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Copper in PDB 8gcq: Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution

Enzymatic activity of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution

All present enzymatic activity of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution, PDB code: 8gcq was solved by I.Ishigami, S.-R.Yeh, D.L.Rousseau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.00 / 2.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.6, 189.5, 211.1, 90, 90, 90
R / Rfree (%) 23.2 / 26.6

Other elements in 8gcq:

The structure of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution 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 Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution (pdb code 8gcq). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution, PDB code: 8gcq:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 8gcq

Go back to Copper Binding Sites List in 8gcq
Copper binding site 1 out of 6 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:12.0
occ:1.00
 NE2 A:HIS291 1.8 12.7 1.0
ND1 A:HIS240 2.1 12.8 1.0
O A:HOH728 2.1 9.2 1.0
NE2 A:HIS290 2.2 10.7 1.0
CE1 A:HIS291 2.7 13.8 1.0
CE1 A:HIS240 2.9 13.6 1.0
CD2 A:HIS291 2.9 12.7 1.0
CE1 A:HIS290 3.1 10.3 1.0
O A:OH607 3.1 9.2 1.0
CD2 A:HIS290 3.2 10.8 1.0
CG A:HIS240 3.2 12.1 1.0
CB A:HIS240 3.7 11.2 1.0
ND1 A:HIS291 3.9 13.4 1.0
CG A:HIS291 4.0 13.9 1.0
CA A:HIS240 4.0 10.4 1.0
NE2 A:HIS240 4.1 13.9 1.0
ND1 A:HIS290 4.2 10.9 1.0
CD2 A:HIS240 4.3 13.1 1.0
CG A:HIS290 4.3 11.6 1.0
NA A:HEA605 4.3 10.9 1.0
C1A A:HEA605 4.4 10.0 1.0
C4A A:HEA605 4.6 10.8 1.0
CHA A:HEA605 4.7 11.1 1.0
FE A:HEA605 4.7 10.9 1.0
N A:HIS240 4.8 9.7 1.0
C4D A:HEA605 4.8 11.2 1.0
ND A:HEA605 4.8 11.2 1.0
C2A A:HEA605 4.8 9.2 1.0
C3A A:HEA605 5.0 9.8 1.0

Copper binding site 2 out of 6 in 8gcq

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Copper binding site 2 out of 6 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:20.0
occ:1.00
 CU1 B:CUA301 0.0 20.0 1.0
ND1 B:HIS161 2.0 14.2 1.0
SG B:CYS200 2.3 13.2 1.0
SG B:CYS196 2.3 18.0 1.0
SD B:MET207 2.3 11.4 1.0
CE1 B:HIS161 2.5 12.6 1.0
CU2 B:CUA301 2.6 19.0 1.0
CB B:CYS200 3.0 12.5 1.0
CG B:HIS161 3.1 13.6 1.0
CE B:MET207 3.2 10.8 1.0
CB B:CYS196 3.6 17.4 1.0
CG B:MET207 3.6 10.5 1.0
NE2 B:HIS161 3.7 12.4 1.0
CB B:HIS161 3.8 14.4 1.0
O B:GLU198 4.0 13.8 1.0
CD2 B:HIS161 4.0 13.4 1.0
CA B:HIS161 4.3 13.6 1.0
CA B:CYS200 4.5 11.4 1.0
ND1 B:HIS204 4.5 12.4 1.0
O B:LEU160 4.5 13.7 1.0
CD1 B:TRP104 4.6 8.6 1.0
O B:HOH439 4.6 15.8 1.0
O B:HIS102 4.6 7.0 1.0
CA B:HIS204 4.7 11.9 1.0
N B:CYS200 4.8 11.8 1.0
CA B:CYS196 5.0 16.6 1.0
O B:HIS204 5.0 10.1 1.0
CB B:MET207 5.0 10.6 1.0

