Sodium in PDB 3ag1: Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K, PDB code: 3ag1 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 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	189.493, 210.887, 178.301, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19.2

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 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 280 K (pdb code 3ag1). 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 280 K, PDB code: 3ag1:
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 280 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 280 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na519 b:47.7 occ:1.00 O A:HOH2258 2.2 42.1 1.0 O A:GLY45 2.3 52.3 1.0 OE1 A:GLU40 2.3 50.9 1.0 O A:SER441 2.3 44.2 1.0 O A:GLU40 2.3 44.6 1.0 CD A:GLU40 3.2 50.7 1.0 C A:GLU40 3.4 41.5 1.0 O A:HOH2563 3.4 58.9 1.0 C A:GLY45 3.5 49.7 1.0 C A:SER441 3.5 41.7 1.0 CG A:GLU40 3.6 42.7 1.0 CA A:ASP442 3.9 42.4 1.0 CA A:THR46 3.9 53.6 1.0 CB A:ASP442 4.0 41.1 1.0 O A:GLN43 4.0 45.5 1.0 O A:HOH2691 4.0 60.1 1.0 OD2 A:ASP442 4.1 46.0 1.0 N A:THR46 4.1 49.5 1.0 CG A:ASP442 4.1 45.0 1.0 N A:ASP442 4.2 41.0 1.0 N A:LEU41 4.3 40.4 1.0 CA A:GLU40 4.3 42.1 1.0 CA A:LEU41 4.3 39.0 1.0 OE2 A:GLU40 4.4 48.5 1.0 CD2 A:LEU41 4.5 36.7 1.0 CB A:GLU40 4.5 41.9 1.0 N A:GLY45 4.6 45.5 1.0 N A:LEU47 4.6 53.6 1.0 CA A:GLY45 4.6 46.8 1.0 C A:THR46 4.7 54.4 1.0 CA A:SER441 4.7 43.3 1.0 OD1 A:ASP442 5.0 45.2 1.0 CB A:SER441 5.0 42.6 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 280 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 280 K within 5.0Å range: probe atom residue distance (Å) B Occ N:Na519 b:58.7 occ:1.00 O N:HOH3258 2.1 58.4 1.0 O N:GLU40 2.3 54.6 1.0 O N:GLY45 2.3 65.3 1.0 O N:SER441 2.3 51.9 1.0 OE1 N:GLU40 2.3 60.5 1.0 CD N:GLU40 3.2 61.0 1.0 C N:GLU40 3.4 54.0 1.0 O N:HOH3563 3.4 63.7 1.0 C N:SER441 3.5 51.8 1.0 C N:GLY45 3.5 65.1 1.0 CG N:GLU40 3.5 53.4 1.0 CA N:ASP442 3.8 53.1 1.0 CB N:ASP442 4.0 53.6 1.0 O N:GLN43 4.0 59.8 1.0 OD2 N:ASP442 4.0 53.6 1.0 CA N:THR46 4.1 67.5 1.0 N N:ASP442 4.1 50.8 1.0 CG N:ASP442 4.2 53.8 1.0 N N:THR46 4.2 66.3 1.0 CA N:GLU40 4.2 53.8 1.0 N N:LEU41 4.3 54.6 1.0 O N:HOH3691 4.3 89.4 1.0 CA N:LEU41 4.3 53.5 1.0 OE2 N:GLU40 4.4 59.3 1.0 N N:LEU47 4.5 68.1 1.0 CB N:GLU40 4.5 53.6 1.0 N N:GLY45 4.5 61.3 1.0 CD2 N:LEU41 4.5 50.7 1.0 C N:THR46 4.6 68.1 1.0 CA N:GLY45 4.6 63.5 1.0 CA N:SER441 4.7 53.0 1.0 O N:HOH3693 4.9 1.0 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