Sodium in PDB 1ocr: Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 1ocr was solved by T.Tsukihara, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	189.100, 210.500, 178.600, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 24.7

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb code 1ocr). 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 Fully Reduced State, PDB code: 1ocr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


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 Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na519 b:22.7 occ:1.00 O A:SER441 2.4 25.9 1.0 O A:GLY45 2.4 29.4 1.0 OE2 A:GLU40 2.4 26.4 1.0 O A:GLU40 2.5 25.2 1.0 CD A:GLU40 3.3 29.4 1.0 C A:GLU40 3.4 20.9 1.0 CG A:GLU40 3.5 22.8 1.0 C A:SER441 3.6 21.6 1.0 C A:GLY45 3.6 24.7 1.0 CA A:THR46 3.9 33.1 1.0 O A:GLN43 3.9 26.6 1.0 CA A:ASP442 4.0 17.6 1.0 N A:LEU41 4.2 16.0 1.0 N A:THR46 4.2 24.5 1.0 CB A:ASP442 4.2 17.4 1.0 N A:ASP442 4.2 20.4 1.0 CA A:GLU40 4.2 21.8 1.0 CA A:LEU41 4.2 12.6 1.0 CG A:ASP442 4.3 17.6 1.0 CB A:GLU40 4.4 22.4 1.0 OD1 A:ASP442 4.4 23.7 1.0 N A:GLY45 4.5 22.0 1.0 OE1 A:GLU40 4.5 29.1 1.0 CD2 A:LEU41 4.5 20.6 1.0 N A:LEU47 4.6 41.2 1.0 CA A:SER441 4.7 21.9 1.0 C A:THR46 4.7 39.4 1.0 CA A:GLY45 4.7 23.9 1.0 OD2 A:ASP442 4.7 28.5 1.0 CB A:THR46 4.9 35.1 1.0

Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


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 Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ N:Na519 b:40.3 occ:1.00 O N:GLU40 2.4 38.8 1.0 O N:SER441 2.4 32.4 1.0 O N:GLY45 2.4 46.1 1.0 OE2 N:GLU40 2.5 45.2 1.0 C N:GLU40 3.3 36.1 1.0 CD N:GLU40 3.4 45.8 1.0 CG N:GLU40 3.5 37.9 1.0 C N:GLY45 3.6 43.3 1.0 C N:SER441 3.6 31.5 1.0 O N:GLN43 3.9 44.0 1.0 CA N:THR46 3.9 48.1 1.0 CA N:ASP442 4.0 33.5 1.0 N N:LEU41 4.2 32.7 1.0 N N:THR46 4.2 44.0 1.0 CA N:LEU41 4.2 32.1 1.0 CA N:GLU40 4.2 34.0 1.0 CB N:ASP442 4.3 40.4 1.0 CG N:ASP442 4.3 40.7 1.0 N N:ASP442 4.3 31.1 1.0 CB N:GLU40 4.4 35.1 1.0 OD1 N:ASP442 4.5 41.3 1.0 N N:GLY45 4.5 39.4 1.0 OE1 N:GLU40 4.6 44.6 1.0 CD2 N:LEU41 4.6 34.3 1.0 N N:LEU47 4.6 48.9 1.0 C N:THR46 4.7 49.0 1.0 OD2 N:ASP442 4.7 52.1 1.0 CA N:GLY45 4.7 39.4 1.0 CA N:SER441 4.7 32.9 1.0 CB N:THR46 4.9 51.8 1.0

S.Yoshikawa, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, E.Yamashita, N.Inoue, M.Yao, M.J.Fei, C.P.Libeu, T.Mizushima, H.Yamaguchi, T.Tomizaki, T.Tsukihara. Redox-Coupled Crystal Structural Changes in Bovine Heart Cytochrome C Oxidase. Science V. 280 1723 1998.
ISSN: ISSN 0036-8075
PubMed: 9624044
DOI: 10.1126/SCIENCE.280.5370.1723