Magnesium in PDB 2dyr: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

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

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 2dyr was solved by K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, T.Kurauchi, T.Mizushima, 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 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	182.590, 205.140, 178.250, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 22.7

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State 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 at the Fully Oxidized State (pdb code 2dyr). 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 at the Fully Oxidized State, PDB code: 2dyr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State


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 at the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg518 b:20.7 occ:1.00 OD1 A:ASP369 2.1 21.4 1.0 OE1 B:GLU198 2.1 26.4 1.0 NE2 A:HIS368 2.2 17.7 1.0 O B:HOH2032 2.3 20.4 1.0 O B:HOH2031 2.3 23.5 1.0 O B:HOH2033 2.3 24.7 1.0 CE1 A:HIS368 3.2 17.7 1.0 CD2 A:HIS368 3.2 17.7 1.0 CG A:ASP369 3.2 25.4 1.0 CD B:GLU198 3.3 29.7 1.0 O B:SER197 3.8 21.0 1.0 O A:HOH2035 3.9 22.7 1.0 OE2 B:GLU198 3.9 34.8 1.0 CB A:ASP369 4.0 18.1 1.0 OD2 A:ASP369 4.2 25.0 1.0 ND1 A:HIS368 4.3 16.7 1.0 OD2 B:ASP173 4.3 26.2 1.0 O A:HOH2038 4.3 18.4 1.0 OD1 B:ASP173 4.3 22.4 1.0 CG A:HIS368 4.3 15.7 1.0 O A:HOH2010 4.3 19.4 1.0 CG B:GLU198 4.4 22.4 1.0 CB B:GLU198 4.6 20.5 1.0 OG1 A:THR294 4.6 21.7 1.0 O A:HOH2023 4.6 19.8 1.0 O A:HOH2020 4.7 21.8 1.0 CG B:ASP173 4.7 25.4 1.0 CA B:GLU198 4.8 20.3 1.0 O B:HOH2055 4.9 39.6 1.0 C B:SER197 4.9 22.1 1.0

Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State


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 at the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg1518 b:26.7 occ:1.00 OE1 O:GLU198 2.1 33.3 1.0 OD1 N:ASP369 2.1 29.0 1.0 NE2 N:HIS368 2.2 22.7 1.0 O O:HOH3031 2.3 28.4 1.0 O O:HOH3032 2.3 26.4 1.0 O O:HOH3033 2.4 28.2 1.0 CD O:GLU198 3.1 33.0 1.0 CD2 N:HIS368 3.2 22.3 1.0 CE1 N:HIS368 3.2 20.8 1.0 CG N:ASP369 3.3 30.7 1.0 OE2 O:GLU198 3.6 31.1 1.0 O O:SER197 3.9 28.2 1.0 O N:HOH3035 3.9 28.0 1.0 CB N:ASP369 4.0 25.0 1.0 OD2 N:ASP369 4.2 30.1 1.0 OD2 O:ASP173 4.2 33.9 1.0 ND1 N:HIS368 4.3 20.9 1.0 CG N:HIS368 4.3 19.9 1.0 O N:HOH3038 4.3 20.6 1.0 CG O:GLU198 4.4 26.9 1.0 O N:HOH3010 4.4 20.9 1.0 OD1 O:ASP173 4.5 28.2 1.0 OG1 N:THR294 4.5 23.6 1.0 O N:HOH3023 4.6 23.3 1.0 CB O:GLU198 4.6 23.6 1.0 O N:HOH3020 4.7 23.4 1.0 CG O:ASP173 4.8 32.1 1.0 CA O:GLU198 4.9 23.3 1.0 O O:HOH3055 4.9 40.5 1.0 C O:SER197 5.0 27.1 1.0

K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, H.Terada, T.Kurauchi, Y.Tadehara, A.Yamasaki, T.Sugimura, S.Kurono, K.Tsujimoto, T.Mizushima, E.Yamashita, T.Tsukihara, S.Yoshikawa. Structures and Physiological Roles of 13 Integral Lipids of Bovine Heart Cytochrome C Oxidase Embo J. V. 26 1713 2007.
ISSN: ISSN 0261-4189
PubMed: 17332748
DOI: 10.1038/SJ.EMBOJ.7601618