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

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

All present enzymatic activity of 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 Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure, PDB code: 7tih 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) 39.34 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.037, 182.696, 205.854, 90, 90, 90
R / Rfree (%) 19.3 / 23.5

Other elements in 7tih:

The structure of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure (pdb code 7tih). 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 Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure, PDB code: 7tih:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7tih

Go back to Magnesium Binding Sites List in 7tih
Magnesium binding site 1 out of 2 in the 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 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:Mg602

b:31.5
occ:1.00
 NE2 A:HIS368 2.0 29.5 1.0
OE1 B:GLU198 2.1 28.5 1.0
OD2 A:ASP369 2.1 25.6 1.0
O B:HOH417 2.2 32.1 1.0
O B:HOH435 2.2 31.7 1.0
O B:HOH409 2.2 27.5 1.0
CE1 A:HIS368 2.9 27.4 1.0
CD2 A:HIS368 3.0 28.4 1.0
CG A:ASP369 3.2 27.3 1.0
CD B:GLU198 3.3 34.1 1.0
CB A:ASP369 3.7 27.1 1.0
O B:SER197 3.9 29.2 1.0
OE2 B:GLU198 3.9 43.5 1.0
O A:HOH845 4.0 24.8 1.0
ND1 A:HIS368 4.0 24.5 1.0
OD1 B:ASP173 4.1 31.5 1.0
CG A:HIS368 4.1 26.4 1.0
OG1 A:THR294 4.2 30.6 1.0
OD1 A:ASP369 4.3 25.3 1.0
OD2 B:ASP173 4.3 35.2 1.0
O A:HOH820 4.3 30.0 1.0
O A:HOH752 4.4 35.8 1.0
CG B:GLU198 4.5 31.8 1.0
O A:HOH779 4.5 28.1 1.0
O A:HOH761 4.6 17.0 1.0
CG B:ASP173 4.6 33.6 1.0
CB B:GLU198 4.7 32.3 1.0
CA A:ASP369 4.9 27.0 1.0

Magnesium binding site 2 out of 2 in 7tih

Go back to Magnesium Binding Sites List in 7tih
Magnesium binding site 2 out of 2 in the 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 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:Mg602

b:35.2
occ:1.00
 NE2 N:HIS368 2.0 33.1 1.0
OE1 O:GLU198 2.1 35.2 1.0
O O:HOH410 2.2 33.0 1.0
O O:HOH413 2.2 32.4 1.0
O O:HOH418 2.2 30.3 1.0
OD2 N:ASP369 2.2 37.8 1.0
CD2 N:HIS368 2.9 30.9 1.0
CE1 N:HIS368 3.0 29.9 1.0
CD O:GLU198 3.1 34.1 1.0
CG N:ASP369 3.3 36.5 1.0
OE2 O:GLU198 3.3 29.6 1.0
O N:HOH838 3.9 34.8 1.0
CB N:ASP369 3.9 36.4 1.0
O O:SER197 4.0 34.0 1.0
CG N:HIS368 4.0 30.1 1.0
ND1 N:HIS368 4.1 28.1 1.0
O N:HOH768 4.1 30.4 1.0
OG1 N:THR294 4.2 31.1 1.0
OD2 O:ASP173 4.3 44.8 1.0
OD1 N:ASP369 4.3 37.0 1.0
O N:HOH814 4.4 34.0 1.0
O N:HOH710 4.4 30.8 1.0
O N:HOH777 4.4 31.2 1.0
CG O:GLU198 4.4 33.5 1.0
OD1 O:ASP173 4.5 39.6 1.0
CG O:ASP173 4.8 41.0 1.0
CB O:GLU198 4.9 34.9 1.0
O N:HOH800 4.9 31.2 1.0
CA N:ASP369 4.9 37.4 1.0
O N:HOH804 4.9 27.0 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 09:17:51 2024

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