Sodium in PDB 3ag4: Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K

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

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K, PDB code: 3ag4 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 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	183.364, 206.648, 178.137, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.9

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-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 Cyanide Ion-Bound Fully Reduced State at 100 K (pdb code 3ag4). 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 Cyanide Ion-Bound Fully Reduced State at 100 K, PDB code: 3ag4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-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 Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na519 b:30.3 occ:1.00 O A:HOH2258 2.2 28.5 1.0 O A:SER441 2.3 28.6 1.0 O A:GLU40 2.3 29.8 1.0 OE1 A:GLU40 2.3 34.4 1.0 O A:GLY45 2.3 33.9 1.0 CD A:GLU40 3.2 33.6 1.0 C A:GLU40 3.4 29.4 1.0 O A:HOH2563 3.5 32.9 1.0 C A:GLY45 3.5 34.9 1.0 CG A:GLU40 3.5 27.1 1.0 C A:SER441 3.6 27.2 1.0 O A:HOH2691 3.9 35.2 1.0 O A:GLN43 3.9 29.5 1.0 CA A:THR46 4.0 39.5 1.0 CA A:ASP442 4.0 28.2 1.0 CB A:ASP442 4.0 29.6 1.0 CG A:ASP442 4.1 32.9 1.0 OD2 A:ASP442 4.1 30.8 1.0 N A:THR46 4.2 36.4 1.0 CA A:GLU40 4.2 29.8 1.0 N A:LEU41 4.2 27.8 1.0 OE2 A:GLU40 4.3 34.2 1.0 N A:ASP442 4.3 28.5 1.0 CA A:LEU41 4.4 27.1 1.0 N A:GLY45 4.4 30.6 1.0 N A:LEU47 4.4 39.5 1.0 CB A:GLU40 4.5 28.6 1.0 CA A:GLY45 4.6 33.1 1.0 C A:THR46 4.6 40.6 1.0 CA A:SER441 4.7 27.7 1.0 OD1 A:ASP442 4.7 32.2 1.0 CD2 A:LEU41 4.8 22.9 1.0 O A:HOH2693 5.0 41.7 1.0

Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-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 Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ N:Na519 b:40.0 occ:1.00 O N:HOH3258 2.2 35.8 1.0 O N:GLY45 2.2 44.1 1.0 OE1 N:GLU40 2.2 42.3 1.0 O N:GLU40 2.3 37.7 1.0 O N:SER441 2.3 39.2 1.0 CD N:GLU40 3.2 44.6 1.0 O N:HOH3563 3.3 47.0 1.0 C N:GLY45 3.4 45.8 1.0 C N:GLU40 3.4 37.7 1.0 C N:SER441 3.6 39.5 1.0 CG N:GLU40 3.6 40.4 1.0 O N:GLN43 3.9 42.1 1.0 CA N:THR46 3.9 48.2 1.0 O N:HOH3691 4.0 50.4 1.0 CA N:ASP442 4.0 38.7 1.0 OD2 N:ASP442 4.1 39.2 1.0 N N:THR46 4.1 46.5 1.0 CG N:ASP442 4.1 39.3 1.0 CB N:ASP442 4.1 37.8 1.0 CA N:GLU40 4.2 37.3 1.0 N N:ASP442 4.3 39.4 1.0 N N:LEU41 4.3 36.0 1.0 N N:GLY45 4.3 43.5 1.0 OE2 N:GLU40 4.3 45.7 1.0 N N:LEU47 4.4 50.0 1.0 CA N:LEU41 4.4 37.1 1.0 CA N:GLY45 4.5 43.9 1.0 CB N:GLU40 4.5 37.3 1.0 C N:THR46 4.6 49.7 1.0 OD1 N:ASP442 4.7 36.9 1.0 CA N:SER441 4.8 40.6 1.0 CD2 N:LEU41 4.9 32.0 1.0 C N:PRO44 4.9 43.1 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