Magnesium in PDB 8h8r: Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State:
7.1.1.9;

The structure of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State, PDB code: 8h8r was solved by K.Muramoto, K.Shinzawa-Itoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	182.8, 205.7, 177.9, 90, 90, 90
R / Rfree (%)	12.2 / 15.3

The structure of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State also contains other interesting chemical elements:

Copper	(Cu)	6 atoms
Iron	(Fe)	4 atoms
Calcium	(Ca)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Magnesium atom in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State (pdb code 8h8r). 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 Calcium-Bound Fully Oxidized State, PDB code: 8h8r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State


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 Calcium-Bound Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:30.4 occ:1.00 OE1 B:GLU198 2.0 35.2 1.0 OD2 A:ASP369 2.1 31.1 1.0 O B:HOH455 2.1 30.3 1.0 O A:HOH890 2.1 29.9 1.0 O B:HOH422 2.2 32.0 1.0 NE2 A:HIS368 2.2 27.7 1.0 CD B:GLU198 3.0 31.6 1.0 CD2 A:HIS368 3.2 31.4 1.0 CE1 A:HIS368 3.2 28.9 1.0 CG A:ASP369 3.3 32.3 1.0 OE2 B:GLU198 3.4 38.2 1.0 O B:SER197 3.9 29.7 1.0 O A:HOH878 4.0 32.0 1.0 CB A:ASP369 4.0 30.6 1.0 OD1 B:ASP173 4.3 31.4 1.0 O A:HOH784 4.3 30.9 1.0 OD2 B:ASP173 4.3 34.6 1.0 OD1 A:ASP369 4.3 33.9 1.0 CG A:HIS368 4.3 27.4 1.0 CG B:GLU198 4.3 30.2 1.0 ND1 A:HIS368 4.3 28.7 1.0 OG1 A:THR294 4.4 32.2 1.0 O B:HOH535 4.5 31.3 0.6 O A:HOH729 4.5 30.3 1.0 CB B:GLU198 4.6 28.5 1.0 O A:HOH806 4.6 32.1 1.0 O A:HOH876 4.6 28.5 1.0 CG B:ASP173 4.7 32.1 1.0 O B:HOH477 4.8 38.7 0.6 CA B:GLU198 4.9 27.0 1.0 O A:HOH871 5.0 33.0 0.7 C B:SER197 5.0 27.8 1.0

Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State


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 Calcium-Bound Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg606 b:37.3 occ:1.00 OE1 O:GLU198 2.0 43.4 1.0 O O:HOH451 2.1 36.0 1.0 O O:HOH429 2.1 39.1 1.0 OD2 N:ASP369 2.1 38.6 1.0 O O:HOH517 2.1 36.9 1.0 NE2 N:HIS368 2.3 35.5 1.0 CD O:GLU198 3.0 38.8 1.0 CD2 N:HIS368 3.2 35.5 1.0 CE1 N:HIS368 3.3 35.7 1.0 CG N:ASP369 3.3 38.2 1.0 OE2 O:GLU198 3.5 45.6 1.0 O O:SER197 3.9 38.3 1.0 O N:HOH2979 4.0 37.5 1.0 CB N:ASP369 4.0 37.4 1.0 O N:HOH2911 4.2 36.8 1.0 OD2 O:ASP173 4.3 41.2 1.0 CG O:GLU198 4.3 38.1 1.0 O O:HOH485 4.3 40.0 0.4 OD1 N:ASP369 4.3 39.7 1.0 CG N:HIS368 4.3 34.6 1.0 OD1 O:ASP173 4.4 38.9 1.0 ND1 N:HIS368 4.4 34.8 1.0 OG1 N:THR294 4.4 37.1 1.0 O N:HOH2815 4.5 37.4 1.0 CB O:GLU198 4.5 35.2 1.0 O O:HOH524 4.5 42.5 0.6 O N:HOH2961 4.6 35.3 1.0 O N:HOH2950 4.6 37.4 1.0 CG O:ASP173 4.7 37.4 1.0 O N:HOH2932 4.9 39.6 0.7 CA O:GLU198 4.9 37.1 1.0 C O:SER197 5.0 37.0 1.0

K.Muramoto, K.Shinzawa-Itoh. Calcium-Bound Structure of Bovine Cytochrome C Oxidase. Biochim Biophys Acta 48956 2023BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 36708913
DOI: 10.1016/J.BBABIO.2023.148956