Magnesium in PDB 2eim: Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

All present enzymatic activity of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State:
1.9.3.1;

The structure of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eim was solved by K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, 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 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	183.909, 206.721, 178.337, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.6

The structure of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb code 2eim). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eim:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg518 b:23.3 occ:1.00 OD1 A:ASP369 2.0 21.1 1.0 OE1 B:GLU198 2.1 35.0 1.0 NE2 A:HIS368 2.2 20.8 1.0 O B:HOH2032 2.3 25.7 1.0 O B:HOH2031 2.3 17.8 1.0 O B:HOH2033 2.4 16.0 1.0 CE1 A:HIS368 3.0 25.1 1.0 CD B:GLU198 3.1 32.0 1.0 CG A:ASP369 3.2 27.6 1.0 CD2 A:HIS368 3.3 32.7 1.0 OE2 B:GLU198 3.5 31.4 1.0 O B:SER197 3.7 39.0 1.0 CB A:ASP369 3.8 18.7 1.0 O A:HOH2035 3.9 25.9 1.0 OD2 A:ASP369 4.1 26.2 1.0 O A:HOH2010 4.2 20.5 1.0 ND1 A:HIS368 4.2 23.0 1.0 CG B:GLU198 4.3 34.3 1.0 CG A:HIS368 4.4 27.4 1.0 O A:HOH2038 4.4 23.8 1.0 OD1 B:ASP173 4.4 34.9 1.0 O B:HOH2055 4.4 38.5 1.0 CB B:GLU198 4.5 27.4 1.0 OD2 B:ASP173 4.6 40.5 1.0 O A:HOH2020 4.6 37.6 1.0 OG1 A:THR294 4.6 25.9 1.0 CA B:GLU198 4.7 31.2 1.0 O A:HOH2023 4.8 12.6 1.0 C B:SER197 4.8 41.0 1.0 CG B:ASP173 4.9 46.8 1.0 O A:HOH2054 4.9 47.5 1.0 CA A:ASP369 4.9 17.8 1.0

Magnesium binding site 2 out of 2 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg1518 b:25.3 occ:1.00 OE1 O:GLU198 2.0 41.8 1.0 OD1 N:ASP369 2.1 38.6 1.0 NE2 N:HIS368 2.2 34.3 1.0 O O:HOH3032 2.3 22.8 1.0 O O:HOH3031 2.3 16.4 1.0 O O:HOH3033 2.4 30.1 1.0 CE1 N:HIS368 3.0 33.4 1.0 CG N:ASP369 3.2 42.1 1.0 CD O:GLU198 3.2 48.7 1.0 CD2 N:HIS368 3.4 27.3 1.0 O O:SER197 3.7 47.0 1.0 OE2 O:GLU198 3.8 47.9 1.0 CB N:ASP369 3.8 38.1 1.0 O N:HOH3035 3.8 36.0 1.0 O N:HOH3010 4.2 27.8 1.0 ND1 N:HIS368 4.2 27.5 1.0 OD2 N:ASP369 4.2 46.7 1.0 O N:HOH3038 4.4 19.6 1.0 CG O:GLU198 4.4 40.7 1.0 CG N:HIS368 4.5 26.1 1.0 O O:HOH3055 4.5 35.8 1.0 CB O:GLU198 4.5 41.6 1.0 OD1 O:ASP173 4.5 43.1 1.0 O N:HOH3020 4.6 54.5 1.0 CA O:GLU198 4.6 45.3 1.0 O N:HOH3023 4.7 23.4 1.0 OD2 O:ASP173 4.7 56.2 1.0 OG1 N:THR294 4.8 44.4 1.0 C O:SER197 4.8 46.2 1.0 CA N:ASP369 4.9 35.1 1.0 O N:HOH3054 4.9 39.8 1.0

K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa. A Histidine Residue Acting As A Controlling Site For Dioxygen Reduction and Proton Pumping By Cytochrome C Oxidase Proc.Natl.Acad.Sci.Usa V. 104 7881 2007.
ISSN: ISSN 0027-8424
PubMed: 17470809
DOI: 10.1073/PNAS.0610031104