1.0
O B:HIS102 4.8 26.1 1.0
CA B:CYS200 4.8 24.7 1.0
CA B:CYS196 4.8 25.0 1.0
CB B:MET207 4.9 26.8 1.0
O B:HIS204 4.9 26.6 1.0

Copper binding site 3 out of 6 in 3x2q

Go back to Copper Binding Sites List in 3x2q
Copper binding site 3 out of 6 in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:26.4
occ:1.00
 CU2 B:CUA301 0.0 26.4 1.0
ND1 B:HIS204 2.0 27.2 1.0
O B:GLU198 2.3 25.9 1.0
SG B:CYS196 2.3 26.7 1.0
SG B:CYS200 2.3 25.2 1.0
CU1 B:CUA301 2.5 27.9 1.0
CE1 B:HIS204 2.8 29.7 1.0
CG B:HIS204 3.2 25.3 1.0
CB B:CYS196 3.4 23.6 1.0
C B:GLU198 3.4 24.7 1.0
CB B:CYS200 3.5 23.8 1.0
CA B:HIS204 3.6 26.6 1.0
N B:CYS200 3.6 24.5 1.0
CB B:HIS204 3.7 22.0 1.0
O B:HIS204 3.8 26.6 1.0
NE2 B:HIS204 4.0 29.7 1.0
C B:ILE199 4.1 24.2 1.0
N B:GLU198 4.1 24.2 1.0
C B:HIS204 4.2 25.2 1.0
CD2 B:HIS204 4.2 25.7 1.0
ND1 B:HIS161 4.2 22.8 1.0
C B:CYS196 4.2 25.0 1.0
CA B:CYS200 4.2 24.7 1.0
CA B:ILE199 4.2 25.0 1.0
N B:ILE199 4.2 25.6 1.0
O B:CYS196 4.2 21.9 1.0
SD B:MET207 4.4 26.8 1.0
CA B:CYS196 4.4 25.0 1.0
CA B:GLU198 4.5 24.2 1.0
N B:SER197 4.6 24.3 1.0
CG B:MET207 4.6 27.4 1.0
N B:HIS204 4.9 23.9 1.0
CA B:HIS161 4.9 24.0 1.0
O B:ILE199 5.0 23.2 1.0

Copper binding site 4 out of 6 in 3x2q

Go back to Copper Binding Sites List in 3x2q
Copper binding site 4 out of 6 in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu604

b:30.3
occ:1.00
 NE2 N:HIS291 2.0 32.9 1.0
N N:CYN601 2.0 30.8 1.0
ND1 N:HIS240 2.0 26.9 1.0
NE2 N:HIS290 2.1 30.1 1.0
CE1 N:HIS291 2.8 30.0 1.0
CD2 N:HIS291 3.0 28.4 1.0
CE1 N:HIS240 3.0 24.8 1.0
CE1 N:HIS290 3.0 30.4 1.0
CG N:HIS240 3.1 29.1 1.0
C N:CYN601 3.1 31.5 1.0
CD2 N:HIS290 3.2 26.9 1.0
CB N:HIS240 3.4 28.4 1.0
CA N:HIS240 3.9 28.3 1.0
ND1 N:HIS291 4.0 28.2 1.0
CG N:HIS291 4.1 31.8 1.0
NE2 N:HIS240 4.2 30.5 1.0
ND1 N:HIS290 4.2 27.3 1.0
CD2 N:HIS240 4.2 25.9 1.0
CG N:HIS290 4.3 29.6 1.0
CG2 N:VAL243 4.6 28.1 1.0
NA N:HEA603 4.7 31.1 1.0
C1A N:HEA603 4.7 29.5 1.0
N N:HIS240 4.8 27.1 1.0
C4A N:HEA603 4.8 27.6 1.0
FE N:HEA603 4.9 30.2 1.0
C2A N:HEA603 5.0 30.7 1.0
C3A N:HEA603 5.0 29.6 1.0
O N:HOH737 5.0 40.1 0.4

