Magnesium in PDB 7d5x: Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution:
7.1.1.9;

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution, PDB code: 7d5x 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)	39.70 / 1.74
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	181.767, 203.304, 177.566, 90, 90, 90
R / Rfree (%)	15.6 / 18.4

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution (pdb code 7d5x). 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, IO10, at 1.74 Angstrom Resolution, PDB code: 7d5x:
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, IO10, at 1.74 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, IO10, at 1.74 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:20.2 occ:1.00 OD1 A:ASP369 2.0 24.1 1.0 OE1 B:GLU198 2.1 26.3 1.0 O B:HOH475 2.1 23.0 1.0 O B:HOH438 2.1 24.8 1.0 NE2 A:HIS368 2.1 22.3 1.0 O B:HOH519 2.2 23.2 1.0 CE1 A:HIS368 3.1 23.0 1.0 CD2 A:HIS368 3.1 23.8 1.0 CG A:ASP369 3.2 26.5 1.0 CD B:GLU198 3.3 27.2 1.0 O B:SER197 3.9 23.7 1.0 O A:HOH882 3.9 21.2 1.0 CB A:ASP369 4.0 21.8 1.0 OE2 B:GLU198 4.0 27.7 1.0 OD2 A:ASP369 4.1 25.0 1.0 O A:HOH705 4.2 21.8 1.0 ND1 A:HIS368 4.2 22.2 1.0 CG A:HIS368 4.3 22.0 1.0 O A:HOH819 4.3 23.4 1.0 OD2 B:ASP173 4.4 25.2 1.0 CG B:GLU198 4.4 23.7 1.0 OD1 B:ASP173 4.4 25.3 1.0 O B:HOH434 4.4 31.0 1.0 CB B:GLU198 4.5 25.6 1.0 O A:HOH811 4.5 22.1 1.0 OG1 A:THR294 4.5 26.4 1.0 O A:HOH855 4.6 21.8 1.0 O B:HOH419 4.7 38.4 1.0 CA B:GLU198 4.7 26.8 1.0 CG B:ASP173 4.8 25.1 1.0 C B:SER197 5.0 24.6 1.0 CA A:ASP369 5.0 21.7 1.0

Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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, IO10, at 1.74 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg604 b:23.8 occ:1.00 OD1 N:ASP369 2.0 27.5 1.0 O O:HOH470 2.0 27.7 1.0 OE1 O:GLU198 2.1 32.9 1.0 O O:HOH430 2.1 26.0 1.0 O O:HOH484 2.1 24.8 1.0 NE2 N:HIS368 2.2 26.1 1.0 CE1 N:HIS368 3.1 26.3 1.0 CD2 N:HIS368 3.2 25.7 1.0 CG N:ASP369 3.2 26.4 1.0 CD O:GLU198 3.3 29.1 1.0 O O:SER197 3.9 27.2 1.0 O N:HOH892 4.0 23.4 1.0 CB N:ASP369 4.0 28.4 1.0 OE2 O:GLU198 4.1 31.6 1.0 O N:HOH702 4.2 25.2 1.0 OD2 N:ASP369 4.2 28.0 1.0 ND1 N:HIS368 4.2 25.4 1.0 O N:HOH817 4.2 24.2 1.0 CG N:HIS368 4.3 26.4 1.0 OD2 O:ASP173 4.3 28.9 1.0 O O:HOH419 4.3 29.5 1.0 CG O:GLU198 4.4 26.3 1.0 CB O:GLU198 4.4 25.3 1.0 OD1 O:ASP173 4.5 26.7 1.0 O N:HOH803 4.5 26.8 1.0 OG1 N:THR294 4.5 27.5 1.0 O N:HOH841 4.6 23.4 1.0 CA O:GLU198 4.7 28.5 1.0 CG O:ASP173 4.8 25.7 1.0 O O:HOH415 4.9 40.5 1.0 C O:SER197 5.0 30.4 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