Magnesium in PDB 7cp5: Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution:
7.1.1.9;

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution, PDB code: 7cp5 was solved by T.Tsukihara, A.Shimada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.91 / 1.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	181.589, 203.218, 177.702, 90, 90, 90
R / Rfree (%)	16 / 18.9

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution (pdb code 7cp5). 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution, PDB code: 7cp5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:19.1 occ:1.00 OD2 A:ASP369 2.0 22.6 1.0 O B:HOH447 2.0 21.3 1.0 OE1 B:GLU198 2.0 26.8 1.0 O B:HOH434 2.1 23.6 1.0 NE2 A:HIS368 2.1 21.3 1.0 O B:HOH516 2.1 22.0 1.0 CE1 A:HIS368 3.1 22.0 1.0 CD B:GLU198 3.1 24.7 1.0 CD2 A:HIS368 3.1 21.6 1.0 CG A:ASP369 3.2 23.5 1.0 OE2 B:GLU198 3.5 24.8 1.0 O B:SER197 3.8 22.8 1.0 CB A:ASP369 3.9 21.2 1.0 O A:HOH893 4.0 21.9 1.0 ND1 A:HIS368 4.2 21.5 1.0 CG A:HIS368 4.2 22.6 1.0 OD1 A:ASP369 4.2 23.3 1.0 OD1 B:ASP173 4.3 23.5 1.0 O A:HOH810 4.3 21.8 1.0 OD2 B:ASP173 4.3 24.9 1.0 OG1 A:THR294 4.4 24.6 1.0 CG B:GLU198 4.4 20.4 1.0 O A:HOH712 4.5 22.9 1.0 O A:HOH883 4.5 21.3 1.0 O A:HOH852 4.6 23.5 1.0 O B:HOH542 4.6 30.7 1.0 CB B:GLU198 4.6 20.3 1.0 CG B:ASP173 4.7 24.0 1.0 CA B:GLU198 4.9 24.5 1.0 CA A:ASP369 5.0 22.7 1.0 C B:SER197 5.0 22.8 1.0

Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg605 b:21.1 occ:1.00 O O:HOH421 2.0 24.1 1.0 O O:HOH442 2.0 27.4 1.0 OD2 N:ASP369 2.0 28.0 1.0 OE1 O:GLU198 2.0 33.8 1.0 NE2 N:HIS368 2.1 25.0 1.0 O N:HOH901 2.1 25.2 1.0 CD2 N:HIS368 3.0 22.4 1.0 CD O:GLU198 3.1 27.5 1.0 CE1 N:HIS368 3.1 24.9 1.0 CG N:ASP369 3.2 27.9 1.0 OE2 O:GLU198 3.5 28.3 1.0 O O:SER197 3.8 27.4 1.0 CB N:ASP369 4.0 25.1 1.0 O N:HOH897 4.0 26.1 1.0 CG N:HIS368 4.2 23.1 1.0 OD1 N:ASP369 4.2 27.5 1.0 ND1 N:HIS368 4.2 23.6 1.0 O N:HOH816 4.2 24.9 1.0 OD2 O:ASP173 4.3 28.8 1.0 OG1 N:THR294 4.3 26.1 1.0 OD1 O:ASP173 4.4 25.7 1.0 CG O:GLU198 4.4 28.9 1.0 O N:HOH715 4.4 26.9 1.0 O N:HOH870 4.5 23.3 1.0 O N:HOH837 4.6 26.0 1.0 CB O:GLU198 4.6 24.3 1.0 O O:HOH535 4.7 40.6 1.0 CG O:ASP173 4.7 28.4 1.0 CA O:GLU198 4.8 28.3 1.0 O N:HOH823 5.0 39.1 1.0 CA N:ASP369 5.0 25.8 1.0 C O:SER197 5.0 32.0 1.0

A.Shimada, F.Hara, K.Shinzawa-Itoh, N.Kanehisa, E.Yamashita, K.Muramoto, T.Tsukihara, S.Yoshikawa. Critical Roles of the Cub Site in Efficient Proton Pumping As Revealed By Crystal Structures of Mammalian Cytochrome C Oxidase Catalytic Intermediates J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X