Magnesium in PDB 5xdx: Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution, PDB code: 5xdx was solved by F.J.Luo, A.Shimada, N.Hagimoto, S.Shimada, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	183.044, 205.691, 177.797, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 20.3

The structure of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution (pdb code 5xdx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution, PDB code: 5xdx:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:30.6 occ:1.00 NE2 A:HIS368 2.0 25.9 1.0 OD1 A:ASP369 2.2 27.2 1.0 OE1 B:GLU198 2.2 29.0 1.0 O B:HOH418 2.3 27.8 1.0 O B:HOH538 2.3 24.5 1.0 O B:HOH407 2.4 29.2 1.0 CE1 A:HIS368 3.0 26.2 1.0 CD2 A:HIS368 3.0 26.0 1.0 CG A:ASP369 3.3 27.3 1.0 CD B:GLU198 3.4 30.5 1.0 O B:SER197 3.9 26.9 1.0 O A:HOH888 4.0 27.2 1.0 CB A:ASP369 4.0 27.8 1.0 O A:HOH707 4.1 27.5 1.0 ND1 A:HIS368 4.1 26.4 1.0 OE2 B:GLU198 4.2 30.8 1.0 CG A:HIS368 4.2 26.9 1.0 O A:HOH821 4.2 27.0 1.0 OD2 B:ASP173 4.3 30.4 1.0 OD2 A:ASP369 4.3 27.9 1.0 O B:HOH451 4.3 27.5 0.9 OD1 B:ASP173 4.4 31.0 1.0 CG B:GLU198 4.4 29.5 1.0 CB B:GLU198 4.4 29.6 1.0 O A:HOH834 4.5 26.9 1.0 OG1 A:THR294 4.5 28.6 1.0 O B:HOH436 4.6 25.8 0.6 O A:HOH863 4.6 29.4 1.0 CG B:ASP173 4.8 30.6 1.0 CA B:GLU198 4.9 29.4 1.0 C B:SER197 5.0 28.6 1.0

Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg604 b:44.4 occ:1.00 NE2 N:HIS368 2.0 39.2 1.0 OD1 N:ASP369 2.2 42.4 1.0 OE1 O:GLU198 2.2 41.4 1.0 O O:HOH432 2.4 37.0 1.0 O N:HOH897 2.4 34.7 1.0 O O:HOH404 2.4 38.8 1.0 CD2 N:HIS368 3.0 36.8 1.0 CE1 N:HIS368 3.0 37.3 1.0 CG N:ASP369 3.3 41.0 1.0 CD O:GLU198 3.4 40.9 1.0 O O:SER197 3.9 38.9 1.0 O N:HOH841 3.9 38.2 1.0 CB N:ASP369 4.1 40.8 1.0 O N:HOH703 4.1 36.5 1.0 ND1 N:HIS368 4.1 36.9 1.0 OE2 O:GLU198 4.1 42.0 1.0 CG N:HIS368 4.1 37.6 1.0 O N:HOH773 4.3 34.9 1.0 OD2 N:ASP369 4.3 39.5 1.0 OD2 O:ASP173 4.3 41.0 1.0 O N:HOH779 4.3 36.8 1.0 CG O:GLU198 4.5 40.4 1.0 O N:HOH853 4.5 35.3 1.0 OG1 N:THR294 4.5 39.3 1.0 OD1 O:ASP173 4.6 41.3 1.0 O N:HOH839 4.6 37.6 1.0 CB O:GLU198 4.6 41.0 1.0 CG O:ASP173 4.8 41.2 1.0 CA O:GLU198 4.9 41.8 1.0 O O:HOH430 5.0 48.9 1.0

F.Luo, K.Shinzawa-Itoh, K.Hagimoto, A.Shimada, S.Shimada, E.Yamashita, S.Yoshikawa, T.Tsukihara. Structure of Bovine Cytochrome C Oxidase in the Ligand-Free Reduced State at Neutral pH. Acta Crystallogr F Struct V. 74 92 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 29400318
DOI: 10.1107/S2053230X17018532