Sodium in PDB 7coh: Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

All present enzymatic activity of Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State:
7.1.1.9;

The structure of Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 7coh was solved by K.Shinzawa-Itoh, K.Muramoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	181.998, 204.193, 177.759, 90, 90, 90
R / Rfree (%)	14.9 / 17

The structure of Dimeric Form of Bovine Heart Cytochrome C Oxidase in 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 Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State (pdb code 7coh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 7coh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in 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 Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na519 b:21.8 occ:1.00 O A:GLY45 2.3 25.1 1.0 OE1 A:GLU40 2.3 23.4 1.0 O A:HOH1020 2.3 22.7 1.0 O A:SER441 2.3 21.2 1.0 O A:GLU40 2.4 21.4 1.0 CD A:GLU40 3.2 21.8 1.0 O A:HOH1042 3.4 32.5 1.0 C A:GLY45 3.5 22.8 1.0 CG A:GLU40 3.5 21.8 1.0 C A:GLU40 3.5 20.2 1.0 C A:SER441 3.5 20.4 1.0 O A:GLN43 4.0 22.1 1.0 CA A:ASP442 4.0 21.5 1.0 CB A:ASP442 4.1 20.6 1.0 CA A:THR46 4.1 24.5 1.0 N A:THR46 4.2 24.0 1.0 OD1 A:ASP442 4.2 23.4 1.0 CG A:ASP442 4.2 22.9 1.0 CA A:GLU40 4.2 19.9 1.0 N A:ASP442 4.2 21.4 1.0 N A:LEU41 4.2 19.2 1.0 N A:LEU47 4.3 25.3 1.0 CB A:GLU40 4.4 20.4 1.0 OE2 A:GLU40 4.4 23.9 1.0 CA A:LEU41 4.4 19.5 1.0 N A:GLY45 4.5 22.7 1.0 CA A:GLY45 4.5 22.3 1.0 CA A:SER441 4.6 20.0 1.0 C A:THR46 4.7 25.2 1.0 CD2 A:LEU41 4.7 23.1 1.0 CB A:SER441 4.9 21.5 1.0 OD2 A:ASP442 4.9 23.9 1.0

Sodium binding site 2 out of 2 in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in 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 Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ N:Na519 b:28.0 occ:1.00 O N:GLY45 2.3 32.0 1.0 OE1 N:GLU40 2.3 31.5 1.0 O N:HOH2020 2.3 28.6 1.0 O N:SER441 2.3 26.6 1.0 O N:GLU40 2.4 30.1 1.0 CD N:GLU40 3.2 28.8 1.0 O N:HOH2042 3.4 40.8 1.0 C N:GLU40 3.4 28.1 1.0 C N:GLY45 3.4 29.3 1.0 CG N:GLU40 3.5 28.0 1.0 C N:SER441 3.5 27.9 1.0 CA N:ASP442 4.0 28.6 1.0 O N:GLN43 4.0 29.7 1.0 CB N:ASP442 4.0 28.0 1.0 CA N:THR46 4.1 31.0 1.0 OD1 N:ASP442 4.1 28.7 1.0 N N:THR46 4.1 30.9 1.0 CA N:GLU40 4.2 26.3 1.0 N N:ASP442 4.2 27.3 1.0 N N:LEU41 4.2 26.1 1.0 CG N:ASP442 4.2 31.2 1.0 CA N:LEU41 4.4 26.4 1.0 CB N:GLU40 4.4 26.0 1.0 OE2 N:GLU40 4.5 30.4 1.0 N N:LEU47 4.5 35.5 1.0 N N:GLY45 4.5 30.4 1.0 CA N:GLY45 4.5 28.7 1.0 CA N:SER441 4.6 25.6 1.0 CD2 N:LEU41 4.6 28.4 1.0 C N:THR46 4.7 35.2 1.0 CB N:SER441 4.9 29.1 1.0 OD2 N:ASP442 5.0 31.3 1.0

K.Shinzawa-Itoh, M.Hatanaka, K.Fujita, N.Yano, Y.Ogasawara, J.Iwata, E.Yamashita, T.Tsukihara, S.Yoshikawa, K.Muramoto. The 1.3-A Resolution Structure of Bovine Cytochrome C Oxidase Suggests A Dimerization Mechanism Biochim.Biophys.Acta 2021.
ISSN: ISSN 0006-3002
DOI: 10.1016/J.BBADVA.2021.100009