Sodium in PDB 3aso: Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength, PDB code: 3aso was solved by M.Suga, N.Yano, K.Muramoto, K.Shinzawa-Itoh, T.Maeda, 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)	15.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	181.874, 204.106, 177.874, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.5

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Magnesium	(Mg)	2 atoms
Copper	(Cu)	6 atoms
Iron	(Fe)	4 atoms

The binding sites of Sodium atom in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength (pdb code 3aso). 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 Fully Oxidized State Measured at 0.9 Angstrom Wavelength, PDB code: 3aso:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength


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 Fully Oxidized State Measured at 0.9 Angstrom Wavelength within 5.0Å range: probe atom residue distance (Å) B Occ A:Na519 b:22.1 occ:1.00 O A:HOH2258 2.2 23.1 1.0 OE1 A:GLU40 2.2 21.5 1.0 O A:SER441 2.3 22.2 1.0 O A:GLY45 2.3 21.9 1.0 O A:GLU40 2.3 21.8 1.0 CD A:GLU40 3.2 23.1 1.0 C A:GLU40 3.3 20.1 1.0 C A:GLY45 3.5 21.4 1.0 C A:SER441 3.5 20.5 1.0 CG A:GLU40 3.5 20.6 1.0 O A:HOH2563 3.6 33.1 1.0 CA A:ASP442 3.9 18.4 1.0 OD2 A:ASP442 4.0 22.4 1.0 O A:GLN43 4.0 21.7 1.0 CB A:ASP442 4.0 18.8 1.0 CG A:ASP442 4.1 20.2 1.0 N A:ASP442 4.2 18.5 1.0 N A:LEU41 4.2 19.4 1.0 CA A:THR46 4.2 23.6 1.0 CA A:GLU40 4.2 20.7 1.0 N A:THR46 4.2 22.1 1.0 CA A:LEU41 4.3 18.6 1.0 N A:GLY45 4.3 20.8 1.0 OE2 A:GLU40 4.4 20.7 1.0 CB A:GLU40 4.5 20.4 1.0 N A:LEU47 4.5 25.8 1.0 CD2 A:LEU41 4.5 16.6 1.0 CA A:GLY45 4.5 20.7 1.0 CA A:SER441 4.6 21.1 1.0 C A:THR46 4.8 25.8 1.0 OD1 A:ASP442 4.9 24.0 1.0 CB A:SER441 4.9 20.1 1.0

Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength


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 Fully Oxidized State Measured at 0.9 Angstrom Wavelength within 5.0Å range: probe atom residue distance (Å) B Occ N:Na519 b:24.3 occ:1.00 O N:HOH3258 2.2 23.9 1.0 OE1 N:GLU40 2.3 20.8 1.0 O N:SER441 2.3 25.0 1.0 O N:GLY45 2.3 26.8 1.0 O N:GLU40 2.3 23.3 1.0 CD N:GLU40 3.2 21.7 1.0 C N:GLU40 3.3 22.9 1.0 C N:GLY45 3.4 25.8 1.0 O N:HOH3563 3.5 28.8 1.0 C N:SER441 3.5 23.8 1.0 CG N:GLU40 3.5 22.7 1.0 O N:GLN43 3.9 24.8 1.0 O N:HOH3466 4.0 0.4 1.0 CA N:ASP442 4.0 22.7 1.0 CA N:THR46 4.0 27.4 1.0 CB N:ASP442 4.1 22.6 1.0 N N:THR46 4.1 26.2 1.0 CA N:GLU40 4.2 22.9 1.0 OD2 N:ASP442 4.2 23.8 1.0 N N:ASP442 4.2 22.9 1.0 N N:LEU41 4.2 23.0 1.0 CG N:ASP442 4.2 23.2 1.0 N N:LEU47 4.3 29.8 1.0 CA N:LEU41 4.3 21.4 1.0 OE2 N:GLU40 4.4 22.2 1.0 CB N:GLU40 4.4 22.5 1.0 N N:GLY45 4.4 24.7 1.0 CD2 N:LEU41 4.5 18.4 1.0 CA N:GLY45 4.6 24.7 1.0 CA N:SER441 4.6 24.7 1.0 C N:THR46 4.6 29.1 1.0 CB N:SER441 4.9 24.9 1.0 OD1 N:ASP442 4.9 23.0 1.0

M.Suga, N.Yano, K.Muramoto, K.Shinzawa-Itoh, T.Maeda, E.Yamashita, T.Tsukihara, S.Yoshikawa. Distinguishing Between Cl- and O2(2-) As the Bridging Element Between FE3+ and CU2+ in Resting-Oxidized Cytochrome C Oxidase Acta Crystallogr.,Sect.D V. 67 742 2011.
ISSN: ISSN 0907-4449
PubMed: 21795816
DOI: 10.1107/S0907444911022803