Sodium in PDB 8ijn: Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K:
7.1.1.9;

The structure of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K, PDB code: 8ijn was solved by T.Tsukihara, A.Shimada, K.Muramoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.37 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	182.289, 208.358, 177.916, 90, 90, 90
R / Rfree (%)	16.9 / 19.2

The structure of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Magnesium	(Mg)	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 Nitric Oxide-Bound Fully Reduced State at 100 K (pdb code 8ijn). 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 Nitric Oxide-Bound Fully Reduced State at 100 K, PDB code: 8ijn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K


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 Nitric Oxide-Bound Fully Reduced State at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:29.6 occ:1.00 O A:HOH872 2.2 28.6 1.0 OE1 A:GLU40 2.3 30.8 1.0 O A:GLY45 2.3 28.1 1.0 O A:SER441 2.4 27.1 1.0 O A:GLU40 2.4 28.9 1.0 CD A:GLU40 3.2 31.8 1.0 O A:HOH749 3.4 34.2 1.0 C A:GLU40 3.4 32.0 1.0 CG A:GLU40 3.5 24.9 1.0 C A:GLY45 3.5 32.0 1.0 C A:SER441 3.5 27.2 1.0 O A:HOH894 3.8 33.2 1.0 CB A:ASP442 3.9 25.9 1.0 CA A:ASP442 3.9 26.6 1.0 CA A:THR46 4.0 34.3 1.0 O A:GLN43 4.0 29.7 1.0 CG A:ASP442 4.1 29.0 1.0 OD2 A:ASP442 4.2 27.1 1.0 N A:ASP442 4.2 27.5 1.0 N A:THR46 4.2 30.6 1.0 N A:LEU41 4.3 23.2 1.0 CA A:GLU40 4.3 22.4 1.0 CA A:LEU41 4.3 29.5 1.0 OE2 A:GLU40 4.4 32.2 1.0 N A:LEU47 4.5 33.4 1.0 CB A:GLU40 4.5 24.3 1.0 N A:GLY45 4.5 27.3 1.0 C A:THR46 4.6 37.1 1.0 CA A:GLY45 4.6 31.3 1.0 CD2 A:LEU41 4.6 25.5 1.0 CA A:SER441 4.7 26.1 1.0 OD1 A:ASP442 4.7 28.6 1.0 O A:HOH714 5.0 34.3 1.0

Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K


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 Nitric Oxide-Bound Fully Reduced State at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ N:Na606 b:34.6 occ:1.00 O N:HOH824 2.2 33.2 1.0 O N:GLY45 2.3 41.2 1.0 OE1 N:GLU40 2.3 38.1 1.0 O N:GLU40 2.4 34.7 1.0 O N:SER441 2.4 33.6 1.0 CD N:GLU40 3.2 44.9 1.0 C N:GLU40 3.4 35.8 1.0 O N:HOH816 3.4 42.0 1.0 C N:GLY45 3.5 40.0 1.0 CG N:GLU40 3.5 32.8 1.0 C N:SER441 3.6 30.8 1.0 O N:HOH876 3.8 39.1 1.0 CA N:ASP442 4.0 35.4 1.0 O N:GLN43 4.0 39.3 1.0 CB N:ASP442 4.0 31.8 1.0 CA N:THR46 4.0 43.9 1.0 OD2 N:ASP442 4.1 36.0 1.0 CG N:ASP442 4.1 33.1 1.0 N N:ASP442 4.2 30.5 1.0 N N:THR46 4.2 37.9 1.0 CA N:GLU40 4.3 31.0 1.0 N N:LEU41 4.3 30.3 1.0 CA N:LEU41 4.4 29.4 1.0 OE2 N:GLU40 4.4 39.0 1.0 N N:GLY45 4.4 38.4 1.0 N N:LEU47 4.5 47.5 1.0 CB N:GLU40 4.5 30.9 1.0 CD2 N:LEU41 4.5 29.7 1.0 CA N:GLY45 4.6 37.2 1.0 C N:THR46 4.7 50.3 1.0 CA N:SER441 4.7 33.2 1.0 OD1 N:ASP442 4.8 35.5 1.0 C N:PRO44 5.0 33.8 1.0

K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, S.Yoshikawa. Bovine Cytochrome C Oxidase Structures Enable O2 Reduction with Minimization of Reactive Oxygens and Provide A Proton-Pumping Gate. Proc.Natl.Acad.Sci.Usa V. 107 7740 2010.
ISSN: ESSN 1091-6490
PubMed: 20385840
DOI: 10.1073/PNAS.0910410107