Atomistry » Copper » PDB 8gcq-8po9 » 8gcq
Atomistry »
  Copper »
    PDB 8gcq-8po9 »
      8gcq »

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

Go back to Copper Binding Sites List in 8gcq
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

Go back to Copper Binding Sites List in 8gcq
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

Go back to Copper Binding Sites List in 8gcq
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

Go back to Copper Binding Sites List in 8gcq
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

Go back to Copper Binding Sites List in 8gcq
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy