Sodium in PDB 2eik: Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

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

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eik was solved by K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, 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 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	183.321, 206.525, 178.159, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 22.8

The structure of Cadmium Ion Binding 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
Cadmium	(Cd)	6 atoms
Iron	(Fe)	4 atoms
Copper	(Cu)	6 atoms

The binding sites of Sodium atom in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb code 2eik). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eik:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cadmium Ion Binding Structure of 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 Cadmium Ion Binding Structure 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:28.4 occ:1.00 OE1 A:GLU40 2.2 27.7 1.0 O A:GLU40 2.3 23.6 1.0 O A:SER441 2.3 28.1 1.0 O A:GLY45 2.4 31.3 1.0 O A:HOH2026 2.5 22.3 1.0 CD A:GLU40 3.1 29.6 1.0 C A:GLU40 3.3 21.8 1.0 CG A:GLU40 3.4 26.1 1.0 O A:HOH2060 3.4 37.2 1.0 C A:SER441 3.5 24.6 1.0 C A:GLY45 3.6 28.5 1.0 CA A:ASP442 4.0 22.3 1.0 O A:GLN43 4.0 27.5 1.0 CA A:THR46 4.1 31.5 1.0 O A:HOH2069 4.1 40.1 1.0 CA A:GLU40 4.2 22.3 1.0 N A:LEU41 4.2 19.3 1.0 CB A:ASP442 4.2 21.9 1.0 CG A:ASP442 4.2 26.6 1.0 OE2 A:GLU40 4.2 28.9 1.0 N A:ASP442 4.2 23.7 1.0 N A:THR46 4.3 29.0 1.0 OD2 A:ASP442 4.3 23.8 1.0 CA A:LEU41 4.3 18.0 1.0 CB A:GLU40 4.4 21.5 1.0 N A:LEU47 4.5 37.1 1.0 CD2 A:LEU41 4.6 19.4 1.0 N A:GLY45 4.6 24.8 1.0 CA A:SER441 4.7 22.3 1.0 C A:THR46 4.7 36.0 1.0 CA A:GLY45 4.7 25.0 1.0 OD1 A:ASP442 4.8 25.6 1.0

Sodium binding site 2 out of 2 in the Cadmium Ion Binding Structure of 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 Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ N:Na1519 b:37.3 occ:1.00 OE1 N:GLU40 2.2 41.0 1.0 O N:GLU40 2.3 29.5 1.0 O N:SER441 2.3 33.5 1.0 O N:GLY45 2.4 38.9 1.0 O N:HOH3026 2.6 34.6 1.0 CD N:GLU40 3.1 41.1 1.0 CG N:GLU40 3.3 37.1 1.0 C N:GLU40 3.3 29.5 1.0 O N:HOH3060 3.4 40.7 1.0 C N:SER441 3.5 30.7 1.0 C N:GLY45 3.5 37.0 1.0 CA N:THR46 3.9 42.5 1.0 O N:HOH3069 4.1 49.1 1.0 CA N:ASP442 4.1 28.8 1.0 CA N:GLU40 4.2 28.2 1.0 N N:THR46 4.2 37.8 1.0 O N:GLN43 4.2 35.5 1.0 OD2 N:ASP442 4.2 34.6 1.0 CB N:ASP442 4.2 32.9 1.0 N N:LEU41 4.2 30.8 1.0 OE2 N:GLU40 4.3 42.6 1.0 N N:ASP442 4.3 28.5 1.0 CB N:GLU40 4.3 32.0 1.0 CG N:ASP442 4.3 35.6 1.0 N N:LEU47 4.4 45.4 1.0 CA N:LEU41 4.4 30.4 1.0 C N:THR46 4.5 45.3 1.0 CA N:SER441 4.6 31.6 1.0 N N:GLY45 4.7 35.7 1.0 CA N:GLY45 4.7 35.6 1.0 CD2 N:LEU41 4.8 27.5 1.0 CB N:THR46 4.9 45.6 1.0 CB N:SER441 5.0 32.6 1.0

K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa. A Histidine Residue Acting As A Controlling Site For Dioxygen Reduction and Proton Pumping By Cytochrome C Oxidase Proc.Natl.Acad.Sci.Usa V. 104 7881 2007.
ISSN: ISSN 0027-8424
PubMed: 17470809
DOI: 10.1073/PNAS.0610031104