Copper binding site 3 out of 6 in 8gcq

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Copper binding site 3 out of 6 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:19.0
occ:1.00
 CU2 B:CUA301 0.0 19.0 1.0
O B:GLU198 2.0 13.8 1.0
ND1 B:HIS204 2.0 12.4 1.0
SG B:CYS196 2.2 18.0 1.0
SG B:CYS200 2.3 13.2 1.0
CU1 B:CUA301 2.6 20.0 1.0
CE1 B:HIS204 2.9 11.5 1.0
CG B:HIS204 3.0 11.5 1.0
CB B:CYS196 3.0 17.4 1.0
C B:GLU198 3.2 13.1 1.0
CB B:CYS200 3.3 12.5 1.0
CB B:HIS204 3.4 12.1 1.0
CA B:HIS204 3.6 11.9 1.0
N B:CYS200 3.6 11.8 1.0
O B:HIS204 4.0 10.1 1.0
N B:ILE199 4.0 11.5 1.0
NE2 B:HIS204 4.1 11.0 1.0
CA B:CYS200 4.1 11.4 1.0
CD2 B:HIS204 4.1 10.9 1.0
CA B:ILE199 4.1 10.2 1.0
C B:ILE199 4.2 10.9 1.0
N B:GLU198 4.2 15.4 1.0
C B:HIS204 4.2 11.0 1.0
CA B:CYS196 4.3 16.6 1.0
SD B:MET207 4.3 11.4 1.0
CA B:GLU198 4.3 14.4 1.0
ND1 B:HIS161 4.3 14.2 1.0
C B:CYS196 4.4 17.9 1.0
O B:CYS196 4.6 15.9 1.0
CG B:MET207 4.7 10.5 1.0
N B:HIS204 4.8 13.3 1.0
O B:LEU160 4.9 13.7 1.0
N B:SER197 4.9 19.9 1.0
CE1 B:HIS161 5.0 12.6 1.0

Copper binding site 4 out of 6 in 8gcq

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Copper binding site 4 out of 6 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu601

b:29.6
occ:1.00
 O N:HOH707 1.7 23.0 1.0
NE2 N:HIS291 2.1 30.5 1.0
ND1 N:HIS240 2.2 28.4 1.0
NE2 N:HIS290 2.3 25.1 1.0
O N:OH608 2.7 14.0 1.0
CE1 N:HIS291 3.0 29.9 1.0
CE1 N:HIS240 3.1 28.9 1.0
CE1 N:HIS290 3.1 25.6 1.0
CD2 N:HIS291 3.1 34.1 1.0
CG N:HIS240 3.2 26.8 1.0
CD2 N:HIS290 3.3 25.9 1.0
CB N:HIS240 3.5 25.5 1.0
CA N:HIS240 4.0 26.1 1.0
ND1 N:HIS291 4.1 30.5 1.0
NE2 N:HIS240 4.2 26.6 1.0
CG N:HIS291 4.2 31.2 1.0
CD2 N:HIS240 4.2 25.8 1.0
NA N:HEA606 4.2 18.4 1.0
ND1 N:HIS290 4.3 27.0 1.0
C1A N:HEA606 4.4 20.4 1.0
CG N:HIS290 4.4 29.0 1.0
C4A N:HEA606 4.5 19.6 1.0
FE N:HEA606 4.6 19.4 1.0
CG1 N:VAL243 4.6 30.3 1.0
ND N:HEA606 4.8 20.0 1.0
CHA N:HEA606 4.8 21.0 1.0
N N:HIS240 4.8 25.6 1.0
C4D N:HEA606 4.9 19.9 1.0
C2A N:HEA606 4.9 19.7 1.0
C3A N:HEA606 5.0 21.1 1.0

