Sodium in PDB 3ag2: Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 100 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 100 K:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 100 K, PDB code: 3ag2 was solved by K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, 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 (°)	182.834, 206.933, 178.090, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.3

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 100 K 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 in the Carbon Monoxide-Bound Fully Reduced State at 100 K (pdb code 3ag2). 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 Carbon Monoxide-Bound Fully Reduced State at 100 K, PDB code: 3ag2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-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 Carbon Monoxide-Bound Fully Reduced State at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na519 b:30.7 occ:1.00 O A:HOH2258 2.2 25.9 1.0 OE1 A:GLU40 2.3 30.9 1.0 O A:GLY45 2.3 34.5 1.0 O A:GLU40 2.3 27.2 1.0 O A:SER441 2.3 29.1 1.0 CD A:GLU40 3.2 32.5 1.0 C A:GLU40 3.3 25.2 1.0 O A:HOH2563 3.5 36.3 1.0 C A:GLY45 3.5 34.6 1.0 CG A:GLU40 3.5 25.9 1.0 C A:SER441 3.6 28.1 1.0 O A:HOH2691 3.8 32.0 1.0 O A:GLN43 3.9 27.3 1.0 CA A:ASP442 3.9 25.5 1.0 CB A:ASP442 4.0 26.6 1.0 CG A:ASP442 4.0 30.1 1.0 CA A:THR46 4.0 35.2 1.0 N A:ASP442 4.2 27.6 1.0 CA A:GLU40 4.2 24.2 1.0 OD2 A:ASP442 4.2 26.2 1.0 CA A:LEU41 4.2 22.7 1.0 N A:THR46 4.2 33.8 1.0 N A:LEU41 4.3 24.6 1.0 OE2 A:GLU40 4.3 31.8 1.0 N A:GLY45 4.5 28.6 1.0 N A:LEU47 4.5 36.0 1.0 CB A:GLU40 4.5 22.8 1.0 CA A:GLY45 4.6 30.0 1.0 CD2 A:LEU41 4.6 25.5 1.0 C A:THR46 4.7 37.3 1.0 CA A:SER441 4.7 28.8 1.0 OD1 A:ASP442 4.8 27.2 1.0 C A:PRO44 5.0 27.2 1.0

Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-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 Carbon Monoxide-Bound Fully Reduced State at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ N:Na519 b:36.5 occ:1.00 O N:HOH3258 2.1 34.0 1.0 OE1 N:GLU40 2.3 38.3 1.0 O N:GLY45 2.3 38.1 1.0 O N:GLU40 2.3 34.2 1.0 O N:SER441 2.3 35.6 1.0 CD N:GLU40 3.2 35.9 1.0 O N:HOH3563 3.4 46.0 1.0 C N:GLU40 3.4 32.6 1.0 C N:GLY45 3.5 37.7 1.0 C N:SER441 3.5 34.3 1.0 CG N:GLU40 3.6 34.5 1.0 CA N:THR46 3.9 42.0 1.0 O N:GLN43 3.9 36.8 1.0 CA N:ASP442 3.9 33.6 1.0 CB N:ASP442 4.1 32.6 1.0 OD2 N:ASP442 4.1 32.7 1.0 CG N:ASP442 4.1 34.4 1.0 O N:HOH3691 4.2 46.7 1.0 N N:THR46 4.2 40.1 1.0 N N:ASP442 4.2 34.8 1.0 CA N:GLU40 4.3 31.2 1.0 N N:LEU41 4.3 30.1 1.0 OE2 N:GLU40 4.4 39.5 1.0 CA N:LEU41 4.4 31.3 1.0 N N:GLY45 4.4 35.1 1.0 CB N:GLU40 4.5 30.6 1.0 N N:LEU47 4.5 43.8 1.0 C N:THR46 4.6 43.7 1.0 CA N:GLY45 4.6 35.7 1.0 CA N:SER441 4.7 35.3 1.0 OD1 N:ASP442 4.7 34.3 1.0 CD2 N:LEU41 4.8 32.6 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: ISSN 0027-8424
PubMed: 20385840
DOI: 10.1073/PNAS.0910410107