Zinc in PDB 7thu: Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays

Enzymatic activity of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays

All present enzymatic activity of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays:
1.9.3.1;

Protein crystallography data

The structure of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays, PDB code: 7thu was solved by I.Ishigami, D.L.Rousseau, S.-R.Yeh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.182, 182.282, 208.683, 90, 90, 90
R / Rfree (%) 18.4 / 21.3

Other elements in 7thu:

The structure of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays also contains other interesting chemical elements:

Copper (Cu) 6 atoms
Iron (Fe) 4 atoms
Magnesium (Mg) 2 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays (pdb code 7thu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays, PDB code: 7thu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7thu

Go back to Zinc Binding Sites List in 7thu
Zinc binding site 1 out of 2 in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn703

b:38.2
occ:1.00
SG F:CYS82 2.3 38.1 1.0
SG F:CYS60 2.3 38.8 1.0
SG F:CYS85 2.3 38.7 1.0
SG F:CYS62 2.4 40.0 1.0
CB F:CYS82 3.2 39.0 1.0
CB F:CYS60 3.3 36.0 1.0
CB F:CYS85 3.3 36.3 1.0
CB F:CYS62 3.4 37.2 1.0
CA F:CYS62 3.6 42.8 1.0
N F:CYS85 3.7 35.3 1.0
CA F:CYS85 4.1 37.9 1.0
N F:CYS62 4.1 40.5 1.0
CB F:SER84 4.4 42.7 1.0
O F:CYS60 4.5 37.1 1.0
CA F:CYS60 4.5 32.0 1.0
C F:CYS60 4.5 36.5 1.0
CA F:CYS82 4.6 38.7 1.0
C F:SER84 4.7 37.1 1.0
OG F:SER84 4.7 46.6 1.0
C F:CYS85 4.8 38.5 1.0
OG1 F:THR87 4.8 53.1 1.0
CA F:SER84 4.9 40.9 1.0
C F:ILE61 4.9 39.2 1.0
CB F:THR87 4.9 48.1 1.0
CB F:ILE70 5.0 36.4 1.0
N F:SER84 5.0 40.0 1.0

Zinc binding site 2 out of 2 in 7thu

Go back to Zinc Binding Sites List in 7thu
Zinc binding site 2 out of 2 in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn2202

b:42.6
occ:1.00
SG S:CYS85 2.3 44.5 1.0
SG S:CYS82 2.3 41.9 1.0
SG S:CYS62 2.3 42.2 1.0
SG S:CYS60 2.4 42.1 1.0
CB S:CYS82 3.1 40.1 1.0
CB S:CYS60 3.2 37.9 1.0
CB S:CYS85 3.2 40.4 1.0
CB S:CYS62 3.3 40.6 1.0
CA S:CYS62 3.6 45.7 1.0
N S:CYS85 3.7 43.2 1.0
CA S:CYS85 4.0 42.7 1.0
N S:CYS62 4.1 45.3 1.0
CA S:CYS60 4.4 38.8 1.0
CB S:SER84 4.5 45.8 1.0
O S:CYS60 4.5 37.4 1.0
OG1 S:THR87 4.5 58.1 1.0
C S:CYS60 4.5 40.6 1.0
CA S:CYS82 4.6 40.2 1.0
C S:SER84 4.7 45.9 1.0
OG S:SER84 4.8 48.0 1.0
C S:CYS85 4.8 39.0 1.0
N S:GLY86 4.9 41.3 1.0
CA S:SER84 5.0 46.2 1.0
C S:ILE61 5.0 42.0 1.0
CG1 S:ILE70 5.0 38.6 1.0
N S:SER84 5.0 48.0 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: Sat Apr 8 03:30:52 2023

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