Magnesium in PDB 5b1a: Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 5b1a was solved by N.Yano, K.Muramoto, A.Shimada, S.Takemura, J.Baba, H.Fujisawa, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	181.938, 204.400, 177.896, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 17.2

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

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

The binding sites of Magnesium atom in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution (pdb code 5b1a). 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 Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 5b1a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the 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 the Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:20.0 occ:1.00 OD1 A:ASP369 2.0 21.4 1.0 O B:HOH486 2.1 22.8 1.0 OE1 B:GLU198 2.1 23.4 1.0 NE2 A:HIS368 2.1 19.8 1.0 O B:HOH447 2.1 23.4 1.0 O B:HOH521 2.1 21.8 1.0 CD B:GLU198 3.0 23.6 1.0 CD2 A:HIS368 3.1 20.7 1.0 CE1 A:HIS368 3.1 19.7 1.0 CG A:ASP369 3.2 21.1 1.0 OE2 B:GLU198 3.3 23.9 1.0 O B:SER197 3.9 19.8 1.0 CB A:ASP369 4.0 20.5 1.0 O A:HOH902 4.0 22.8 1.0 OD1 B:ASP173 4.2 20.8 1.0 CG A:HIS368 4.2 19.4 1.0 O A:HOH811 4.3 21.9 1.0 OD2 A:ASP369 4.3 22.9 1.0 O B:HOH492 4.3 23.2 0.4 ND1 A:HIS368 4.3 19.3 1.0 OD2 B:ASP173 4.3 21.9 1.0 OG1 A:THR294 4.3 22.0 1.0 CG B:GLU198 4.4 20.5 1.0 O B:HOH570 4.5 22.4 0.6 O A:HOH793 4.5 23.3 1.0 O A:HOH859 4.6 21.3 1.0 O A:HOH733 4.6 21.9 1.0 CB B:GLU198 4.6 19.6 1.0 CG B:ASP173 4.7 20.9 1.0 CA B:GLU198 4.9 19.1 1.0 C B:SER197 5.0 19.4 1.0

Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the 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 the Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg604 b:25.4 occ:1.00 OD1 N:ASP369 2.0 26.3 1.0 NE2 N:HIS368 2.1 22.6 1.0 OE1 O:GLU198 2.1 29.3 1.0 O O:HOH479 2.1 27.6 1.0 O O:HOH548 2.1 26.8 1.0 O O:HOH439 2.2 28.4 1.0 CD2 N:HIS368 3.0 23.5 1.0 CD O:GLU198 3.1 27.9 1.0 CE1 N:HIS368 3.1 22.9 1.0 CG N:ASP369 3.2 26.3 1.0 OE2 O:GLU198 3.3 30.0 1.0 O O:SER197 3.9 25.6 1.0 CB N:ASP369 4.0 24.5 1.0 O N:HOH911 4.0 27.7 1.0 CG N:HIS368 4.2 22.8 1.0 ND1 N:HIS368 4.3 23.5 1.0 OD2 N:ASP369 4.3 27.2 1.0 O N:HOH792 4.3 25.6 1.0 OD1 O:ASP173 4.3 25.5 1.0 OD2 O:ASP173 4.3 27.4 1.0 OG1 N:THR294 4.4 25.5 1.0 O O:HOH509 4.4 26.7 0.4 CG O:GLU198 4.4 24.7 1.0 O N:HOH721 4.5 26.6 1.0 O N:HOH867 4.5 25.2 1.0 O N:HOH803 4.6 26.6 1.0 O O:HOH564 4.6 27.4 0.6 CB O:GLU198 4.6 25.3 1.0 CG O:ASP173 4.7 25.5 1.0 CA O:GLU198 4.9 24.8 1.0

N.Yano, K.Muramoto, A.Shimada, S.Takemura, J.Baba, H.Fujisawa, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, 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