Magnesium in PDB 6nmp: Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature

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

The structure of Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature, PDB code: 6nmp 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 / 2.90
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 (%)	19.2 / 24.4

The structure of Sfx Structure of Oxidized 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 Oxidized Cytochrome C Oxidase at Room Temperature (pdb code 6nmp). 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 Room Temperature, PDB code: 6nmp:
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 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 Oxidized Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:39.0 occ:1.00 NE2 A:HIS368 2.0 40.4 1.0 OE1 B:GLU198 2.2 44.8 1.0 O B:HOH419 2.2 40.5 1.0 OD2 A:ASP369 2.2 43.5 1.0 O B:HOH401 2.2 34.4 1.0 CE1 A:HIS368 2.7 40.4 1.0 CD B:GLU198 3.1 46.5 1.0 CD2 A:HIS368 3.2 40.1 1.0 CG A:ASP369 3.3 41.9 1.0 OE2 B:GLU198 3.3 48.9 1.0 O A:HOH771 3.5 37.4 1.0 ND1 A:HIS368 3.9 39.0 1.0 O A:HOH762 4.0 31.7 1.0 CB A:ASP369 4.1 39.2 1.0 CG A:HIS368 4.1 39.8 1.0 OD1 A:ASP369 4.3 41.1 1.0 O A:HOH705 4.3 29.1 1.0 O A:HOH709 4.4 39.8 1.0 O B:SER197 4.5 41.0 1.0 O A:HOH746 4.5 45.9 1.0 OD2 B:ASP173 4.5 59.7 1.0 CG B:GLU198 4.5 43.1 1.0 O A:HOH711 4.7 13.6 1.0 OD1 B:ASP173 4.8 48.2 1.0 CB B:GLU198 5.0 41.9 1.0 CA A:ASP369 5.0 38.4 1.0

Magnesium binding site 2 out of 2 in the Sfx Structure of Oxidized 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 Oxidized Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg602 b:46.8 occ:1.00 NE2 N:HIS368 2.0 57.5 1.0 O O:HOH404 2.2 44.7 1.0 O O:HOH413 2.2 48.1 1.0 OE1 O:GLU198 2.2 57.2 1.0 OD2 N:ASP369 2.2 50.9 1.0 CD2 N:HIS368 2.8 57.0 1.0 CE1 N:HIS368 3.0 57.1 1.0 CG N:ASP369 3.3 52.7 1.0 CD O:GLU198 3.5 60.9 1.0 O N:HOH735 3.6 24.2 1.0 O O:SER197 3.9 57.9 1.0 CB N:ASP369 4.0 52.7 1.0 CG N:HIS368 4.0 53.2 1.0 ND1 N:HIS368 4.0 53.3 1.0 OD2 O:ASP173 4.2 53.3 1.0 OE2 O:GLU198 4.2 52.9 1.0 OD1 N:ASP369 4.3 54.3 1.0 O N:HOH712 4.4 51.3 1.0 OG1 N:THR294 4.4 55.4 1.0 CG O:GLU198 4.5 62.1 1.0 OD1 O:ASP173 4.5 55.5 1.0 CB O:GLU198 4.6 60.1 1.0 CG O:ASP173 4.8 50.4 1.0 N N:ASP369 4.8 48.6 1.0 CA N:ASP369 4.9 50.7 1.0 O O:HOH417 5.0 45.5 1.0 CA O:GLU198 5.0 60.1 1.0 C O:SER197 5.0 61.6 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