Copper binding site 5 out of 6 in 3x2q

Go back to Copper Binding Sites List in 3x2q
Copper binding site 5 out of 6 in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:38.8
occ:1.00
 CU1 O:CUA301 0.0 38.8 1.0
ND1 O:HIS161 2.0 36.0 1.0
SG O:CYS200 2.3 40.5 1.0
SG O:CYS196 2.3 36.2 1.0
SD O:MET207 2.3 42.1 1.0
CU2 O:CUA301 2.6 38.5 1.0
CE1 O:HIS161 2.7 36.9 1.0
CE O:MET207 3.1 37.9 1.0
CG O:HIS161 3.2 34.7 1.0
CB O:CYS200 3.4 36.8 1.0
CB O:CYS196 3.4 39.2 1.0
CG O:MET207 3.5 39.4 1.0
CB O:HIS161 3.7 36.5 1.0
NE2 O:HIS161 3.9 31.0 1.0
O O:GLU198 4.0 35.2 1.0
CD2 O:HIS161 4.2 37.5 1.0
CA O:HIS161 4.3 36.6 1.0
CD1 O:TRP104 4.5 43.0 1.0
ND1 O:HIS204 4.5 37.3 1.0
O O:HIS102 4.7 40.0 1.0
CA O:HIS204 4.7 38.3 1.0
O O:LEU160 4.7 32.4 1.0
CA O:CYS200 4.8 38.7 1.0
CA O:CYS196 4.8 38.7 1.0
CB O:MET207 4.9 40.0 1.0
O O:HIS204 4.9 38.1 1.0

Copper binding site 6 out of 6 in 3x2q

Go back to Copper Binding Sites List in 3x2q
Copper binding site 6 out of 6 in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:38.5
occ:1.00
 CU2 O:CUA301 0.0 38.5 1.0
ND1 O:HIS204 2.0 37.3 1.0
O O:GLU198 2.2 35.2 1.0
SG O:CYS200 2.3 40.5 1.0
SG O:CYS196 2.3 36.2 1.0
CU1 O:CUA301 2.6 38.8 1.0
CE1 O:HIS204 2.9 36.5 1.0
CG O:HIS204 3.1 36.8 1.0
CB O:CYS196 3.3 39.2 1.0
C O:GLU198 3.4 34.0 1.0
CB O:CYS200 3.4 36.8 1.0
CB O:HIS204 3.5 35.9 1.0
CA O:HIS204 3.6 38.3 1.0
N O:CYS200 3.7 38.5 1.0
O O:HIS204 3.9 38.1 1.0
NE2 O:HIS204 4.0 36.6 1.0
N O:GLU198 4.1 33.9 1.0
ND1 O:HIS161 4.1 36.0 1.0
CD2 O:HIS204 4.1 37.3 1.0
C O:ILE199 4.2 37.1 1.0
C O:HIS204 4.2 38.5 1.0
CA O:CYS200 4.2 38.7 1.0
C O:CYS196 4.2 38.5 1.0
O O:CYS196 4.2 37.8 1.0
CA O:ILE199 4.2 36.0 1.0
N O:ILE199 4.2 32.6 1.0
CA O:CYS196 4.4 38.7 1.0
CA O:GLU198 4.4 34.2 1.0
SD O:MET207 4.4 42.1 1.0
N O:SER197 4.6 36.1 1.0
CG O:MET207 4.7 39.4 1.0
N O:HIS204 4.8 39.0 1.0
CE1 O:HIS161 4.9 36.9 1.0
O O:ILE199 4.9 33.5 1.0
CA O:HIS161 5.0 36.6 1.0

Reference:

N.Yano, K.Muramoto, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara. X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution. Acta Crystallogr F Struct V. 71 726 2015BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 26057802
DOI: 10.1107/S2053230X15007025
Page generated: Wed Jul 31 02:29:48 2024

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