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Copper in PDB 7thu: Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays

Enzymatic activity of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays

All present enzymatic activity of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays:
1.9.3.1;

Protein crystallography data

The structure of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays, PDB code: 7thu was solved by I.Ishigami, D.L.Rousseau, S.-R.Yeh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.182, 182.282, 208.683, 90, 90, 90
R / Rfree (%) 18.4 / 21.3

Other elements in 7thu:

The structure of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms
Magnesium (Mg) 2 atoms
Sodium (Na) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays (pdb code 7thu). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays, PDB code: 7thu:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7thu

Go back to Copper Binding Sites List in 7thu
Copper binding site 1 out of 6 in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:29.9
occ:1.00
 NE2 A:HIS291 2.0 31.4 1.0
NE2 A:HIS290 2.0 31.6 1.0
ND1 A:HIS240 2.0 30.4 1.0
CD2 A:HIS291 2.9 28.1 1.0
CE1 A:HIS290 3.0 31.4 1.0
CG A:HIS240 3.0 28.5 1.0
CE1 A:HIS240 3.0 28.0 1.0
CD2 A:HIS290 3.0 28.6 1.0
CE1 A:HIS291 3.1 27.8 1.0
CB A:HIS240 3.3 23.5 1.0
CA A:HIS240 3.9 26.4 1.0
CG A:HIS291 4.0 31.3 1.0
ND1 A:HIS291 4.1 28.0 1.0
ND1 A:HIS290 4.1 26.9 1.0
CD2 A:HIS240 4.1 30.6 1.0
CG A:HIS290 4.1 31.1 1.0
NE2 A:HIS240 4.2 33.7 1.0
C1A A:HEA606 4.6 26.7 1.0
NA A:HEA606 4.6 31.0 1.0
N A:HIS240 4.7 26.1 1.0
C4A A:HEA606 4.8 27.1 1.0
CG2 A:VAL243 4.8 28.2 1.0
C2A A:HEA606 4.9 29.1 1.0
CHA A:HEA606 4.9 25.0 1.0
C3A A:HEA606 5.0 29.6 1.0

Copper binding site 2 out of 6 in 7thu

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Copper binding site 2 out of 6 in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:30.2
occ:1.00
 CU1 B:CUA301 0.0 30.2 1.0
ND1 B:HIS161 2.1 29.8 1.0
SG B:CYS196 2.3 29.0 1.0
SG B:CYS200 2.3 30.1 1.0
SD B:MET207 2.4 31.2 1.0
CU2 B:CUA301 2.5 30.4 1.0
CE1 B:HIS161 2.9 28.1 1.0
CE B:MET207 3.1 28.0 1.0
CG B:HIS161 3.2 27.6 1.0
CB B:CYS200 3.2 32.0 1.0
CB B:CYS196 3.4 30.2 1.0
CG B:MET207 3.5 32.6 1.0
CB B:HIS161 3.7 31.7 1.0
O B:GLU198 4.1 30.6 1.0
NE2 B:HIS161 4.1 27.6 1.0
CA B:HIS161 4.2 29.1 1.0
CD2 B:HIS161 4.2 28.9 1.0
ND1 B:HIS204 4.5 31.2 1.0
CD1 B:TRP104 4.6 30.6 1.0
O B:HIS102 4.7 29.8 1.0
CA B:CYS200 4.7 33.0 1.0
O B:LEU160 4.7 29.7 1.0
CA B:HIS204 4.8 30.7 1.0
CA B:CYS196 4.8 30.6 1.0
CB B:MET207 4.9 31.7 1.0
O B:HIS204 5.0 30.7 1.0

Copper binding site 3 out of 6 in 7thu

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Copper binding site 3 out of 6 in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:30.4
occ:1.00
 CU2 B:CUA301 0.0 30.4 1.0
ND1 B:HIS204 2.0 31.2 1.0
SG B:CYS200 2.2 30.1 1.0
SG B:CYS196 2.3 29.0 1.0
O B:GLU198 2.5 30.6 1.0
CU1 B:CUA301 2.5 30.2 1.0
CE1 B:HIS204 2.9 29.4 1.0
CG B:HIS204 3.1 29.1 1.0
CB B:CYS196 3.3 30.2 1.0
CB B:CYS200 3.3 32.0 1.0
CB B:HIS204 3.5 29.9 1.0
CA B:HIS204 3.5 30.7 1.0
C B:GLU198 3.6 31.1 1.0
N B:CYS200 3.7 30.8 1.0
O B:HIS204 3.8 30.7 1.0
NE2 B:HIS204 4.1 27.8 1.0
CD2 B:HIS204 4.1 30.5 1.0
CA B:CYS200 4.1 33.0 1.0
C B:HIS204 4.2 27.0 1.0
N B:GLU198 4.2 29.8 1.0
ND1 B:HIS161 4.2 29.8 1.0
C B:ILE199 4.2 32.3 1.0
CA B:ILE199 4.2 30.7 1.0
C B:CYS196 4.2 30.6 1.0
O B:CYS196 4.3 26.1 1.0
N B:ILE199 4.3 32.0 1.0
CA B:CYS196 4.3 30.6 1.0
SD B:MET207 4.4 31.2 1.0
CA B:GLU198 4.5 29.9 1.0
N B:SER197 4.6 29.8 1.0
CG B:MET207 4.7 32.6 1.0
N B:HIS204 4.8 31.2 1.0
CA B:HIS161 4.9 29.1 1.0

