Zinc in PDB 7tie: Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays

Enzymatic activity of Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays

All present enzymatic activity of Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays:
1.9.3.1;

Protein crystallography data

The structure of Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays, PDB code: 7tie 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) 39.99 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.118, 182.415, 208.547, 90, 90, 90
R / Rfree (%) 18.5 / 21.5

Other elements in 7tie:

The structure of Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays 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 Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays (pdb code 7tie). 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 Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays, PDB code: 7tie:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7tie

Go back to Zinc Binding Sites List in 7tie
Zinc binding site 1 out of 2 in the Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 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 Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn703

b:34.7
occ:1.00
SG F:CYS60 2.3 33.1 1.0
SG F:CYS82 2.3 34.1 1.0
SG F:CYS62 2.4 35.8 1.0
SG F:CYS85 2.4 34.2 1.0
CB F:CYS82 3.2 36.5 1.0
CB F:CYS60 3.2 32.5 1.0
CB F:CYS85 3.3 33.9 1.0
CB F:CYS62 3.4 33.8 1.0
CA F:CYS62 3.6 38.3 1.0
N F:CYS85 3.7 35.0 1.0
CA F:CYS85 4.0 34.7 1.0
N F:CYS62 4.1 36.5 1.0
O F:CYS60 4.4 34.8 1.0
CA F:CYS60 4.4 31.7 1.0
C F:CYS60 4.5 34.7 1.0
OG F:SER84 4.6 38.0 1.0
CA F:CYS82 4.6 36.5 1.0
CB F:SER84 4.6 37.2 1.0
C F:SER84 4.7 34.6 1.0
OG1 F:THR87 4.7 47.5 1.0
C F:CYS85 4.8 37.5 1.0
C F:ILE61 4.9 36.9 1.0
N F:GLY86 4.9 38.3 1.0
CB F:THR87 4.9 44.7 1.0
CB F:ILE70 5.0 30.5 1.0
C F:CYS62 5.0 40.5 1.0

Zinc binding site 2 out of 2 in 7tie

Go back to Zinc Binding Sites List in 7tie
Zinc binding site 2 out of 2 in the Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 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 Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:38.5
occ:1.00
SG S:CYS85 2.3 40.5 1.0
SG S:CYS62 2.3 38.0 1.0
SG S:CYS60 2.3 38.1 1.0
SG S:CYS82 2.4 37.1 1.0
CB S:CYS82 3.1 33.1 1.0
CB S:CYS60 3.1 34.4 1.0
CB S:CYS85 3.3 35.5 1.0
CB S:CYS62 3.3 36.9 1.0
CA S:CYS62 3.6 40.7 1.0
N S:CYS85 3.7 39.8 1.0
CA S:CYS85 4.1 39.2 1.0
N S:CYS62 4.1 39.0 1.0
CA S:CYS60 4.3 34.6 1.0
C S:CYS60 4.4 36.5 1.0
OG1 S:THR87 4.4 53.8 1.0
O S:CYS60 4.4 35.3 1.0
O S:HOH208 4.5 59.9 1.0
CB S:SER84 4.5 38.8 1.0
CA S:CYS82 4.5 35.9 1.0
OG S:SER84 4.7 39.2 1.0
C S:SER84 4.7 40.1 1.0
C S:CYS85 4.8 35.4 1.0
C S:ILE61 4.9 37.1 1.0
C S:CYS62 5.0 41.6 1.0
N S:GLY86 5.0 40.9 1.0
CA S:SER84 5.0 39.1 1.0
N S:SER84 5.0 43.9 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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