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Zinc 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
Copper (Cu) 6 atoms
Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution, PDB code: 8gcq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8gcq

Go back to Zinc Binding Sites List in 8gcq
Zinc binding site 1 out of 2 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
F:Zn101

b:23.8
occ:1.00
SG F:CYS82 2.3 24.4 1.0
SG F:CYS85 2.3 24.4 1.0
SG F:CYS62 2.4 24.7 1.0
SG F:CYS60 2.4 19.2 1.0
CB F:CYS82 3.1 23.8 1.0
CB F:CYS85 3.4 24.7 1.0
CB F:CYS60 3.4 18.4 1.0
N F:CYS85 3.5 22.2 1.0
CB F:CYS62 3.5 24.7 1.0
CA F:CYS62 3.7 25.0 1.0
CA F:CYS85 4.0 24.9 1.0
CB F:SER84 4.2 19.1 1.0
OG1 F:THR87 4.3 21.3 1.0
N F:CYS62 4.3 22.3 1.0
O F:CYS60 4.3 15.3 1.0
C F:SER84 4.5 20.9 1.0
CA F:CYS60 4.6 17.5 1.0
C F:CYS60 4.6 17.0 1.0
CA F:CYS82 4.6 21.6 1.0
C F:CYS85 4.7 26.3 1.0
CA F:SER84 4.7 20.1 1.0
CB F:THR87 4.8 22.7 1.0
N F:GLY86 4.8 27.5 1.0
N F:SER84 4.8 18.9 1.0
C F:CYS62 5.0 27.6 1.0

Zinc binding site 2 out of 2 in 8gcq

Go back to Zinc Binding Sites List in 8gcq
Zinc binding site 2 out of 2 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
S:Zn101

b:30.1
occ:1.00
SG S:CYS82 2.3 37.0 1.0
SG S:CYS60 2.4 22.0 1.0
SG S:CYS85 2.4 30.0 1.0
SG S:CYS62 2.4 26.2 1.0
CB S:CYS82 3.1 36.9 1.0
CB S:CYS60 3.2 25.8 1.0
CB S:CYS85 3.3 32.4 1.0
CB S:CYS62 3.5 32.5 1.0
N S:CYS85 3.5 32.4 1.0
CA S:CYS62 3.6 32.9 1.0
CA S:CYS85 4.0 31.6 1.0
CB S:SER84 4.0 43.1 1.0
N S:CYS62 4.1 34.4 1.0
O S:CYS60 4.4 22.5 1.0
CA S:CYS60 4.4 25.1 1.0
C S:SER84 4.5 33.2 1.0
C S:CYS60 4.5 27.8 1.0
CA S:CYS82 4.6 36.5 1.0
OG S:SER84 4.6 51.1 1.0
CA S:SER84 4.6 41.2 1.0
C S:CYS85 4.7 32.4 1.0
N S:GLY86 4.7 32.8 1.0
OG1 S:THR87 4.8 33.5 1.0
N S:SER84 4.8 44.8 1.0
C S:ILE61 4.8 35.5 1.0
CB S:ILE70 5.0 26.9 1.0
C S:CYS82 5.0 34.6 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: Thu Dec 28 13:05:04 2023

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