Magnesium in PDB 7ypy: Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution:
7.1.1.9;

The structure of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 7ypy was solved by A.Shimada, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.96 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	181.938, 204.4, 177.896, 90, 90, 90
R / Rfree (%)	15.9 / 17.7

The structure of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution (pdb code 7ypy). 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 Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 7ypy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:19.0 occ:1.00 O B:HOH478 2.0 20.1 1.0 O B:HOH475 2.1 20.6 1.0 OD1 A:ASP369 2.1 21.1 1.0 OE1 B:GLU198 2.1 23.8 1.0 O B:HOH522 2.1 20.5 1.0 NE2 A:HIS368 2.2 20.0 1.0 CD B:GLU198 3.1 20.2 1.0 CD2 A:HIS368 3.1 20.7 1.0 CE1 A:HIS368 3.2 19.8 1.0 CG A:ASP369 3.3 20.4 1.0 OE2 B:GLU198 3.4 21.8 1.0 O B:SER197 3.9 20.7 1.0 CB A:ASP369 4.0 21.3 1.0 O A:HOH891 4.0 21.9 1.0 OD1 B:ASP173 4.2 20.1 1.0 O A:HOH792 4.3 20.7 1.0 CG A:HIS368 4.3 20.0 1.0 ND1 A:HIS368 4.3 18.3 1.0 OD2 A:ASP369 4.3 22.6 1.0 O B:HOH499 4.3 22.2 0.4 OG1 A:THR294 4.3 22.0 1.0 OD2 B:ASP173 4.3 21.9 1.0 CG B:GLU198 4.4 20.2 1.0 O B:HOH544 4.5 21.7 0.6 O A:HOH859 4.6 19.9 1.0 O A:HOH802 4.6 22.1 1.0 O A:HOH727 4.6 20.0 1.0 CB B:GLU198 4.6 18.8 1.0 CG B:ASP173 4.7 20.4 1.0 CA B:GLU198 4.9 19.6 1.0

Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg604 b:22.5 occ:1.00 O O:HOH439 2.0 23.7 1.0 OD1 N:ASP369 2.0 25.6 1.0 OE1 O:GLU198 2.1 30.2 1.0 O O:HOH457 2.1 24.6 1.0 O N:HOH895 2.1 24.7 1.0 NE2 N:HIS368 2.1 24.2 1.0 CD O:GLU198 3.0 25.8 1.0 CD2 N:HIS368 3.1 24.5 1.0 CE1 N:HIS368 3.2 22.1 1.0 CG N:ASP369 3.3 25.0 1.0 OE2 O:GLU198 3.4 28.3 1.0 O O:SER197 3.9 26.9 1.0 CB N:ASP369 4.0 25.7 1.0 O N:HOH909 4.1 25.1 1.0 CG N:HIS368 4.2 22.7 1.0 OD1 O:ASP173 4.2 24.7 1.0 O N:HOH781 4.3 23.4 1.0 ND1 N:HIS368 4.3 22.6 1.0 OD2 N:ASP369 4.3 26.8 1.0 OD2 O:ASP173 4.3 27.2 1.0 O O:HOH504 4.3 23.2 0.4 OG1 N:THR294 4.3 26.3 1.0 CG O:GLU198 4.4 24.8 1.0 O O:HOH532 4.5 25.3 0.6 O N:HOH876 4.5 22.2 1.0 O N:HOH733 4.5 23.7 1.0 CB O:GLU198 4.6 25.0 1.0 O N:HOH848 4.6 25.2 1.0 CG O:ASP173 4.7 24.7 1.0 CA O:GLU198 4.9 24.6 1.0

N.Yano, K.Muramoto, A.Shimada, K.Shinzawa-Itoh, T.Tsukihara, S.Yoshikawa. The MG2+-Containing Water Cluster of Mammalian Cytochrome C Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle. J. Biol. Chem. V. 291 23882 2016.
ISSN: ESSN 1083-351X
PubMed: 27605664
DOI: 10.1074/JBC.M115.711770