Sodium in PDB 3abl: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset):
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset), PDB code: 3abl was solved by H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, 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 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	184.137, 207.514, 178.173, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-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 (15-S X-Ray Exposure Dataset) (pdb code 3abl). 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 (15-S X-Ray Exposure Dataset), PDB code: 3abl:
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 (15-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 (15-S X-Ray Exposure Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na519 b:25.5 occ:1.00 O A:HOH2026 2.1 27.5 1.0 O A:SER441 2.3 23.3 1.0 OE1 A:GLU40 2.3 28.7 1.0 O A:GLU40 2.3 23.9 1.0 O A:GLY45 2.3 27.4 1.0 CD A:GLU40 3.2 29.9 1.0 O A:HOH2060 3.3 35.0 1.0 C A:GLU40 3.3 24.8 1.0 CG A:GLU40 3.5 23.3 1.0 C A:GLY45 3.5 29.1 1.0 C A:SER441 3.5 20.6 1.0 O A:GLN43 3.9 27.8 1.0 CA A:ASP442 4.0 24.9 1.0 CA A:THR46 4.1 30.0 1.0 CA A:GLU40 4.1 25.4 1.0 CB A:ASP442 4.1 26.5 1.0 OD2 A:ASP442 4.2 25.3 1.0 N A:THR46 4.2 27.1 1.0 CG A:ASP442 4.3 30.2 1.0 N A:ASP442 4.3 22.8 1.0 N A:LEU41 4.3 21.5 1.0 CA A:LEU41 4.3 22.8 1.0 N A:LEU47 4.3 29.6 1.0 OE2 A:GLU40 4.4 26.9 1.0 N A:GLY45 4.4 27.1 1.0 CB A:GLU40 4.4 21.3 1.0 CA A:GLY45 4.6 27.6 1.0 CA A:SER441 4.6 21.6 1.0 C A:THR46 4.7 30.4 1.0 CD2 A:LEU41 4.7 20.8 1.0 OD1 A:ASP442 5.0 27.3 1.0

Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-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 (15-S X-Ray Exposure Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ N:Na1519 b:30.7 occ:1.00 OE1 N:GLU40 2.2 32.5 1.0 O N:SER441 2.2 30.6 1.0 O N:GLU40 2.3 30.8 1.0 O N:GLY45 2.3 33.1 1.0 O N:HOH3026 2.4 31.3 1.0 CD N:GLU40 3.2 35.6 1.0 O N:HOH3060 3.2 42.8 1.0 C N:GLU40 3.4 31.1 1.0 C N:GLY45 3.5 34.1 1.0 CG N:GLU40 3.5 30.8 1.0 C N:SER441 3.5 31.9 1.0 OD2 N:ASP442 4.1 32.8 1.0 CA N:THR46 4.1 35.5 1.0 CA N:ASP442 4.1 32.5 1.0 O N:GLN43 4.1 32.5 1.0 CG N:ASP442 4.1 34.4 1.0 CB N:ASP442 4.1 31.6 1.0 CA N:GLU40 4.2 31.5 1.0 N N:THR46 4.2 34.2 1.0 N N:LEU41 4.2 31.0 1.0 N N:ASP442 4.3 32.5 1.0 CA N:LEU41 4.3 32.1 1.0 OE2 N:GLU40 4.4 36.1 1.0 CB N:GLU40 4.4 30.3 1.0 N N:GLY45 4.4 33.1 1.0 N N:LEU47 4.4 37.1 1.0 CA N:GLY45 4.6 32.8 1.0 CA N:SER441 4.6 31.4 1.0 CD2 N:LEU41 4.7 29.1 1.0 C N:THR46 4.7 36.8 1.0 OD1 N:ASP442 4.8 31.5 1.0 CB N:SER441 4.9 31.6 1.0 C N:PRO44 5.0 34.2 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