Magnesium 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:

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

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 7thu

Go back to Magnesium Binding Sites List in 7thu
Magnesium 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 Magnesium with other atoms in the Mg 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
A:Mg602

b:32.0
occ:1.00
 OD1 A:ASP369 2.1 27.6 1.0
O B:HOH423 2.1 30.4 1.0
NE2 A:HIS368 2.1 28.6 1.0
OE1 B:GLU198 2.1 40.6 1.0
O B:HOH500 2.2 30.4 1.0
O B:HOH442 2.2 29.9 1.0
CD2 A:HIS368 3.1 28.7 1.0
CE1 A:HIS368 3.2 27.8 1.0
CG A:ASP369 3.3 33.2 1.0
CD B:GLU198 3.4 38.8 1.0
O B:SER197 3.9 29.2 1.0
O A:HOH842 3.9 31.9 1.0
CB A:ASP369 4.0 32.0 1.0
OE2 B:GLU198 4.1 45.3 1.0
OD2 A:ASP369 4.2 34.4 1.0
ND1 A:HIS368 4.3 24.8 1.0
CG A:HIS368 4.3 25.3 1.0
O A:HOH770 4.3 31.2 1.0
OD2 B:ASP173 4.3 35.4 1.0
O A:HOH716 4.3 29.6 1.0
OD1 B:ASP173 4.4 35.2 1.0
CG B:GLU198 4.4 32.9 1.0
CB B:GLU198 4.5 30.5 1.0
OG1 A:THR294 4.5 32.2 1.0
O A:HOH793 4.5 36.8 1.0
O A:HOH845 4.6 28.5 1.0
O A:HOH810 4.6 30.9 1.0
CG B:ASP173 4.8 35.7 1.0
CA B:GLU198 4.8 29.9 1.0

Magnesium binding site 2 out of 2 in 7thu

Go back to Magnesium Binding Sites List in 7thu
Magnesium 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 Magnesium with other atoms in the Mg 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
N:Mg602

b:39.8
occ:1.00
 NE2 N:HIS368 2.1 33.3 1.0
O O:HOH441 2.1 33.8 1.0
O O:HOH466 2.1 36.2 1.0
OD1 N:ASP369 2.1 42.3 1.0
O O:HOH413 2.1 40.2 1.0
OE1 O:GLU198 2.2 43.9 1.0
CD2 N:HIS368 3.0 33.5 1.0
CE1 N:HIS368 3.1 32.3 1.0
CG N:ASP369 3.4 44.5 1.0
CD O:GLU198 3.4 42.3 1.0
O N:HOH826 3.9 39.9 1.0
O O:SER197 3.9 39.4 1.0
OD2 O:ASP173 4.1 41.6 1.0
OE2 O:GLU198 4.1 50.6 1.0
CB N:ASP369 4.1 39.1 1.0
ND1 N:HIS368 4.2 32.6 1.0
CG N:HIS368 4.2 34.2 1.0
O N:HOH764 4.2 36.6 1.0
OD2 N:ASP369 4.3 43.8 1.0
OG1 N:THR294 4.4 33.9 1.0
OD1 O:ASP173 4.4 42.7 1.0
O N:HOH739 4.4 37.3 1.0
CG O:GLU198 4.4 39.3 1.0
O N:HOH814 4.5 35.6 1.0
CB O:GLU198 4.5 33.4 1.0
O N:HOH815 4.6 36.7 1.0
CG O:ASP173 4.6 45.3 1.0
CA O:GLU198 4.8 36.7 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 Apr 6 22:43:39 2023

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