Magnesium in PDB 1v55: Bovine Heart Cytochrome C Oxidase at the Fully Reduced State

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

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State, PDB code: 1v55 was solved by T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	183.060, 206.584, 178.298, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 23

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Reduced 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 Reduced State (pdb code 1v55). 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 Reduced State, PDB code: 1v55:
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 Reduced 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 Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3518 b:17.3 occ:1.00 OD1 A:ASP369 2.1 16.5 1.0 OE1 B:GLU198 2.1 18.7 1.0 NE2 A:HIS368 2.2 13.4 1.0 O B:HOH4093 2.3 20.5 1.0 O B:HOH4091 2.3 17.7 1.0 O B:HOH4092 2.3 15.6 1.0 CE1 A:HIS368 3.1 14.7 1.0 CG A:ASP369 3.3 16.7 1.0 CD2 A:HIS368 3.3 13.8 1.0 CD B:GLU198 3.3 23.4 1.0 O B:SER197 3.9 18.6 1.0 O A:HOH3547 3.9 17.3 1.0 CB A:ASP369 4.1 15.7 1.0 OE2 B:GLU198 4.1 24.2 1.0 OD2 A:ASP369 4.2 18.6 1.0 O A:HOH3532 4.2 17.9 1.0 ND1 A:HIS368 4.3 11.7 1.0 OD2 B:ASP173 4.3 21.1 1.0 O A:HOH3550 4.3 15.0 1.0 CG B:GLU198 4.4 17.6 1.0 CG A:HIS368 4.4 13.1 1.0 OD1 B:ASP173 4.4 19.9 1.0 CB B:GLU198 4.5 17.3 1.0 OG1 A:THR294 4.6 15.8 1.0 O A:HOH3541 4.6 16.3 1.0 O A:HOH3538 4.6 16.9 1.0 O A:HOH3561 4.6 29.0 1.0 O B:HOH4097 4.7 34.1 1.0 CA B:GLU198 4.7 17.6 1.0 CG B:ASP173 4.8 22.8 1.0 C B:SER197 5.0 21.0 1.0

Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at 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 Bovine Heart Cytochrome C Oxidase at the Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg4518 b:27.4 occ:1.00 OE1 O:GLU198 2.1 28.8 1.0 OD1 N:ASP369 2.1 29.9 1.0 NE2 N:HIS368 2.2 20.5 1.0 O O:HOH1032 2.3 24.1 1.0 O O:HOH1033 2.3 25.5 1.0 O O:HOH1031 2.4 26.2 1.0 CE1 N:HIS368 3.2 16.3 1.0 CD2 N:HIS368 3.2 17.5 1.0 CG N:ASP369 3.3 26.0 1.0 CD O:GLU198 3.3 28.0 1.0 O O:SER197 3.9 22.7 1.0 O N:HOH1035 3.9 24.6 1.0 CB N:ASP369 4.0 24.4 1.0 OE2 O:GLU198 4.0 27.7 1.0 O N:HOH1010 4.2 22.7 1.0 OD2 N:ASP369 4.2 28.1 1.0 ND1 N:HIS368 4.3 17.9 1.0 CG N:HIS368 4.3 16.4 1.0 OD2 O:ASP173 4.4 29.5 1.0 CG O:GLU198 4.4 23.2 1.0 O N:HOH1038 4.4 18.8 1.0 CB O:GLU198 4.5 21.1 1.0 OG1 N:THR294 4.6 23.0 1.0 O N:HOH1023 4.6 16.7 1.0 O N:HOH1020 4.6 20.9 1.0 OD1 O:ASP173 4.6 26.9 1.0 O N:HOH1054 4.7 30.0 1.0 CA O:GLU198 4.7 21.3 1.0 O O:HOH1055 4.8 36.3 1.0 CG O:ASP173 4.9 28.9 1.0 C O:SER197 5.0 23.0 1.0

T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa. The Low-Spin Heme of Cytochrome C Oxidase As the Driving Element of the Proton-Pumping Process. Proc.Natl.Acad.Sci.Usa V. 100 15304 2003.
ISSN: ISSN 0027-8424
PubMed: 14673090
DOI: 10.1073/PNAS.2635097100