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

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

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eik 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 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	183.321, 206.525, 178.159, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 22.8

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

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

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

Magnesium binding site 1 out of 2 in the Cadmium 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 Cadmium 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:19.6 occ:1.00 OD1 A:ASP369 2.1 21.0 1.0 OE1 B:GLU198 2.1 22.6 1.0 NE2 A:HIS368 2.2 17.2 1.0 O B:HOH2032 2.3 20.5 1.0 O B:HOH2031 2.3 20.5 1.0 O B:HOH2033 2.3 20.4 1.0 CE1 A:HIS368 3.2 16.5 1.0 CD2 A:HIS368 3.2 17.8 1.0 CG A:ASP369 3.3 21.0 1.0 CD B:GLU198 3.3 25.3 1.0 O B:SER197 3.8 21.4 1.0 O A:HOH2035 3.9 21.2 1.0 CB A:ASP369 4.1 19.8 1.0 OE2 B:GLU198 4.1 27.9 1.0 OD2 A:ASP369 4.2 22.3 1.0 O A:HOH2010 4.3 20.3 1.0 OD2 B:ASP173 4.3 26.1 1.0 ND1 A:HIS368 4.3 17.4 1.0 CG A:HIS368 4.3 18.0 1.0 CG B:GLU198 4.4 19.0 1.0 OD1 B:ASP173 4.4 23.6 1.0 CB B:GLU198 4.4 17.0 1.0 O A:HOH2038 4.4 16.7 1.0 OG1 A:THR294 4.6 18.0 1.0 O A:HOH2054 4.6 33.3 1.0 CA B:GLU198 4.7 19.9 1.0 O A:HOH2023 4.7 16.2 1.0 O B:HOH2055 4.7 36.9 1.0 O A:HOH2020 4.7 18.4 1.0 CG B:ASP173 4.8 28.9 1.0 C B:SER197 4.9 23.8 1.0

Magnesium binding site 2 out of 2 in the Cadmium 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 Cadmium 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:27.0 occ:1.00 OD1 N:ASP369 2.1 31.9 1.0 OE1 O:GLU198 2.1 31.1 1.0 NE2 N:HIS368 2.2 21.8 1.0 O O:HOH3031 2.3 28.2 1.0 O O:HOH3032 2.3 25.6 1.0 O O:HOH3033 2.3 30.0 1.0 CE1 N:HIS368 3.2 18.6 1.0 CD2 N:HIS368 3.2 20.0 1.0 CG N:ASP369 3.3 30.2 1.0 CD O:GLU198 3.3 30.2 1.0 O O:SER197 3.9 26.2 1.0 O N:HOH3035 4.0 26.9 1.0 OD2 O:ASP173 4.0 32.0 1.0 OE2 O:GLU198 4.1 31.2 1.0 CB N:ASP369 4.1 28.6 1.0 OD2 N:ASP369 4.2 31.2 1.0 ND1 N:HIS368 4.3 21.0 1.0 CG N:HIS368 4.4 19.7 1.0 CG O:GLU198 4.4 24.2 1.0 O N:HOH3038 4.4 21.8 1.0 O N:HOH3010 4.4 22.5 1.0 OD1 O:ASP173 4.4 28.8 1.0 CB O:GLU198 4.5 21.8 1.0 OG1 N:THR294 4.5 22.5 1.0 O N:HOH3023 4.6 19.3 1.0 O O:HOH3055 4.6 40.5 1.0 CG O:ASP173 4.7 30.9 1.0 O N:HOH3054 4.7 34.8 1.0 O N:HOH3020 4.7 24.6 1.0 CA O:GLU198 4.7 23.8 1.0 C O:SER197 5.0 26.6 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