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

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

All present enzymatic activity of Annealed 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 Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure, PDB code: 7tii 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) 39.30 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.037, 182.633, 205.453, 90, 90, 90
R / Rfree (%) 20.6 / 25.3

Other elements in 7tii:

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

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

Copper Binding Sites:

The binding sites of Copper atom in the Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure (pdb code 7tii). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure, PDB code: 7tii:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7tii

Go back to Copper Binding Sites List in 7tii
Copper binding site 1 out of 6 in the Annealed 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 Annealed 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:Cu603

b:32.3
occ:1.00
 NE2 A:HIS290 2.0 29.9 1.0
NE2 A:HIS291 2.0 35.7 1.0
ND1 A:HIS240 2.0 34.0 1.0
O A:HOH701 2.4 8.1 0.3
O A:OH610 2.9 27.0 0.6
CE1 A:HIS291 2.9 37.4 1.0
CE1 A:HIS240 3.0 35.3 1.0
CE1 A:HIS290 3.0 28.9 1.0
CD2 A:HIS291 3.0 35.4 1.0
CD2 A:HIS290 3.0 29.1 1.0
CG A:HIS240 3.1 28.9 1.0
CB A:HIS240 3.4 28.7 1.0
ND1 A:HIS291 4.0 34.6 1.0
CA A:HIS240 4.0 27.7 1.0
CG A:HIS291 4.0 33.8 1.0
ND1 A:HIS290 4.1 26.1 1.0
CG A:HIS290 4.1 28.3 1.0
NE2 A:HIS240 4.2 34.4 1.0
CD2 A:HIS240 4.2 31.9 1.0
NA A:HEA602 4.5 29.8 1.0
C1A A:HEA602 4.5 27.4 1.0
CG2 A:VAL243 4.7 29.3 1.0
CHA A:HEA602 4.8 27.8 1.0
C4A A:HEA602 4.8 30.0 1.0
N A:HIS240 4.8 25.3 1.0
FE A:HEA602 4.9 32.0 1.0
ND A:HEA602 5.0 29.8 1.0
C4D A:HEA602 5.0 30.6 1.0
C2A A:HEA602 5.0 29.3 1.0

Copper binding site 2 out of 6 in 7tii

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Copper binding site 2 out of 6 in the Annealed 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 Annealed 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:Cu302

b:29.5
occ:1.00
 CU1 B:CUA302 0.0 29.5 1.0
ND1 B:HIS161 2.0 29.1 1.0
SG B:CYS196 2.3 26.5 1.0
SG B:CYS200 2.3 23.9 1.0
SD B:MET207 2.4 33.4 1.0
CU2 B:CUA302 2.6 31.1 1.0
CE1 B:HIS161 3.0 28.1 1.0
CG B:HIS161 3.0 27.1 1.0
CE B:MET207 3.1 30.9 1.0
CB B:CYS200 3.3 25.5 1.0
CB B:CYS196 3.4 26.7 1.0
CB B:HIS161 3.4 27.6 1.0
CG B:MET207 3.6 31.9 1.0
O B:GLU198 4.0 33.5 1.0
CA B:HIS161 4.1 26.9 1.0
NE2 B:HIS161 4.2 28.3 1.0
CD2 B:HIS161 4.2 26.9 1.0
O B:HIS102 4.5 28.3 1.0
ND1 B:HIS204 4.6 32.9 1.0
CA B:CYS200 4.7 27.6 1.0
CA B:CYS196 4.7 26.8 1.0
CD1 B:TRP104 4.7 31.6 1.0
CA B:HIS204 4.9 34.3 1.0
O B:LEU160 4.9 35.9 1.0
CB B:MET207 4.9 30.4 1.0
N B:CYS200 4.9 27.1 1.0

Copper binding site 3 out of 6 in 7tii

Go back to Copper Binding Sites List in 7tii
Copper binding site 3 out of 6 in the Annealed 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 Annealed 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:Cu302

b:31.1
occ:1.00
 CU2 B:CUA302 0.0 31.1 1.0
ND1 B:HIS204 2.0 32.9 1.0
SG B:CYS196 2.3 26.5 1.0
SG B:CYS200 2.3 23.9 1.0
O B:GLU198 2.3 33.5 1.0
CU1 B:CUA302 2.6 29.5 1.0
CE1 B:HIS204 3.0 32.2 1.0
CG B:HIS204 3.0 33.1 1.0
CB B:CYS196 3.2 26.7 1.0
CB B:HIS204 3.4 32.6 1.0
C B:GLU198 3.5 29.6 1.0
CB B:CYS200 3.5 25.5 1.0
CA B:HIS204 3.6 34.3 1.0
N B:CYS200 3.7 27.1 1.0
O B:HIS204 3.7 27.1 1.0
O B:CYS196 3.8 27.9 1.0
C B:CYS196 4.1 29.2 1.0
NE2 B:HIS204 4.1 35.7 1.0
C B:HIS204 4.1 33.5 1.0
C B:ILE199 4.1 26.9 1.0
CA B:ILE199 4.1 29.5 1.0
CD2 B:HIS204 4.1 33.8 1.0
N B:ILE199 4.2 28.9 1.0
N B:GLU198 4.2 29.2 1.0
CA B:CYS200 4.2 27.6 1.0
CA B:CYS196 4.3 26.8 1.0
ND1 B:HIS161 4.3 29.1 1.0
SD B:MET207 4.3 33.4 1.0
CA B:GLU198 4.5 28.8 1.0
CG B:MET207 4.7 31.9 1.0
N B:SER197 4.7 30.2 1.0
CA B:HIS161 4.9 26.9 1.0
N B:HIS204 4.9 38.5 1.0
CB B:HIS161 4.9 27.6 1.0

