Sodium in PDB 7vuw: Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K:
7.1.1.9;

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K, PDB code: 7vuw was solved by A.Shimada, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.92 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	182.076, 204.481, 177.68, 90, 90, 90
R / Rfree (%)	15.4 / 17.5

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K (pdb code 7vuw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K, PDB code: 7vuw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:23.2 occ:1.00 O A:HOH869 2.2 23.3 1.0 O A:GLY45 2.3 27.3 1.0 OE1 A:GLU40 2.3 25.2 1.0 O A:SER441 2.4 23.5 1.0 O A:GLU40 2.4 22.4 1.0 CD A:GLU40 3.2 25.9 1.0 O A:HOH730 3.4 32.9 1.0 C A:GLU40 3.4 23.2 1.0 CG A:GLU40 3.5 22.4 1.0 C A:GLY45 3.5 27.1 1.0 C A:SER441 3.6 24.7 1.0 O A:GLN43 4.0 24.9 1.0 CA A:ASP442 4.0 22.3 1.0 CB A:ASP442 4.0 22.3 1.0 CA A:THR46 4.1 25.7 1.0 OD2 A:ASP442 4.2 26.9 1.0 CG A:ASP442 4.2 24.6 1.0 N A:THR46 4.2 27.1 1.0 CA A:GLU40 4.2 23.5 1.0 N A:ASP442 4.2 21.7 1.0 N A:LEU41 4.3 23.1 1.0 N A:LEU47 4.4 26.5 1.0 CA A:LEU41 4.4 22.4 1.0 OE2 A:GLU40 4.4 27.1 1.0 N A:GLY45 4.4 25.2 1.0 CB A:GLU40 4.5 21.2 1.0 CA A:GLY45 4.6 27.4 1.0 CD2 A:LEU41 4.7 23.5 1.0 C A:THR46 4.7 28.2 1.0 CA A:SER441 4.7 23.5 1.0 OD1 A:ASP442 4.9 25.2 1.0 CB A:SER441 5.0 21.6 1.0

Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K within 5.0Å range: probe atom residue distance (Å) B Occ N:Na605 b:29.4 occ:1.00 O N:HOH873 2.2 28.7 1.0 O N:SER441 2.3 28.1 1.0 O N:GLY45 2.3 31.9 1.0 OE1 N:GLU40 2.3 31.6 1.0 O N:GLU40 2.4 33.0 1.0 CD N:GLU40 3.3 37.5 1.0 C N:GLU40 3.4 32.0 1.0 O N:HOH768 3.5 38.6 1.0 C N:GLY45 3.5 34.4 1.0 C N:SER441 3.5 29.9 1.0 CG N:GLU40 3.5 31.7 1.0 CA N:ASP442 4.0 28.4 1.0 O N:GLN43 4.0 32.0 1.0 CB N:ASP442 4.0 30.7 1.0 OD2 N:ASP442 4.1 32.1 1.0 CA N:THR46 4.1 32.7 1.0 CG N:ASP442 4.2 31.5 1.0 N N:ASP442 4.2 30.3 1.0 N N:THR46 4.2 35.4 1.0 N N:LEU41 4.2 29.2 1.0 CA N:GLU40 4.2 27.9 1.0 CA N:LEU41 4.3 31.9 1.0 CB N:GLU40 4.4 27.9 1.0 OE2 N:GLU40 4.4 32.6 1.0 N N:LEU47 4.5 36.2 1.0 N N:GLY45 4.5 31.2 1.0 CD2 N:LEU41 4.5 28.6 1.0 CA N:GLY45 4.6 33.4 1.0 CA N:SER441 4.6 28.1 1.0 C N:THR46 4.7 36.6 1.0 OD1 N:ASP442 4.9 32.9 1.0 CB N:SER441 5.0 31.7 1.0

A.Shimada, T.Tsukihara. Bovine Cytochrome C Oxidese in Cn-Bound Fully Oxidized State at 50 K To Be Published.