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Magnesium 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:

Sodium (Na) 2 atoms
Copper (Cu) 6 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7tii

Go back to Magnesium Binding Sites List in 7tii
Magnesium 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 Magnesium with other atoms in the Mg 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
A:Mg604

b:29.6
occ:1.00
 NE2 A:HIS368 2.0 29.9 1.0
OE1 B:GLU198 2.2 28.4 1.0
O B:HOH432 2.2 28.6 1.0
OD2 A:ASP369 2.2 27.1 1.0
O B:HOH437 2.2 30.2 1.0
O B:HOH408 2.2 31.4 1.0
CE1 A:HIS368 2.9 31.6 1.0
CD2 A:HIS368 3.0 30.5 1.0
CG A:ASP369 3.3 27.2 1.0
CD B:GLU198 3.4 32.9 1.0
CB A:ASP369 3.9 27.3 1.0
O B:SER197 4.0 27.6 1.0
O A:HOH813 4.0 18.7 1.0
ND1 A:HIS368 4.0 28.9 1.0
OE2 B:GLU198 4.0 36.5 1.0
CG A:HIS368 4.1 28.9 1.0
O A:HOH787 4.3 27.6 1.0
O A:HOH715 4.3 25.6 1.0
OD2 B:ASP173 4.3 37.2 1.0
OD1 A:ASP369 4.3 27.6 1.0
OD1 B:ASP173 4.4 35.4 1.0
OG1 A:THR294 4.4 30.2 1.0
O A:HOH745 4.4 10.4 1.0
CG B:GLU198 4.5 32.5 1.0
O A:HOH743 4.5 33.8 1.0
CG B:ASP173 4.8 35.5 1.0
CB B:GLU198 4.8 32.0 1.0
CA A:ASP369 5.0 27.9 1.0

Magnesium binding site 2 out of 2 in 7tii

Go back to Magnesium Binding Sites List in 7tii
Magnesium 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 Magnesium with other atoms in the Mg 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
N:Mg604

b:34.0
occ:1.00
 NE2 N:HIS368 2.0 35.6 1.0
OE1 O:GLU198 2.1 34.6 1.0
O O:HOH419 2.1 32.5 1.0
OD2 N:ASP369 2.2 32.1 1.0
O O:HOH404 2.2 32.6 1.0
O O:HOH409 2.2 37.4 1.0
CE1 N:HIS368 2.9 32.9 1.0
CD2 N:HIS368 3.0 33.8 1.0
CG N:ASP369 3.3 33.1 1.0
CD O:GLU198 3.4 39.3 1.0
CB N:ASP369 3.9 33.1 1.0
O O:SER197 3.9 37.0 1.0
O N:HOH796 4.0 48.7 1.0
ND1 N:HIS368 4.0 32.4 1.0
CG N:HIS368 4.1 32.5 1.0
OD2 O:ASP173 4.1 40.8 1.0
OE2 O:GLU198 4.2 41.0 1.0
OG1 N:THR294 4.3 36.6 1.0
O N:HOH732 4.3 29.4 1.0
CG O:GLU198 4.3 38.6 1.0
OD1 N:ASP369 4.3 37.5 1.0
O N:HOH703 4.4 25.8 1.0
OD1 O:ASP173 4.4 36.9 1.0
O N:HOH772 4.4 33.1 1.0
CB O:GLU198 4.5 37.9 1.0
O N:HOH748 4.6 30.6 1.0
O O:HOH422 4.7 35.3 1.0
CG O:ASP173 4.7 38.7 1.0
CA O:GLU198 4.9 35.9 1.0
CA N:ASP369 5.0 34.0 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: Thu Oct 3 09:18:20 2024

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