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Copper in PDB 7tih: Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure

Enzymatic activity of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure

All present enzymatic activity of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure:
1.9.3.1;

Protein crystallography data

The structure of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure, PDB code: 7tih was solved by I.Ishigami, D.L.Rousseau, S.-R.Yeh, S.Russi, A.Cohen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.34 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.037, 182.696, 205.854, 90, 90, 90
R / Rfree (%) 19.3 / 23.5

Other elements in 7tih:

The structure of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure also contains other interesting chemical elements:

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

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure (pdb code 7tih). 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 Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure, PDB code: 7tih:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7tih

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Copper binding site 1 out of 6 in the Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:31.7
occ:1.00
 NE2 A:HIS291 2.0 32.1 1.0
NE2 A:HIS290 2.0 30.9 1.0
ND1 A:HIS240 2.0 32.7 1.0
O A:HOH701 2.3 17.4 0.8
CE1 A:HIS291 2.9 32.0 1.0
CE1 A:HIS290 3.0 29.4 1.0
CD2 A:HIS291 3.0 31.4 1.0
CG A:HIS240 3.0 29.2 1.0
CE1 A:HIS240 3.0 32.1 1.0
CD2 A:HIS290 3.1 31.0 1.0
O A:OH618 3.2 21.5 0.9
CB A:HIS240 3.2 28.3 1.0
CA A:HIS240 3.8 28.1 1.0
ND1 A:HIS291 4.0 31.3 1.0
CG A:HIS291 4.0 32.1 1.0
ND1 A:HIS290 4.1 26.5 1.0
CD2 A:HIS240 4.1 30.3 1.0
NE2 A:HIS240 4.2 33.8 1.0
CG A:HIS290 4.2 29.8 1.0
NA A:HEA606 4.5 28.0 1.0
C1A A:HEA606 4.6 26.3 1.0
CG2 A:VAL243 4.7 29.0 1.0
N A:HIS240 4.7 27.2 1.0
C4A A:HEA606 4.7 28.2 1.0
FE A:HEA606 4.8 29.3 1.0
CHA A:HEA606 4.9 26.5 1.0
C A:HIS240 4.9 30.0 1.0
C2A A:HEA606 5.0 28.2 1.0

Copper binding site 2 out of 6 in 7tih

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Copper binding site 2 out of 6 in the Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:30.8
occ:1.00
 CU1 B:CUA301 0.0 30.8 1.0
ND1 B:HIS161 2.0 29.4 1.0
SG B:CYS196 2.2 27.3 1.0
SG B:CYS200 2.3 27.1 1.0
SD B:MET207 2.4 31.9 1.0
CU2 B:CUA301 2.6 31.7 1.0
CE1 B:HIS161 2.9 27.7 1.0
CG B:HIS161 3.1 27.1 1.0
CE B:MET207 3.2 30.8 1.0
CB B:CYS200 3.2 30.1 1.0
CB B:CYS196 3.4 29.8 1.0
CB B:HIS161 3.5 27.7 1.0
CG B:MET207 3.6 30.9 1.0
O B:GLU198 4.0 32.9 1.0
CA B:HIS161 4.1 26.6 1.0
NE2 B:HIS161 4.1 25.6 1.0
CD2 B:HIS161 4.2 26.9 1.0
ND1 B:HIS204 4.5 32.3 1.0
CA B:CYS200 4.6 30.7 1.0
O B:HIS102 4.6 29.1 1.0
O B:LEU160 4.7 29.8 1.0
CA B:HIS204 4.7 31.0 1.0
CA B:CYS196 4.7 30.1 1.0
CD1 B:TRP104 4.7 30.6 1.0
O B:HIS204 4.8 28.9 1.0
N B:CYS200 4.9 29.7 1.0
CB B:MET207 5.0 28.8 1.0

Copper binding site 3 out of 6 in 7tih

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Copper binding site 3 out of 6 in the Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:31.7
occ:1.00
 CU2 B:CUA301 0.0 31.7 1.0
ND1 B:HIS204 2.0 32.3 1.0
SG B:CYS200 2.3 27.1 1.0
O B:GLU198 2.3 32.9 1.0
SG B:CYS196 2.3 27.3 1.0
CU1 B:CUA301 2.6 30.8 1.0
CE1 B:HIS204 2.9 32.5 1.0
CG B:HIS204 3.0 31.2 1.0
CB B:CYS196 3.2 29.8 1.0
CB B:HIS204 3.4 31.2 1.0
C B:GLU198 3.4 30.6 1.0
CB B:CYS200 3.5 30.1 1.0
CA B:HIS204 3.5 31.0 1.0
O B:HIS204 3.6 28.9 1.0
N B:CYS200 3.7 29.7 1.0
O B:CYS196 3.9 32.2 1.0
C B:HIS204 4.0 30.4 1.0
NE2 B:HIS204 4.1 36.0 1.0
CD2 B:HIS204 4.1 33.8 1.0
C B:CYS196 4.1 32.8 1.0
N B:GLU198 4.1 31.0 1.0
C B:ILE199 4.1 29.9 1.0
N B:ILE199 4.2 29.1 1.0
CA B:CYS200 4.2 30.7 1.0
CA B:ILE199 4.2 31.7 1.0
ND1 B:HIS161 4.3 29.4 1.0
CA B:CYS196 4.3 30.1 1.0
SD B:MET207 4.3 31.9 1.0
CA B:GLU198 4.4 30.1 1.0
N B:SER197 4.8 33.0 1.0
CG B:MET207 4.8 30.9 1.0
N B:HIS204 4.9 32.9 1.0
CA B:HIS161 4.9 26.6 1.0
O B:ILE199 5.0 31.9 1.0

