Magnesium in PDB 2dys: Bovine Heart Cytochrome C Oxidase Modified By Dccd

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase Modified By Dccd:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase Modified By Dccd, PDB code: 2dys 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 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	184.130, 207.232, 178.242, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.2

The structure of Bovine Heart Cytochrome C Oxidase Modified By Dccd 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 Modified By Dccd (pdb code 2dys). 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 Modified By Dccd, PDB code: 2dys:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


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 Modified By Dccd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:23.8 occ:1.00 OE1 B:GLU198 2.1 29.8 1.0 OD1 A:ASP369 2.1 18.5 1.0 NE2 A:HIS368 2.2 23.1 1.0 O B:HOH2007 2.3 17.8 1.0 O A:HOH721 2.3 23.9 1.0 O B:HOH2008 2.4 22.1 1.0 CD B:GLU198 3.2 27.9 1.0 CD2 A:HIS368 3.2 29.5 1.0 CE1 A:HIS368 3.2 24.7 1.0 CG A:ASP369 3.3 24.6 1.0 OE2 B:GLU198 3.7 34.0 1.0 O B:SER197 3.8 20.7 1.0 OD1 B:ASP173 4.1 29.8 1.0 CB A:ASP369 4.1 20.6 1.0 OD2 A:ASP369 4.1 16.3 1.0 O A:HOH723 4.1 20.4 1.0 OD2 B:ASP173 4.2 34.7 1.0 O A:HOH726 4.3 19.7 1.0 ND1 A:HIS368 4.3 24.4 1.0 CG B:GLU198 4.4 24.8 1.0 CG A:HIS368 4.4 30.3 1.0 OG1 A:THR294 4.5 24.5 1.0 O A:HOH708 4.5 12.7 1.0 CG B:ASP173 4.5 38.6 1.0 CB B:GLU198 4.6 22.6 1.0 O A:HOH716 4.7 21.3 1.0 O B:HOH2012 4.7 35.9 1.0 O A:HOH713 4.8 18.7 1.0 CA B:GLU198 4.9 23.5 1.0 C B:SER197 5.0 25.0 1.0

Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


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 Modified By Dccd within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg602 b:35.7 occ:1.00 OE1 O:GLU198 2.0 35.2 1.0 OD1 N:ASP369 2.1 35.0 1.0 NE2 N:HIS368 2.2 32.6 1.0 O O:HOH410 2.3 35.1 1.0 O O:HOH409 2.3 27.7 1.0 O O:HOH408 2.4 30.4 1.0 CD2 N:HIS368 3.2 29.0 1.0 CE1 N:HIS368 3.2 32.5 1.0 CG N:ASP369 3.3 32.0 1.0 CD O:GLU198 3.3 38.7 1.0 O O:SER197 3.8 31.1 1.0 CB N:ASP369 4.0 32.1 1.0 OE2 O:GLU198 4.0 36.1 1.0 O N:HOH721 4.2 35.2 1.0 OD2 O:ASP173 4.2 43.0 1.0 OD2 N:ASP369 4.2 32.2 1.0 O N:HOH724 4.3 24.5 1.0 ND1 N:HIS368 4.3 25.8 1.0 CG N:HIS368 4.3 26.7 1.0 CG O:GLU198 4.3 34.9 1.0 OD1 O:ASP173 4.4 39.7 1.0 OG1 N:THR294 4.5 31.6 1.0 CB O:GLU198 4.5 27.7 1.0 O N:HOH707 4.6 29.1 1.0 CG O:ASP173 4.7 42.3 1.0 O N:HOH715 4.7 28.1 1.0 O N:HOH712 4.8 23.1 1.0 O O:HOH413 4.8 57.4 1.0 CA O:GLU198 4.8 27.2 1.0 C O:SER197 5.0 30.7 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