Copper binding site 4 out of 6 in 7thu

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Copper binding site 4 out of 6 in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu601

b:35.5
occ:1.00
 ND1 N:HIS240 2.0 34.5 1.0
NE2 N:HIS291 2.0 34.0 1.0
NE2 N:HIS290 2.0 29.4 1.0
CD2 N:HIS291 2.9 35.5 1.0
CE1 N:HIS290 2.9 31.8 1.0
CG N:HIS240 2.9 38.3 1.0
CE1 N:HIS240 3.0 35.5 1.0
CE1 N:HIS291 3.0 33.9 1.0
CD2 N:HIS290 3.1 29.7 1.0
CB N:HIS240 3.3 32.7 1.0
CA N:HIS240 3.9 33.3 1.0
CG N:HIS291 4.0 33.7 1.0
ND1 N:HIS291 4.0 34.1 1.0
ND1 N:HIS290 4.1 30.2 1.0
CD2 N:HIS240 4.1 35.4 1.0
NE2 N:HIS240 4.1 36.2 1.0
CG N:HIS290 4.2 29.7 1.0
NA N:HEA606 4.5 34.9 1.0
C1A N:HEA606 4.6 33.6 1.0
N N:HIS240 4.7 33.7 1.0
C4A N:HEA606 4.8 33.8 1.0
CG2 N:VAL243 4.8 39.8 1.0
C2A N:HEA606 4.9 36.1 1.0
CHA N:HEA606 5.0 30.8 1.0

Copper binding site 5 out of 6 in 7thu

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Copper binding site 5 out of 6 in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays 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 2.1 41.8 1.0
SG O:CYS200 2.3 36.3 1.0
SG O:CYS196 2.3 38.7 1.0
SD O:MET207 2.4 39.5 1.0
CU2 O:CUA301 2.5 37.0 1.0
CE1 O:HIS161 2.9 41.4 1.0
CG O:HIS161 3.2 37.4 1.0
CE O:MET207 3.2 41.4 1.0
CB O:CYS200 3.2 40.0 1.0
CB O:CYS196 3.4 41.8 1.0
CG O:MET207 3.5 45.6 1.0
CB O:HIS161 3.6 37.1 1.0
O O:GLU198 4.1 38.7 1.0
CA O:HIS161 4.1 38.7 1.0
NE2 O:HIS161 4.2 40.0 1.0
CD2 O:HIS161 4.3 36.9 1.0
ND1 O:HIS204 4.4 38.5 1.0
CD1 O:TRP104 4.6 38.9 1.0
O O:HIS102 4.6 37.7 1.0
CA O:CYS200 4.6 36.5 1.0
CA O:HIS204 4.8 39.4 1.0
CA O:CYS196 4.8 38.8 1.0
O O:LEU160 4.8 35.0 1.0
N O:CYS200 4.9 42.6 1.0
CB O:MET207 4.9 42.5 1.0

Copper binding site 6 out of 6 in 7thu

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Copper binding site 6 out of 6 in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:37.0
occ:1.00
 CU2 O:CUA301 0.0 37.0 1.0
ND1 O:HIS204 2.0 38.5 1.0
SG O:CYS196 2.2 38.7 1.0
SG O:CYS200 2.2 36.3 1.0
O O:GLU198 2.4 38.7 1.0
CU1 O:CUA301 2.5 38.8 1.0
CE1 O:HIS204 2.8 38.3 1.0
CG O:HIS204 3.1 40.6 1.0
CB O:CYS196 3.2 41.8 1.0
CB O:CYS200 3.4 40.0 1.0
C O:GLU198 3.5 33.4 1.0
CA O:HIS204 3.6 39.4 1.0
CB O:HIS204 3.6 40.8 1.0
N O:CYS200 3.6 42.6 1.0
O O:HIS204 3.9 40.9 1.0
NE2 O:HIS204 4.0 37.1 1.0
CD2 O:HIS204 4.1 39.7 1.0
CA O:CYS200 4.2 36.5 1.0
N O:GLU198 4.2 36.6 1.0
C O:HIS204 4.2 36.8 1.0
ND1 O:HIS161 4.2 41.8 1.0
CA O:ILE199 4.2 37.6 1.0
C O:CYS196 4.2 36.4 1.0
C O:ILE199 4.3 40.2 1.0
N O:ILE199 4.3 35.2 1.0
O O:CYS196 4.3 35.2 1.0
CA O:CYS196 4.3 38.8 1.0
SD O:MET207 4.4 39.5 1.0
CA O:GLU198 4.5 36.7 1.0
N O:SER197 4.6 35.8 1.0
CG O:MET207 4.7 45.6 1.0
N O:HIS204 4.8 44.8 1.0
CA O:HIS161 4.8 38.7 1.0

Reference:

I.Ishigami, S.Russi, A.Cohen, S.R.Yeh, D.L.Rousseau. Temperature-Dependent Structural Transition Following X-Ray-Induced Metal Center Reduction in Oxidized Cytochrome C Oxidase. J.Biol.Chem. V. 298 01799 2022.
ISSN: ESSN 1083-351X
PubMed: 35257742
DOI: 10.1016/J.JBC.2022.101799
Page generated: Wed Jul 31 09:16:16 2024

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