Copper binding site 4 out of 6 in 7tih

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Copper binding site 4 out of 6 in the Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu601

b:33.7
occ:1.00
 NE2 N:HIS290 2.0 29.8 1.0
NE2 N:HIS291 2.0 36.0 1.0
ND1 N:HIS240 2.0 35.6 1.0
O N:HOH701 2.4 23.2 0.8
CE1 N:HIS290 2.9 30.6 1.0
CE1 N:HIS291 2.9 37.0 1.0
CD2 N:HIS291 3.0 33.9 1.0
CG N:HIS240 3.0 31.9 1.0
CD2 N:HIS290 3.0 30.9 1.0
CE1 N:HIS240 3.0 36.3 1.0
O N:OH618 3.1 18.6 0.9
CB N:HIS240 3.2 32.0 1.0
CA N:HIS240 3.9 31.7 1.0
ND1 N:HIS291 4.0 35.0 1.0
ND1 N:HIS290 4.0 31.0 1.0
CG N:HIS291 4.1 32.8 1.0
CD2 N:HIS240 4.1 33.7 1.0
CG N:HIS290 4.1 31.0 1.0
NE2 N:HIS240 4.2 38.6 1.0
NA N:HEA605 4.4 30.8 1.0
C1A N:HEA605 4.5 30.1 1.0
C4A N:HEA605 4.6 33.6 1.0
N N:HIS240 4.7 28.8 1.0
CG2 N:VAL243 4.8 35.0 1.0
FE N:HEA605 4.8 30.7 1.0
CHA N:HEA605 4.8 31.9 1.0
C2A N:HEA605 4.9 32.1 1.0
C3A N:HEA605 4.9 33.0 1.0
ND N:HEA605 5.0 30.9 1.0

Copper binding site 5 out of 6 in 7tih

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Copper binding site 5 out of 6 in the Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:35.9
occ:1.00
 CU1 O:CUA301 0.0 35.9 1.0
ND1 O:HIS161 2.0 35.5 1.0
SG O:CYS196 2.3 33.3 1.0
SG O:CYS200 2.3 33.4 1.0
SD O:MET207 2.4 38.4 1.0
CU2 O:CUA301 2.6 37.3 1.0
CE1 O:HIS161 2.9 36.6 1.0
CE O:MET207 3.0 36.3 1.0
CG O:HIS161 3.1 33.6 1.0
CB O:CYS200 3.3 36.3 1.0
CB O:CYS196 3.4 37.2 1.0
CB O:HIS161 3.5 34.7 1.0
CG O:MET207 3.6 39.3 1.0
O O:GLU198 4.1 42.6 1.0
NE2 O:HIS161 4.1 34.7 1.0
CA O:HIS161 4.2 31.7 1.0
CD2 O:HIS161 4.2 36.1 1.0
ND1 O:HIS204 4.6 38.6 1.0
CD1 O:TRP104 4.6 32.6 1.0
CA O:CYS200 4.6 36.5 1.0
O O:HIS102 4.7 32.9 1.0
O O:LEU160 4.7 35.2 1.0
CA O:HIS204 4.8 34.5 1.0
CA O:CYS196 4.8 35.6 1.0
CB O:MET207 4.9 39.2 1.0
N O:CYS200 4.9 37.4 1.0
O O:HIS204 5.0 30.7 1.0
CZ2 O:TRP106 5.0 37.4 1.0

Copper binding site 6 out of 6 in 7tih

Go back to Copper Binding Sites List in 7tih
Copper binding site 6 out of 6 in the Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:37.3
occ:1.00
 CU2 O:CUA301 0.0 37.3 1.0
ND1 O:HIS204 2.0 38.6 1.0
SG O:CYS196 2.2 33.3 1.0
SG O:CYS200 2.3 33.4 1.0
O O:GLU198 2.3 42.6 1.0
CU1 O:CUA301 2.6 35.9 1.0
CE1 O:HIS204 3.0 37.6 1.0
CG O:HIS204 3.0 36.1 1.0
CB O:CYS196 3.3 37.2 1.0
CB O:HIS204 3.4 36.6 1.0
CB O:CYS200 3.4 36.3 1.0
C O:GLU198 3.4 32.0 1.0
CA O:HIS204 3.6 34.5 1.0
N O:CYS200 3.6 37.4 1.0
O O:HIS204 3.8 30.7 1.0
O O:CYS196 3.9 37.3 1.0
N O:GLU198 4.0 32.6 1.0
NE2 O:HIS204 4.1 38.3 1.0
C O:CYS196 4.1 36.8 1.0
CD2 O:HIS204 4.1 37.4 1.0
C O:HIS204 4.1 35.0 1.0
CA O:CYS200 4.2 36.5 1.0
C O:ILE199 4.2 36.5 1.0
ND1 O:HIS161 4.2 35.5 1.0
N O:ILE199 4.2 31.1 1.0
CA O:ILE199 4.3 35.1 1.0
SD O:MET207 4.3 38.4 1.0
CA O:CYS196 4.4 35.6 1.0
CA O:GLU198 4.4 32.9 1.0
N O:SER197 4.6 37.1 1.0
CG O:MET207 4.7 39.3 1.0
N O:HIS204 4.9 36.2 1.0
CA O:HIS161 5.0 31.7 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: Mon Jul 14 08:35:50 2025

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