Copper binding site 5 out of 6 in 8gcq

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Copper binding site 5 out of 6 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu302

b:34.5
occ:1.00
 CU1 O:CUA302 0.0 34.5 1.0
ND1 O:HIS161 2.0 33.1 1.0
SG O:CYS200 2.3 26.6 1.0
SD O:MET207 2.3 29.6 1.0
SG O:CYS196 2.3 26.1 1.0
CU2 O:CUA302 2.7 29.9 1.0
CE O:MET207 2.7 31.1 1.0
CE1 O:HIS161 2.9 34.5 1.0
CG O:HIS161 3.1 35.4 1.0
CB O:CYS200 3.4 28.4 1.0
CG O:MET207 3.5 37.2 1.0
CB O:CYS196 3.5 27.4 1.0
CB O:HIS161 3.5 37.4 1.0
O O:GLU198 4.0 31.8 1.0
NE2 O:HIS161 4.0 35.4 1.0
CA O:HIS161 4.0 36.2 1.0
CD2 O:HIS161 4.1 34.6 1.0
ND1 O:HIS204 4.6 31.8 1.0
O O:HIS204 4.7 34.9 1.0
CA O:CYS200 4.7 30.0 1.0
O O:LEU160 4.8 33.3 1.0
O O:HIS102 4.8 33.3 1.0
CZ2 O:TRP106 4.8 25.5 1.0
CA O:CYS196 4.8 26.2 1.0
CB O:MET207 4.8 40.7 1.0
CA O:HIS204 4.8 40.3 1.0
N O:HIS161 5.0 37.3 1.0
N O:SER162 5.0 36.6 1.0

Copper binding site 6 out of 6 in 8gcq

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Copper binding site 6 out of 6 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu302

b:29.9
occ:1.00
 CU2 O:CUA302 0.0 29.9 1.0
O O:GLU198 2.0 31.8 1.0
ND1 O:HIS204 2.0 31.8 1.0
SG O:CYS196 2.3 26.1 1.0
SG O:CYS200 2.3 26.6 1.0
CU1 O:CUA302 2.7 34.5 1.0
CE1 O:HIS204 2.9 32.2 1.0
CB O:CYS196 2.9 27.4 1.0
CG O:HIS204 3.1 34.9 1.0
C O:GLU198 3.2 26.3 1.0
CB O:HIS204 3.5 36.4 1.0
CB O:CYS200 3.5 28.4 1.0
N O:CYS200 3.5 29.4 1.0
O O:HIS204 3.6 34.9 1.0
CA O:HIS204 3.7 40.3 1.0
NE2 O:HIS204 4.0 31.8 1.0
C O:HIS204 4.0 42.6 1.0
N O:GLU198 4.1 22.4 1.0
CD2 O:HIS204 4.1 33.5 1.0
N O:ILE199 4.1 27.4 1.0
CA O:CYS200 4.1 30.0 1.0
CA O:CYS196 4.2 26.2 1.0
C O:ILE199 4.2 29.7 1.0
CA O:ILE199 4.2 28.6 1.0
CA O:GLU198 4.3 24.3 1.0
ND1 O:HIS161 4.4 33.1 1.0
SD O:MET207 4.4 29.6 1.0
C O:CYS196 4.4 25.7 1.0
CG O:MET207 4.6 37.2 1.0
O O:CYS196 4.7 26.7 1.0
N O:SER197 4.8 22.9 1.0
CA O:HIS161 5.0 36.2 1.0

Reference:

I.Ishigami, R.G.Sierra, Z.Su, A.Peck, C.Wang, F.Poitevin, S.Lisova, B.Hayes, F.R.Moss 3Rd, S.Boutet, R.E.Sublett, C.H.Yoon, S.R.Yeh, D.L.Rousseau. Structural Insights Into Functional Properties of the Oxidized Form of Cytochrome C Oxidase. Nat Commun V. 14 5752 2023.
ISSN: ESSN 2041-1723
PubMed: 37717031
DOI: 10.1038/S41467-023-41533-X
Page generated: Wed Jul 31 09:44:37 2024

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