Copper binding site 4 out of 6 in 7tii

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Copper binding site 4 out of 6 in the Annealed 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 Annealed 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:Cu603

b:36.8
occ:1.00
 NE2 N:HIS291 2.0 39.1 1.0
NE2 N:HIS290 2.0 35.8 1.0
ND1 N:HIS240 2.0 36.2 1.0
O N:HOH701 2.5 17.6 0.3
O N:OH608 2.8 27.4 0.6
CE1 N:HIS290 2.9 35.3 1.0
CE1 N:HIS291 3.0 40.4 1.0
CD2 N:HIS291 3.0 36.8 1.0
CE1 N:HIS240 3.0 36.8 1.0
CG N:HIS240 3.0 34.1 1.0
CD2 N:HIS290 3.1 35.8 1.0
CB N:HIS240 3.3 32.6 1.0
CA N:HIS240 4.0 32.4 1.0
ND1 N:HIS290 4.0 33.0 1.0
ND1 N:HIS291 4.0 38.3 1.0
CG N:HIS291 4.1 35.3 1.0
CD2 N:HIS240 4.2 34.2 1.0
CG N:HIS290 4.2 35.0 1.0
NE2 N:HIS240 4.2 36.2 1.0
NA N:HEA602 4.4 33.7 1.0
C1A N:HEA602 4.5 33.4 1.0
C4A N:HEA602 4.7 36.6 1.0
CG2 N:VAL243 4.8 29.1 1.0
CHA N:HEA602 4.8 33.0 1.0
FE N:HEA602 4.8 33.9 1.0
N N:HIS240 4.9 30.3 1.0
C2A N:HEA602 4.9 34.2 1.0
ND N:HEA602 5.0 31.2 1.0
O N:HOH734 5.0 64.2 1.0

Copper binding site 5 out of 6 in 7tii

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Copper binding site 5 out of 6 in the Annealed 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 Annealed 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:36.2
occ:1.00
 CU1 O:CUA301 0.0 36.2 1.0
ND1 O:HIS161 2.0 35.1 1.0
SG O:CYS200 2.3 30.1 1.0
SG O:CYS196 2.3 32.6 1.0
SD O:MET207 2.4 37.9 1.0
CU2 O:CUA301 2.6 39.0 1.0
CE1 O:HIS161 3.0 33.9 1.0
CE O:MET207 3.0 35.9 1.0
CG O:HIS161 3.1 30.6 1.0
CB O:CYS200 3.3 33.7 1.0
CB O:CYS196 3.4 35.6 1.0
CB O:HIS161 3.5 30.8 1.0
CG O:MET207 3.6 38.6 1.0
NE2 O:HIS161 4.1 32.3 1.0
O O:GLU198 4.1 46.2 1.0
CD2 O:HIS161 4.2 32.4 1.0
CA O:HIS161 4.2 29.8 1.0
O O:HIS102 4.5 31.9 1.0
CD1 O:TRP104 4.5 35.8 1.0
ND1 O:HIS204 4.6 37.2 1.0
CA O:CYS200 4.7 36.5 1.0
CA O:CYS196 4.7 36.9 1.0
CA O:HIS204 4.8 36.8 1.0
O O:LEU160 4.8 38.5 1.0
CB O:MET207 4.9 39.0 1.0
O O:HIS204 5.0 32.9 1.0
N O:CYS200 5.0 38.8 1.0

Copper binding site 6 out of 6 in 7tii

Go back to Copper Binding Sites List in 7tii
Copper binding site 6 out of 6 in the Annealed 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 Annealed 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:39.0
occ:1.00
 CU2 O:CUA301 0.0 39.0 1.0
ND1 O:HIS204 2.0 37.2 1.0
SG O:CYS196 2.3 32.6 1.0
SG O:CYS200 2.3 30.1 1.0
O O:GLU198 2.3 46.2 1.0
CU1 O:CUA301 2.6 36.2 1.0
CE1 O:HIS204 2.9 34.0 1.0
CG O:HIS204 3.0 37.6 1.0
CB O:CYS196 3.1 35.6 1.0
CB O:HIS204 3.4 38.7 1.0
C O:GLU198 3.5 35.2 1.0
CB O:CYS200 3.6 33.7 1.0
CA O:HIS204 3.6 36.8 1.0
O O:HIS204 3.7 32.9 1.0
N O:CYS200 3.8 38.8 1.0
O O:CYS196 3.9 40.0 1.0
NE2 O:HIS204 4.0 37.2 1.0
C O:CYS196 4.0 37.7 1.0
CD2 O:HIS204 4.0 38.4 1.0
N O:GLU198 4.0 34.0 1.0
C O:HIS204 4.1 36.4 1.0
CA O:CYS196 4.2 36.9 1.0
ND1 O:HIS161 4.3 35.1 1.0
CA O:ILE199 4.3 38.1 1.0
N O:ILE199 4.3 34.2 1.0
CA O:CYS200 4.3 36.5 1.0
C O:ILE199 4.3 40.9 1.0
CA O:GLU198 4.4 35.9 1.0
SD O:MET207 4.4 37.9 1.0
N O:SER197 4.6 39.0 1.0
CG O:MET207 4.8 38.6 1.0
N O:HIS204 5.0 38.2 1.0
CA O:HIS161 5.0 29.8 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 09:17:10 2024

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