Magnesium in PDB 8gcq: Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution

All present enzymatic activity of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution:
1.9.3.1;

The structure of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution, PDB code: 8gcq was solved by I.Ishigami, S.-R.Yeh, D.L.Rousseau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.00 / 2.38
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	178.6, 189.5, 211.1, 90, 90, 90
R / Rfree (%)	23.2 / 26.6

The structure of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution (pdb code 8gcq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution, PDB code: 8gcq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:16.0 occ:1.00 NE2 A:HIS368 2.0 16.1 1.0 O A:HOH751 2.2 12.1 1.0 O B:HOH403 2.2 27.2 1.0 OD2 A:ASP369 2.2 16.7 1.0 OE1 B:GLU198 2.2 14.9 1.0 O B:HOH425 2.2 18.3 1.0 CD2 A:HIS368 2.9 15.2 1.0 CE1 A:HIS368 3.0 14.7 1.0 CD B:GLU198 3.3 15.1 1.0 CG A:ASP369 3.4 15.5 1.0 OE2 B:GLU198 3.9 14.7 1.0 O B:SER197 3.9 25.4 1.0 CG A:HIS368 4.1 15.0 1.0 ND1 A:HIS368 4.1 14.4 1.0 OD1 A:ASP369 4.1 17.4 1.0 OD1 B:ASP173 4.1 20.6 1.0 OD2 B:ASP173 4.2 21.5 1.0 OG1 A:THR294 4.3 18.4 1.0 O A:HOH753 4.4 28.1 1.0 CB A:ASP369 4.4 14.8 1.0 O A:HOH766 4.4 13.3 1.0 O A:HOH776 4.4 10.2 1.0 CG B:GLU198 4.6 14.0 1.0 CG B:ASP173 4.6 20.3 1.0 O A:HOH741 4.6 6.7 1.0 CB B:GLU198 4.7 14.7 1.0

Magnesium binding site 2 out of 2 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg602 b:26.8 occ:1.00 NE2 N:HIS368 2.0 30.8 1.0 O N:HOH701 2.2 19.7 1.0 O N:HOH765 2.2 17.9 1.0 OD2 N:ASP369 2.2 20.2 1.0 OE1 O:GLU198 2.2 23.7 1.0 O O:HOH413 2.2 27.5 1.0 CD2 N:HIS368 3.0 31.6 1.0 CE1 N:HIS368 3.0 32.3 1.0 CG N:ASP369 3.1 21.8 1.0 CD O:GLU198 3.3 24.8 1.0 OD1 N:ASP369 3.4 19.9 1.0 OE2 O:GLU198 3.8 27.6 1.0 O N:HOH706 3.9 11.5 1.0 ND1 N:HIS368 4.1 30.2 1.0 CG N:HIS368 4.1 31.1 1.0 O N:HOH704 4.1 16.1 1.0 OG1 N:THR294 4.3 29.0 1.0 OD1 O:ASP173 4.3 32.8 1.0 OD2 O:ASP173 4.4 23.9 1.0 O N:HOH761 4.5 29.1 1.0 CG O:GLU198 4.5 24.2 1.0 CB N:ASP369 4.6 22.6 1.0 O O:SER197 4.6 24.7 1.0 O N:HOH749 4.7 86.4 1.0 CG O:ASP173 4.8 30.3 1.0 OH N:TYR129 5.0 17.9 1.0

I.Ishigami, R.G.Sierra, Z.Su, A.Peck, C.Wang, F.Poitevin, S.Lisova, B.Hayes, F.R.Moss 3Rd, S.Boutet, R.E.Sublett, C.H.Yoon, S.R.Yeh, D.L.Rousseau. Structural Insights Into Functional Properties of the Oxidized Form of Cytochrome C Oxidase. Nat Commun V. 14 5752 2023.
ISSN: ESSN 2041-1723
PubMed: 37717031
DOI: 10.1038/S41467-023-41533-X