Magnesium in PDB 6nkn: Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature

All present enzymatic activity of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature:
1.9.3.1;

The structure of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature, PDB code: 6nkn 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)	10.50 / 2.50
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 / 21.7

The structure of Time-Resolved Sfx Structure of the Pr Intermediate of 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 Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature (pdb code 6nkn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature, PDB code: 6nkn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Time-Resolved Sfx Structure of the Pr Intermediate of 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 Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:38.9 occ:1.00 NE2 A:HIS368 2.0 43.5 1.0 OE1 B:GLU198 2.1 30.9 1.0 O B:HOH427 2.2 37.4 1.0 OD2 A:ASP369 2.2 32.4 1.0 O B:HOH441 2.2 33.4 1.0 O B:HOH447 2.2 36.3 1.0 CE1 A:HIS368 3.0 42.2 1.0 CD2 A:HIS368 3.0 44.0 1.0 CG A:ASP369 3.2 34.7 1.0 CD B:GLU198 3.4 41.3 1.0 CB A:ASP369 3.7 32.3 1.0 O B:SER197 4.0 35.5 1.0 ND1 A:HIS368 4.1 37.8 1.0 CG A:HIS368 4.1 40.5 1.0 OE2 B:GLU198 4.1 47.5 1.0 O A:HOH808 4.1 41.5 1.0 OD2 B:ASP173 4.2 51.3 1.0 O A:HOH820 4.3 78.7 1.0 O A:HOH732 4.3 25.3 1.0 OD1 A:ASP369 4.4 35.9 1.0 CG B:GLU198 4.4 40.8 1.0 OG1 A:THR294 4.5 41.6 1.0 O A:HOH715 4.5 38.5 1.0 OD1 B:ASP173 4.5 51.0 1.0 O A:HOH804 4.5 38.9 1.0 O A:HOH822 4.6 41.5 1.0 CB B:GLU198 4.7 39.4 1.0 O B:HOH436 4.7 47.2 1.0 CG B:ASP173 4.8 49.7 1.0 CA A:ASP369 4.8 35.7 1.0

Magnesium binding site 2 out of 2 in the Time-Resolved Sfx Structure of the Pr Intermediate of 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 Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg603 b:55.8 occ:1.00 NE2 N:HIS368 2.0 63.5 1.0 O O:HOH402 2.2 55.0 1.0 OD2 N:ASP369 2.2 55.1 1.0 O O:HOH403 2.2 44.0 1.0 O O:HOH412 2.2 51.7 1.0 OE1 O:GLU198 2.2 53.1 1.0 CE1 N:HIS368 3.0 57.1 1.0 CD2 N:HIS368 3.0 60.7 1.0 CG N:ASP369 3.2 60.4 1.0 CD O:GLU198 3.5 56.5 1.0 CB N:ASP369 3.7 58.9 1.0 O N:HOH740 3.8 42.0 1.0 O O:SER197 3.8 60.0 1.0 ND1 N:HIS368 4.0 54.5 1.0 CG N:HIS368 4.0 56.0 1.0 OE2 O:GLU198 4.2 52.3 1.0 O N:HOH723 4.3 54.9 1.0 OD1 N:ASP369 4.3 67.3 1.0 OD2 O:ASP173 4.4 61.1 1.0 OD1 O:ASP173 4.5 59.9 1.0 CG O:GLU198 4.5 55.7 1.0 OG1 N:THR294 4.6 50.3 1.0 CB O:GLU198 4.7 60.8 1.0 CA N:ASP369 4.8 58.1 1.0 O N:HOH756 4.8 57.0 1.0 O O:HOH429 4.9 52.8 1.0 CG O:ASP173 4.9 60.3 1.0 C O:SER197 4.9 59.9 1.0 N N:ASP369 4.9 53.1 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