Magnesium in PDB 2y69: Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen, PDB code: 2y69 was solved by V.R.I.Kaila, E.Oksanen, A.Goldman, M.I.Verkhovsky, D.Sundholm, M.Wikstrom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.15 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	183.697, 206.991, 178.251, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.5

The structure of Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen (pdb code 2y69). 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 Re-Refined with Molecular Oxygen, PDB code: 2y69:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1516 b:26.3 occ:1.00 OE1 B:GLU198 2.0 30.6 1.0 OD2 A:ASP369 2.0 26.2 1.0 O B:HOH2089 2.0 21.4 1.0 NE2 A:HIS368 2.1 28.4 1.0 O B:HOH2079 2.1 27.0 1.0 O B:HOH2090 2.2 29.1 1.0 CD2 A:HIS368 3.0 28.6 1.0 CE1 A:HIS368 3.1 26.8 1.0 CD B:GLU198 3.1 25.8 1.0 CG A:ASP369 3.2 26.1 1.0 OE2 B:GLU198 3.7 29.2 1.0 O B:SER197 3.9 25.5 1.0 CB A:ASP369 3.9 27.6 1.0 O A:HOH2075 4.0 29.9 1.0 OD1 B:ASP173 4.1 29.7 1.0 OD1 A:ASP369 4.1 25.2 1.0 CG A:HIS368 4.1 27.9 1.0 ND1 A:HIS368 4.2 23.3 1.0 OD2 B:ASP173 4.3 32.3 1.0 O A:HOH2061 4.4 25.6 1.0 OG1 A:THR294 4.4 25.8 1.0 CG B:GLU198 4.4 25.0 1.0 O A:HOH2068 4.5 27.4 1.0 O A:HOH2077 4.5 23.9 1.0 CG B:ASP173 4.6 31.3 1.0 CB B:GLU198 4.6 27.0 1.0 O A:HOH2066 4.7 28.4 1.0 CA B:GLU198 4.9 27.8 1.0 CA A:ASP369 5.0 27.5 1.0

Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg1516 b:35.6 occ:1.00 OE1 O:GLU198 1.9 43.6 1.0 OD2 N:ASP369 1.9 37.0 1.0 O O:HOH2080 2.0 32.4 1.0 O N:HOH2076 2.0 36.1 1.0 NE2 N:HIS368 2.1 29.9 1.0 O O:HOH2069 2.1 33.1 1.0 CD2 N:HIS368 3.0 33.0 1.0 CD O:GLU198 3.0 24.3 1.0 CE1 N:HIS368 3.1 23.4 1.0 CG N:ASP369 3.2 48.4 1.0 OE2 O:GLU198 3.5 38.7 1.0 O O:SER197 3.8 36.2 1.0 CB N:ASP369 4.0 38.9 1.0 O N:HOH2073 4.0 33.6 1.0 OD1 N:ASP369 4.1 33.7 1.0 CG N:HIS368 4.2 22.3 1.0 ND1 N:HIS368 4.2 28.9 1.0 OD2 O:ASP173 4.3 42.6 1.0 CG O:GLU198 4.4 30.5 1.0 OD1 O:ASP173 4.5 43.1 1.0 OG1 N:THR294 4.5 31.4 1.0 O N:HOH2016 4.5 31.6 1.0 O N:HOH2077 4.5 31.1 1.0 O N:HOH2064 4.6 29.0 1.0 CB O:GLU198 4.6 26.7 1.0 CG O:ASP173 4.7 39.9 1.0 O N:HOH2063 4.7 34.2 1.0 CA O:GLU198 4.9 37.6 1.0 C O:SER197 5.0 37.6 1.0 CA N:ASP369 5.0 42.0 1.0

V.R.I.Kaila, E.Oksanen, A.Goldman, D.A.Bloch, M.I.Verkhovsky, D.Sundholm, M.Wikstrom. A Combined Quantum Chemical and Crystallographic Study on the Oxidized Binuclear Center of Cytochrome C Oxidase. Biochim.Biophys.Acta V.1807 769 2011.
ISSN: ISSN 0006-3002
PubMed: 21211513
DOI: 10.1016/J.BBABIO.2010.12.016