Magnesium in PDB 3ag4: Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K, PDB code: 3ag4 was solved by K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, 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 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	183.364, 206.648, 178.137, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.9

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K 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 Cyanide Ion-Bound Fully Reduced State at 100 K (pdb code 3ag4). 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 Cyanide Ion-Bound Fully Reduced State at 100 K, PDB code: 3ag4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg518 b:25.2 occ:1.00 OE1 B:GLU198 2.1 29.9 1.0 OD1 A:ASP369 2.1 25.6 1.0 NE2 A:HIS368 2.1 25.3 1.0 O B:HOH2267 2.3 25.1 1.0 O B:HOH2266 2.3 28.0 1.0 O B:HOH2268 2.3 25.8 1.0 CD2 A:HIS368 3.1 26.3 1.0 CE1 A:HIS368 3.1 28.0 1.0 CG A:ASP369 3.3 28.3 1.0 CD B:GLU198 3.3 30.6 1.0 O B:SER197 3.8 25.3 1.0 O A:HOH2278 3.9 25.1 1.0 CB A:ASP369 4.0 27.2 1.0 OE2 B:GLU198 4.0 34.7 1.0 O A:HOH2116 4.1 23.8 1.0 OD2 A:ASP369 4.2 29.8 1.0 ND1 A:HIS368 4.2 24.6 1.0 CG A:HIS368 4.3 27.0 1.0 O B:HOH2475 4.3 25.9 1.0 OD2 B:ASP173 4.3 26.8 1.0 O A:HOH2297 4.3 25.3 1.0 OD1 B:ASP173 4.4 30.1 1.0 CG B:GLU198 4.4 22.8 1.0 CB B:GLU198 4.4 25.1 1.0 OG1 A:THR294 4.6 26.7 1.0 O A:HOH2209 4.6 28.0 1.0 O A:HOH2219 4.6 27.2 1.0 CA B:GLU198 4.7 26.9 1.0 CG B:ASP173 4.8 27.8 1.0 C B:SER197 4.9 27.8 1.0 O B:HOH2480 4.9 36.1 1.0

Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg518 b:33.6 occ:1.00 NE2 N:HIS368 2.1 34.8 1.0 OD1 N:ASP369 2.1 32.9 1.0 OE1 O:GLU198 2.2 36.2 1.0 O O:HOH3266 2.3 32.4 1.0 O O:HOH3267 2.3 34.4 1.0 O O:HOH3268 2.3 34.5 1.0 CD2 N:HIS368 3.1 31.5 1.0 CE1 N:HIS368 3.1 39.6 1.0 CG N:ASP369 3.3 37.3 1.0 CD O:GLU198 3.4 35.6 1.0 O O:SER197 3.8 35.5 1.0 O N:HOH3278 3.9 38.9 1.0 CB N:ASP369 4.1 34.0 1.0 OE2 O:GLU198 4.1 39.8 1.0 O N:HOH3116 4.2 31.4 1.0 ND1 N:HIS368 4.2 38.2 1.0 OD2 N:ASP369 4.2 33.0 1.0 CG N:HIS368 4.2 34.2 1.0 OD2 O:ASP173 4.3 38.5 1.0 O N:HOH3297 4.3 38.3 1.0 CG O:GLU198 4.4 31.2 1.0 O N:HOH3475 4.4 40.4 1.0 CB O:GLU198 4.4 33.9 1.0 OD1 O:ASP173 4.5 37.8 1.0 OG1 N:THR294 4.6 35.4 1.0 O O:HOH3480 4.6 44.6 1.0 O N:HOH3219 4.6 30.9 1.0 O N:HOH3209 4.7 32.6 1.0 CG O:ASP173 4.8 37.5 1.0 CA O:GLU198 4.8 34.9 1.0 C O:SER197 4.9 36.8 1.0

K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, S.Yoshikawa. Bovine Cytochrome C Oxidase Structures Enable O2 Reduction with Minimization of Reactive Oxygens and Provide A Proton-Pumping Gate Proc.Natl.Acad.Sci.Usa V. 107 7740 2010.
ISSN: ISSN 0027-8424
PubMed: 20385840
DOI: 10.1073/PNAS.0910410107