Magnesium in PDB 6nmf: Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature

All present enzymatic activity of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature:
1.9.3.1;

The structure of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature, PDB code: 6nmf was solved by D.L.Rousseau, S.-R.Yeh, I.Ishigami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	178.700, 189.800, 211.300, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 23.2

The structure of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature (pdb code 6nmf). 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 Reduced Cytochrome C Oxidase at Room Temperature, PDB code: 6nmf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature


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 Reduced Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:43.4 occ:1.00 NE2 A:HIS368 2.0 46.4 1.0 OE1 B:GLU198 2.1 38.0 1.0 O B:HOH409 2.2 36.0 1.0 O B:HOH458 2.2 45.0 1.0 OD2 A:ASP369 2.2 43.8 1.0 O B:HOH401 2.2 37.7 1.0 CE1 A:HIS368 2.8 45.2 1.0 CD2 A:HIS368 3.1 42.5 1.0 CG A:ASP369 3.3 42.9 1.0 CD B:GLU198 3.3 45.6 1.0 OE2 B:GLU198 3.9 48.0 1.0 CB A:ASP369 3.9 39.5 1.0 ND1 A:HIS368 4.0 43.8 1.0 O A:HOH733 4.0 47.9 1.0 CG A:HIS368 4.1 42.7 1.0 O A:HOH757 4.2 53.2 1.0 O B:SER197 4.2 45.5 1.0 O A:HOH771 4.3 85.5 1.0 O B:HOH435 4.3 29.6 1.0 OD2 B:ASP173 4.3 54.9 1.0 O A:HOH772 4.4 38.1 1.0 OD1 A:ASP369 4.4 42.1 1.0 O A:HOH775 4.4 33.4 1.0 CG B:GLU198 4.6 46.2 1.0 O A:HOH745 4.6 54.4 1.0 OD1 B:ASP173 4.6 50.1 1.0 OG1 A:THR294 4.7 40.4 1.0 CB B:GLU198 4.8 46.5 1.0 CA A:ASP369 4.9 40.8 1.0 CG B:ASP173 4.9 52.2 1.0 N A:ASP369 5.0 40.7 1.0

Magnesium binding site 2 out of 2 in the Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature


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 Reduced Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg604 b:60.5 occ:1.00 NE2 N:HIS368 2.0 78.1 1.0 O O:HOH422 2.2 61.3 1.0 O O:HOH401 2.2 56.9 1.0 OD2 N:ASP369 2.2 60.1 1.0 OE1 O:GLU198 2.2 58.9 1.0 CE1 N:HIS368 2.8 75.2 1.0 CD2 N:HIS368 3.1 73.0 1.0 CG N:ASP369 3.4 65.1 1.0 CD O:GLU198 3.4 66.0 1.0 O N:HOH771 3.4 58.4 1.0 OD2 O:ASP173 3.8 62.1 1.0 O O:SER197 3.9 68.2 1.0 ND1 N:HIS368 4.0 72.6 1.0 CG N:HIS368 4.1 68.8 1.0 CB N:ASP369 4.2 64.7 1.0 O N:HOH735 4.2 48.8 1.0 CG O:GLU198 4.3 68.1 1.0 OD1 O:ASP173 4.3 61.3 1.0 OE2 O:GLU198 4.4 59.4 1.0 CB O:GLU198 4.4 69.2 1.0 OD1 N:ASP369 4.4 65.6 1.0 OG1 N:THR294 4.4 61.3 1.0 CG O:ASP173 4.5 60.8 1.0 O N:HOH732 4.6 50.7 1.0 O N:HOH706 4.7 56.3 1.0 O N:HOH734 4.8 65.0 1.0 CA O:GLU198 4.9 66.9 1.0

I.Ishigami, A.Lewis-Ballester, A.Echelmeier, G.Brehm, N.A.Zatsepin, T.D.Grant, J.D.Coe, S.Lisova, G.Nelson, S.Zhang, Z.F.Dobson, S.Boutet, R.G.Sierra, A.Batyuk, P.Fromme, R.Fromme, J.C.H.Spence, A.Ros, S.R.Yeh, D.L.Rousseau. Snapshot of An Oxygen Intermediate in the Catalytic Reaction of Cytochromecoxidase. Proc. Natl. Acad. Sci. V. 116 3572 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30808749
DOI: 10.1073/PNAS.1814526116