Sodium in PDB 1oco: Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State, PDB code: 1oco was solved by T.Tsukihara, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	189.100, 210.500, 178.600, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 25.6

The structure of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State 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 Carbon Monoxide-Bound State (pdb code 1oco). 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 Carbon Monoxide-Bound State, PDB code: 1oco:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State


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 Carbon Monoxide-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na519 b:14.4 occ:1.00 O A:GLU40 2.4 23.2 1.0 O A:SER441 2.4 8.9 1.0 O A:GLY45 2.4 27.5 1.0 OE2 A:GLU40 2.5 15.4 1.0 C A:GLU40 3.5 12.1 1.0 C A:SER441 3.5 8.2 1.0 C A:GLY45 3.6 26.8 1.0 O A:GLN43 3.6 25.1 1.0 CD A:GLU40 3.7 17.9 1.0 CA A:ASP442 3.8 10.8 1.0 OD1 A:ASP442 3.8 17.2 1.0 CA A:LEU41 3.9 7.0 1.0 CG A:ASP442 4.0 16.2 1.0 CD2 A:LEU41 4.0 24.9 1.0 N A:GLY45 4.1 23.8 1.0 CB A:ASP442 4.1 9.5 1.0 N A:ASP442 4.1 7.0 1.0 CG A:GLU40 4.1 19.2 1.0 N A:LEU41 4.1 7.0 1.0 CA A:GLY45 4.5 25.3 1.0 CE2 A:TYR443 4.5 21.7 1.0 N A:THR46 4.5 25.6 1.0 CA A:THR46 4.6 33.6 1.0 CA A:GLU40 4.6 10.2 1.0 OD2 A:ASP442 4.6 18.2 1.0 CG A:LEU41 4.7 9.2 1.0 CA A:SER441 4.7 10.7 1.0 C A:LEU41 4.8 8.1 1.0 C A:GLN43 4.8 21.9 1.0 OE1 A:GLU40 4.8 16.2 1.0 CB A:LEU41 4.8 7.0 1.0 C A:PRO44 4.9 23.7 1.0 CD2 A:TYR443 4.9 20.6 1.0 CB A:GLU40 5.0 13.8 1.0

Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State


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 Carbon Monoxide-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ N:Na519 b:30.1 occ:1.00 O N:GLY45 2.4 42.2 1.0 O N:SER441 2.4 22.9 1.0 O N:GLU40 2.5 34.3 1.0 OE2 N:GLU40 2.6 39.2 1.0 C N:GLY45 3.5 37.7 1.0 C N:SER441 3.5 19.4 1.0 C N:GLU40 3.6 30.9 1.0 O N:GLN43 3.6 34.4 1.0 CD N:GLU40 3.7 39.7 1.0 OD1 N:ASP442 3.7 36.6 1.0 CA N:ASP442 3.7 20.3 1.0 CG N:ASP442 3.9 34.9 1.0 N N:GLY45 4.0 25.6 1.0 CA N:LEU41 4.0 27.4 1.0 CB N:ASP442 4.0 30.9 1.0 CD2 N:LEU41 4.1 35.1 1.0 N N:ASP442 4.1 13.3 1.0 CG N:GLU40 4.2 37.1 1.0 N N:LEU41 4.2 28.3 1.0 CA N:GLY45 4.4 30.9 1.0 CE1 N:TYR443 4.4 21.6 1.0 N N:THR46 4.5 38.8 1.0 OD2 N:ASP442 4.5 40.6 1.0 CA N:THR46 4.5 43.4 1.0 CA N:GLU40 4.7 28.0 1.0 C N:GLN43 4.7 31.6 1.0 C N:PRO44 4.7 27.8 1.0 CA N:SER441 4.8 23.6 1.0 CG N:LEU41 4.8 34.9 1.0 OE1 N:GLU40 4.8 40.5 1.0 C N:LEU41 4.8 28.1 1.0 CD1 N:TYR443 4.9 18.1 1.0 CB N:LEU41 4.9 29.6 1.0 CA N:PRO44 5.0 23.9 1.0

S.Yoshikawa, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, E.Yamashita, N.Inoue, M.Yao, M.J.Fei, C.P.Libeu, T.Mizushima, H.Yamaguchi, T.Tomizaki, T.Tsukihara. Redox-Coupled Crystal Structural Changes in Bovine Heart Cytochrome C Oxidase. Science V. 280 1723 1998.
ISSN: ISSN 0036-8075
PubMed: 9624044
DOI: 10.1126/SCIENCE.280.5370.1723