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

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

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 2eil 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 (°)	183.379, 205.898, 178.182, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.1

The structure of Cadmium Ion Binding Structure 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
Cadmium	(Cd)	3 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 Oxidized State (pdb code 2eil). 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 Oxidized State, PDB code: 2eil:
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 Oxidized 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 Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na519 b:41.2 occ:1.00 OE1 A:GLU40 2.2 42.9 1.0 O A:GLU40 2.3 30.8 1.0 O A:SER441 2.4 28.2 1.0 O A:GLY45 2.4 45.6 1.0 O A:HOH2026 2.5 47.4 1.0 O A:HOH2060 2.8 37.7 1.0 CD A:GLU40 3.2 38.3 1.0 C A:GLU40 3.4 25.2 1.0 CG A:GLU40 3.5 33.2 1.0 C A:SER441 3.6 26.1 1.0 C A:GLY45 3.6 42.2 1.0 O A:GLN43 3.7 31.5 1.0 CA A:ASP442 4.1 25.1 1.0 CA A:GLU40 4.2 26.9 1.0 CA A:THR46 4.2 49.3 1.0 N A:LEU41 4.2 23.6 1.0 CB A:ASP442 4.3 28.2 1.0 OE2 A:GLU40 4.3 38.9 1.0 OD2 A:ASP442 4.3 32.8 1.0 N A:ASP442 4.3 25.8 1.0 CG A:ASP442 4.3 31.7 1.0 CA A:LEU41 4.3 20.9 1.0 N A:THR46 4.4 45.2 1.0 N A:LEU47 4.4 56.9 1.0 N A:GLY45 4.4 26.6 1.0 CB A:GLU40 4.4 27.3 1.0 CD2 A:LEU41 4.6 21.7 1.0 CA A:GLY45 4.7 34.0 1.0 CA A:SER441 4.7 24.4 1.0 C A:THR46 4.8 56.0 1.0 C A:PRO44 4.9 29.0 1.0 C A:GLN43 4.9 34.1 1.0 OD1 A:ASP442 4.9 33.8 1.0

Sodium binding site 2 out of 2 in the Cadmium Ion Binding Structure 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 Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ N:Na1519 b:47.4 occ:1.00 OE1 N:GLU40 2.2 47.8 1.0 O N:GLU40 2.3 38.9 1.0 O N:SER441 2.4 36.8 1.0 O N:GLY45 2.4 51.0 1.0 O N:HOH3026 2.6 54.0 1.0 O N:HOH3060 2.9 47.6 1.0 CD N:GLU40 3.0 43.5 1.0 CG N:GLU40 3.3 42.0 1.0 C N:GLU40 3.3 35.4 1.0 C N:SER441 3.6 35.1 1.0 C N:GLY45 3.6 48.5 1.0 O N:GLN43 3.9 36.2 1.0 CA N:THR46 4.0 56.0 1.0 CA N:GLU40 4.1 35.8 1.0 OE2 N:GLU40 4.2 43.1 1.0 CA N:ASP442 4.2 32.2 1.0 N N:LEU47 4.2 62.4 1.0 N N:LEU41 4.3 34.9 1.0 N N:THR46 4.3 51.6 1.0 CB N:GLU40 4.3 37.2 1.0 N N:ASP442 4.3 33.5 1.0 CB N:ASP442 4.4 35.9 1.0 OD2 N:ASP442 4.4 39.5 1.0 CG N:ASP442 4.4 40.2 1.0 CA N:LEU41 4.5 32.2 1.0 N N:GLY45 4.5 43.0 1.0 C N:THR46 4.6 60.5 1.0 CA N:SER441 4.7 36.3 1.0 CA N:GLY45 4.7 44.1 1.0 CD2 N:LEU41 4.8 27.2 1.0 C N:PRO44 5.0 42.0 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