Sodium in PDB 2dyr: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

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

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 2dyr was solved by K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, T.Kurauchi, T.Mizushima, E.Yamashita, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	182.590, 205.140, 178.250, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 22.7

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized 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 at the Fully Oxidized State (pdb code 2dyr). 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 at the Fully Oxidized State, PDB code: 2dyr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized 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 at the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na519 b:27.3 occ:1.00 OE1 A:GLU40 2.2 25.1 1.0 O A:SER441 2.3 25.5 1.0 O A:GLU40 2.3 24.2 1.0 O A:GLY45 2.4 28.1 1.0 O A:HOH2026 2.5 23.4 1.0 CD A:GLU40 3.2 28.2 1.0 C A:GLU40 3.3 23.3 1.0 CG A:GLU40 3.5 27.2 1.0 O A:HOH2060 3.5 40.2 1.0 C A:SER441 3.5 24.2 1.0 C A:GLY45 3.5 26.4 1.0 CA A:ASP442 4.0 21.9 1.0 O A:GLN43 4.0 23.4 1.0 CA A:THR46 4.1 27.9 1.0 CB A:ASP442 4.1 22.8 1.0 OD2 A:ASP442 4.2 24.8 1.0 CA A:GLU40 4.2 24.3 1.0 N A:ASP442 4.2 21.5 1.0 N A:LEU41 4.2 20.1 1.0 N A:THR46 4.3 26.3 1.0 CG A:ASP442 4.3 25.1 1.0 OE2 A:GLU40 4.3 27.8 1.0 CA A:LEU41 4.3 19.8 1.0 CB A:GLU40 4.4 25.5 1.0 N A:LEU47 4.4 32.0 1.0 N A:GLY45 4.5 21.5 1.0 CD2 A:LEU41 4.6 21.3 1.0 CA A:GLY45 4.6 23.1 1.0 CA A:SER441 4.6 23.8 1.0 C A:THR46 4.7 32.1 1.0 CB A:SER441 5.0 23.3 1.0

Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized 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 at the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ N:Na1519 b:30.8 occ:1.00 OE1 N:GLU40 2.2 28.5 1.0 O N:SER441 2.3 28.0 1.0 O N:GLU40 2.3 28.7 1.0 O N:GLY45 2.4 34.2 1.0 O N:HOH3026 2.6 30.9 1.0 CD N:GLU40 3.1 27.4 1.0 C N:GLU40 3.3 26.9 1.0 CG N:GLU40 3.4 28.6 1.0 O N:HOH3060 3.4 40.2 1.0 C N:SER441 3.5 27.3 1.0 C N:GLY45 3.5 32.0 1.0 CA N:THR46 4.0 33.2 1.0 CA N:ASP442 4.1 26.4 1.0 CA N:GLU40 4.1 26.8 1.0 O N:GLN43 4.1 29.4 1.0 CB N:ASP442 4.2 31.4 1.0 N N:THR46 4.2 32.1 1.0 N N:LEU41 4.2 25.4 1.0 N N:ASP442 4.2 27.0 1.0 OE2 N:GLU40 4.3 30.5 1.0 OD2 N:ASP442 4.3 34.0 1.0 N N:LEU47 4.3 37.0 1.0 CB N:GLU40 4.3 27.4 1.0 CG N:ASP442 4.4 35.1 1.0 CA N:LEU41 4.4 24.8 1.0 N N:GLY45 4.6 29.7 1.0 CA N:SER441 4.6 28.2 1.0 C N:THR46 4.6 35.5 1.0 CA N:GLY45 4.7 29.9 1.0 CD2 N:LEU41 4.7 24.4 1.0 CB N:SER441 4.9 31.0 1.0

K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, H.Terada, T.Kurauchi, Y.Tadehara, A.Yamasaki, T.Sugimura, S.Kurono, K.Tsujimoto, T.Mizushima, E.Yamashita, T.Tsukihara, S.Yoshikawa. Structures and Physiological Roles of 13 Integral Lipids of Bovine Heart Cytochrome C Oxidase Embo J. V. 26 1713 2007.
ISSN: ISSN 0261-4189
PubMed: 17332748
DOI: 10.1038/SJ.EMBOJ.7601618