Magnesium in PDB 7y44: Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution

All present enzymatic activity of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution:
7.1.1.9;

The structure of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution, PDB code: 7y44 was solved by T.Tsukihara, K.Hirata, H.Ago, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.31 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	182.6, 204.51, 178.29, 90, 90, 90
R / Rfree (%)	18.5 / 22.7

The structure of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution (pdb code 7y44). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution, PDB code: 7y44:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:13.4 occ:1.00 OD2 A:ASP369 2.0 12.7 1.0 OE1 B:GLU198 2.1 18.1 1.0 O B:HOH511 2.1 15.1 1.0 O B:HOH432 2.1 17.2 1.0 O B:HOH461 2.2 16.9 1.0 NE2 A:HIS368 2.2 14.8 1.0 CD B:GLU198 3.1 24.9 1.0 CD2 A:HIS368 3.1 17.9 1.0 CE1 A:HIS368 3.2 27.9 1.0 CG A:ASP369 3.2 21.2 1.0 OE2 B:GLU198 3.5 20.0 1.0 O B:SER197 3.8 18.2 1.0 O A:HOH872 3.9 16.0 1.0 CB A:ASP369 3.9 20.1 1.0 OD1 A:ASP369 4.2 17.0 1.0 OD1 B:ASP173 4.2 20.4 1.0 ND1 A:HIS368 4.3 15.0 1.0 CG A:HIS368 4.3 15.4 1.0 O A:HOH809 4.3 14.7 1.0 OD2 B:ASP173 4.3 17.2 1.0 CG B:GLU198 4.4 14.4 1.0 OG1 A:THR294 4.5 19.0 1.0 O A:HOH710 4.5 15.2 1.0 O B:HOH516 4.5 35.0 1.0 O A:HOH880 4.5 18.8 1.0 O A:HOH897 4.6 24.0 1.0 CB B:GLU198 4.6 16.3 1.0 CG B:ASP173 4.7 15.4 1.0 CA B:GLU198 4.9 18.9 1.0 CA A:ASP369 5.0 17.9 1.0

Magnesium binding site 2 out of 2 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg604 b:16.6 occ:1.00 O O:HOH440 2.0 22.6 1.0 O O:HOH432 2.0 18.6 1.0 O O:HOH493 2.0 19.4 1.0 OE1 O:GLU198 2.1 25.0 1.0 OD2 N:ASP369 2.1 19.6 1.0 NE2 N:HIS368 2.2 20.4 1.0 CE1 N:HIS368 3.1 20.9 1.0 CD O:GLU198 3.1 30.9 1.0 CD2 N:HIS368 3.1 18.8 1.0 CG N:ASP369 3.3 27.7 1.0 OE2 O:GLU198 3.5 19.6 1.0 O O:SER197 3.9 23.5 1.0 CB N:ASP369 4.0 22.2 1.0 O N:HOH886 4.1 20.8 1.0 OD1 N:ASP369 4.2 24.5 1.0 ND1 N:HIS368 4.2 20.7 1.0 CG N:HIS368 4.3 21.4 1.0 O N:HOH793 4.3 16.0 1.0 OD2 O:ASP173 4.3 27.9 1.0 OD1 O:ASP173 4.4 23.9 1.0 OG1 N:THR294 4.4 22.8 1.0 O O:HOH497 4.4 38.2 1.0 CG O:GLU198 4.4 29.6 1.0 O N:HOH842 4.5 17.2 1.0 O N:HOH736 4.5 19.3 1.0 O N:HOH822 4.5 24.5 1.0 CB O:GLU198 4.7 23.4 1.0 CG O:ASP173 4.7 23.0 1.0 CA O:GLU198 4.9 20.6 1.0

K.Hirata, T.Tsukihara, H.Ago. Determination of Damage-Free Crystal Structure of An X-Ray-Sensitive Protein Using An Xfel Nature Methods V. 11 734 2014.
DOI: 10.1038/NMETH.2962