Sodium in PDB 2zxw: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset):
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset), PDB code: 2zxw was solved by H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, K.Hirata, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	184.156, 207.621, 178.247, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23.3

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset) 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 at the Fully Oxidized State (1-S X- Ray Exposure Dataset) (pdb code 2zxw). 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 at the Fully Oxidized State (1-S X- Ray Exposure Dataset), PDB code: 2zxw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset)


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 at the Fully Oxidized State (1-S X- Ray Exposure Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na519 b:16.4 occ:1.00 O A:SER441 2.2 16.6 1.0 OE1 A:GLU40 2.2 15.1 1.0 O A:GLU40 2.3 17.1 1.0 O A:GLY45 2.3 18.2 1.0 O A:HOH2026 2.4 16.5 1.0 CD A:GLU40 3.2 18.6 1.0 C A:GLU40 3.4 16.6 1.0 C A:SER441 3.4 17.4 1.0 C A:GLY45 3.5 17.7 1.0 CG A:GLU40 3.5 15.2 1.0 CA A:ASP442 3.9 16.6 1.0 CB A:ASP442 4.0 16.9 1.0 O A:GLN43 4.0 18.9 1.0 OD2 A:ASP442 4.0 24.5 1.0 CG A:ASP442 4.1 18.3 1.0 N A:ASP442 4.1 16.6 1.0 CA A:THR46 4.2 19.9 1.0 N A:THR46 4.2 18.2 1.0 CA A:GLU40 4.2 16.6 1.0 N A:LEU41 4.2 16.0 1.0 CA A:LEU41 4.3 14.9 1.0 OE2 A:GLU40 4.4 21.6 1.0 CB A:GLU40 4.4 17.2 1.0 N A:GLY45 4.5 14.6 1.0 N A:LEU47 4.5 22.0 1.0 CA A:GLY45 4.5 16.6 1.0 CA A:SER441 4.6 17.4 1.0 CD2 A:LEU41 4.6 16.4 1.0 OD1 A:ASP442 4.7 21.4 1.0 C A:THR46 4.8 21.2 1.0 CB A:SER441 4.9 17.9 1.0

Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset)


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 at the Fully Oxidized State (1-S X- Ray Exposure Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ N:Na1519 b:24.1 occ:1.00 OE1 N:GLU40 2.2 23.5 1.0 O N:SER441 2.3 23.0 1.0 O N:GLY45 2.3 26.6 1.0 O N:GLU40 2.3 26.9 1.0 O N:HOH3026 2.4 22.2 1.0 CD N:GLU40 3.2 25.2 1.0 C N:GLU40 3.4 26.8 1.0 CG N:GLU40 3.4 25.9 1.0 C N:SER441 3.4 23.7 1.0 C N:GLY45 3.4 26.6 1.0 CA N:ASP442 4.0 22.6 1.0 CA N:THR46 4.0 28.6 1.0 CB N:ASP442 4.1 23.4 1.0 O N:GLN43 4.1 26.5 1.0 N N:THR46 4.1 27.3 1.0 N N:ASP442 4.2 22.4 1.0 CA N:GLU40 4.2 26.6 1.0 CG N:ASP442 4.2 24.3 1.0 OD2 N:ASP442 4.2 28.7 1.0 N N:LEU41 4.3 27.4 1.0 N N:LEU47 4.3 32.6 1.0 CB N:GLU40 4.3 26.6 1.0 OE2 N:GLU40 4.4 28.1 1.0 CA N:LEU41 4.4 27.5 1.0 N N:GLY45 4.5 27.0 1.0 CA N:GLY45 4.5 26.7 1.0 CA N:SER441 4.6 25.4 1.0 C N:THR46 4.6 30.6 1.0 CD2 N:LEU41 4.7 25.5 1.0 CB N:SER441 4.8 26.3 1.0 OD1 N:ASP442 4.9 18.7 1.0

H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, K.Hirata, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa. A Peroxide Bridge Between Fe and Cu Ions in the O2 Reduction Site of Fully Oxidized Cytochrome C Oxidase Could Suppress the Proton Pump Proc.Natl.Acad.Sci.Usa V. 106 2165 2009.
ISSN: ISSN 0027-8424
PubMed: 19164527
DOI: 10.1073/PNAS.0806391106