Magnesium in PDB 7d5w: Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution:
7.1.1.9;

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution, PDB code: 7d5w 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)	39.92 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	181.435, 203.092, 177.794, 90, 90, 90
R / Rfree (%)	15.4 / 18.4

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 O at 1.84 Angstrom Resolution (pdb code 7d5w). 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 O at 1.84 Angstrom Resolution, PDB code: 7d5w:
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 O at 1.84 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 O at 1.84 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:18.8 occ:1.00 O B:HOH425 1.9 21.0 1.0 OE1 B:GLU198 2.1 30.2 1.0 OD1 A:ASP369 2.1 23.2 1.0 O B:HOH426 2.1 22.4 1.0 NE2 A:HIS368 2.1 22.3 1.0 O B:HOH535 2.1 21.3 1.0 CE1 A:HIS368 3.1 22.3 1.0 CD B:GLU198 3.1 26.8 1.0 CD2 A:HIS368 3.2 22.6 1.0 CG A:ASP369 3.2 21.3 1.0 OE2 B:GLU198 3.5 25.9 1.0 O B:SER197 3.9 21.6 1.0 CB A:ASP369 4.0 21.5 1.0 O A:HOH904 4.0 21.8 1.0 ND1 A:HIS368 4.2 19.0 1.0 O A:HOH825 4.2 21.9 1.0 OD2 A:ASP369 4.2 22.6 1.0 CG A:HIS368 4.3 20.4 1.0 OD2 B:ASP173 4.3 25.6 1.0 OD1 B:ASP173 4.3 23.1 1.0 OG1 A:THR294 4.4 24.7 1.0 O A:HOH713 4.4 22.3 1.0 CG B:GLU198 4.4 18.9 1.0 O A:HOH859 4.6 21.5 1.0 O A:HOH819 4.6 24.5 1.0 O B:HOH536 4.6 38.9 1.0 CB B:GLU198 4.6 21.3 1.0 CG B:ASP173 4.7 24.4 1.0 CA B:GLU198 4.9 25.1 1.0

Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 O at 1.84 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg605 b:21.5 occ:1.00 O O:HOH421 2.0 24.8 1.0 O N:HOH904 2.0 22.7 1.0 OD1 N:ASP369 2.0 25.5 1.0 OE1 O:GLU198 2.0 35.3 1.0 NE2 N:HIS368 2.2 25.4 1.0 O O:HOH476 2.4 28.9 1.0 CD2 N:HIS368 3.1 26.9 1.0 CD O:GLU198 3.1 31.9 1.0 CE1 N:HIS368 3.2 24.1 1.0 CG N:ASP369 3.2 26.3 1.0 OE2 O:GLU198 3.5 28.4 1.0 O N:HOH888 3.9 24.4 1.0 O O:SER197 3.9 26.6 1.0 CB N:ASP369 4.0 27.6 1.0 OD2 N:ASP369 4.2 26.7 1.0 CG N:HIS368 4.3 23.0 1.0 ND1 N:HIS368 4.3 22.2 1.0 O N:HOH766 4.3 22.8 1.0 O N:HOH709 4.3 24.9 1.0 CG O:GLU198 4.4 26.9 1.0 OD2 O:ASP173 4.4 31.5 1.0 OG1 N:THR294 4.4 27.9 1.0 OD1 O:ASP173 4.4 26.2 1.0 O N:HOH828 4.5 25.1 1.0 O N:HOH853 4.5 23.1 1.0 CB O:GLU198 4.6 25.4 1.0 O N:HOH832 4.7 35.7 1.0 O O:HOH508 4.7 52.2 1.0 CG O:ASP173 4.8 31.3 1.0 CA O:GLU198 4.8 28.9 1.0 CA N:ASP369 5.0 31.1 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