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Zinc in PDB 7tii: Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure

Enzymatic activity of Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure

All present enzymatic activity of Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure:
1.9.3.1;

Protein crystallography data

The structure of Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure, PDB code: 7tii was solved by I.Ishigami, D.L.Rousseau, S.-R.Yeh, S.Russi, A.Cohen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.30 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.037, 182.633, 205.453, 90, 90, 90
R / Rfree (%) 20.6 / 25.3

Other elements in 7tii:

The structure of Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure 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 Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure (pdb code 7tii). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure, PDB code: 7tii:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7tii

Go back to Zinc Binding Sites List in 7tii
Zinc binding site 1 out of 2 in the Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:36.7
occ:1.00
 SG F:CYS60 2.3 34.1 1.0
SG F:CYS62 2.3 35.7 1.0
SG F:CYS82 2.3 38.0 1.0
SG F:CYS85 2.4 38.8 1.0
CB F:CYS82 3.1 37.3 1.0
CB F:CYS60 3.2 34.5 1.0
CB F:CYS85 3.3 38.2 1.0
CB F:CYS62 3.3 37.0 1.0
CA F:CYS62 3.5 39.9 1.0
N F:CYS85 3.8 39.2 1.0
N F:CYS62 4.1 36.7 1.0
CA F:CYS85 4.1 40.5 1.0
O F:CYS60 4.2 35.2 1.0
O F:HOH211 4.2 43.5 1.0
CA F:CYS60 4.4 34.3 1.0
C F:CYS60 4.4 34.0 1.0
OG1 F:THR87 4.4 46.1 1.0
OG F:SER84 4.5 44.5 1.0
CB F:SER84 4.6 43.8 1.0
CA F:CYS82 4.6 36.9 1.0
C F:SER84 4.8 43.5 1.0
C F:CYS62 4.9 43.1 1.0
C F:CYS85 4.9 41.7 1.0
C F:ILE61 4.9 34.8 1.0
CG1 F:ILE70 4.9 30.8 1.0

Zinc binding site 2 out of 2 in 7tii

Go back to Zinc Binding Sites List in 7tii
Zinc binding site 2 out of 2 in the Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:40.0
occ:1.00
 SG S:CYS82 2.3 36.3 1.0
SG S:CYS85 2.3 37.4 1.0
SG S:CYS62 2.3 43.3 1.0
SG S:CYS60 2.3 33.4 1.0
CB S:CYS82 3.1 38.3 1.0
CB S:CYS60 3.2 33.2 1.0
CB S:CYS85 3.4 39.4 1.0
CB S:CYS62 3.4 42.5 1.0
N S:CYS85 3.7 38.9 1.0
CA S:CYS62 3.7 42.5 1.0
CA S:CYS85 4.1 40.7 1.0
OG1 S:THR87 4.1 41.0 0.5
N S:CYS62 4.2 40.4 1.0
O S:CYS60 4.2 38.0 1.0
CB S:SER84 4.3 42.1 1.0
O S:HOH215 4.3 66.5 1.0
C S:CYS60 4.4 35.5 1.0
CA S:CYS60 4.4 34.7 1.0
CG2 S:THR87 4.5 43.4 0.5
CA S:CYS82 4.5 35.2 1.0
C S:SER84 4.6 39.5 1.0
OG S:SER84 4.7 40.5 1.0
CA S:SER84 4.8 39.5 1.0
C S:CYS85 4.9 44.9 1.0
CB S:ILE70 4.9 33.7 1.0
CG1 S:ILE70 4.9 36.3 1.0
N S:SER84 4.9 38.4 1.0
OH S:TYR89 5.0 45.0 1.0
N S:GLY86 5.0 45.2 1.0
C S:ILE61 5.0 37.3 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: Wed Oct 30 11:37:02 2024

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