Sodium in PDB 7ypy: Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution:
7.1.1.9;

The structure of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 7ypy 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)	39.96 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	181.938, 204.4, 177.896, 90, 90, 90
R / Rfree (%)	15.9 / 17.7

The structure of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution (pdb code 7ypy). 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 Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 7ypy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution


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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:22.6 occ:1.00 O A:GLY45 2.2 27.0 1.0 OE1 A:GLU40 2.3 25.2 1.0 O A:HOH839 2.3 23.6 1.0 O A:SER441 2.3 22.4 1.0 O A:GLU40 2.4 23.3 1.0 CD A:GLU40 3.2 25.5 1.0 CG A:GLU40 3.4 22.6 1.0 C A:GLU40 3.4 22.2 1.0 C A:GLY45 3.4 25.3 1.0 O A:HOH837 3.5 34.0 1.0 C A:SER441 3.6 21.1 1.0 O A:GLN43 4.0 24.0 1.0 CA A:ASP442 4.0 24.1 1.0 CB A:ASP442 4.0 21.4 1.0 CA A:THR46 4.1 25.9 1.0 OD1 A:ASP442 4.1 25.9 1.0 CG A:ASP442 4.1 23.1 1.0 N A:THR46 4.2 27.6 1.0 CA A:GLU40 4.2 21.3 1.0 N A:ASP442 4.3 21.5 1.0 N A:LEU41 4.3 22.4 1.0 N A:LEU47 4.4 28.0 1.0 CA A:LEU41 4.4 21.1 1.0 OE2 A:GLU40 4.4 27.2 1.0 CB A:GLU40 4.4 20.5 1.0 N A:GLY45 4.5 24.9 1.0 CA A:GLY45 4.6 24.8 1.0 CD2 A:LEU41 4.6 22.6 1.0 C A:THR46 4.7 27.2 1.0 CA A:SER441 4.7 22.1 1.0 CB A:SER441 4.9 21.9 1.0 OD2 A:ASP442 5.0 24.4 1.0

Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution


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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ N:Na605 b:28.7 occ:1.00 O N:GLY45 2.2 32.9 1.0 O N:HOH858 2.3 28.0 1.0 OE1 N:GLU40 2.3 31.8 1.0 O N:SER441 2.3 27.0 1.0 O N:GLU40 2.4 30.7 1.0 CD N:GLU40 3.2 39.0 1.0 C N:GLU40 3.4 31.0 1.0 CG N:GLU40 3.4 29.5 1.0 C N:GLY45 3.4 35.1 1.0 O N:HOH854 3.5 37.3 1.0 C N:SER441 3.5 28.2 1.0 CA N:ASP442 4.0 30.0 1.0 O N:GLN43 4.0 31.3 1.0 CB N:ASP442 4.0 28.4 1.0 OD1 N:ASP442 4.1 32.3 1.0 CA N:THR46 4.1 34.2 1.0 CG N:ASP442 4.1 28.9 1.0 N N:THR46 4.2 36.1 1.0 N N:ASP442 4.2 29.9 1.0 CA N:GLU40 4.2 27.7 1.0 N N:LEU41 4.2 27.9 1.0 CA N:LEU41 4.3 30.3 1.0 CB N:GLU40 4.4 27.6 1.0 N N:GLY45 4.4 32.5 1.0 OE2 N:GLU40 4.4 32.7 1.0 N N:LEU47 4.4 34.2 1.0 CA N:GLY45 4.5 32.1 1.0 CD2 N:LEU41 4.6 29.3 1.0 CA N:SER441 4.6 27.8 1.0 C N:THR46 4.7 35.2 1.0 OD2 N:ASP442 4.9 31.0 1.0 CB N:SER441 5.0 29.4 1.0

N.Yano, K.Muramoto, A.Shimada, K.Shinzawa-Itoh, T.Tsukihara, S.Yoshikawa. The MG2+-Containing Water Cluster of Mammalian Cytochrome C Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle. J. Biol. Chem. V. 291 23882 2016.
ISSN: ESSN 1083-351X
PubMed: 27605664
DOI: 10.1074/JBC.M115.711770