Sodium in PDB 2dys: Bovine Heart Cytochrome C Oxidase Modified By Dccd

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase Modified By Dccd:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase Modified By Dccd, PDB code: 2dys was solved by K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, T.Kurauchi, T.Mizushima, 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 (°)	184.130, 207.232, 178.242, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.2

The structure of Bovine Heart Cytochrome C Oxidase Modified By Dccd 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 Modified By Dccd (pdb code 2dys). 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 Modified By Dccd, PDB code: 2dys:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


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 Modified By Dccd within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:44.5 occ:1.00 OE1 A:GLU40 2.2 41.5 1.0 O A:SER441 2.3 29.1 1.0 O A:GLU40 2.3 34.6 1.0 O A:GLY45 2.4 45.1 1.0 O A:HOH719 2.5 39.9 1.0 CD A:GLU40 3.2 33.5 1.0 C A:GLU40 3.3 28.8 1.0 O A:HOH739 3.5 51.1 1.0 CG A:GLU40 3.5 28.5 1.0 C A:SER441 3.5 30.6 1.0 C A:GLY45 3.6 41.2 1.0 O A:GLN43 4.0 29.9 1.0 CA A:ASP442 4.1 24.2 1.0 CA A:THR46 4.2 47.3 1.0 CA A:GLU40 4.2 29.1 1.0 N A:LEU41 4.2 27.7 1.0 N A:ASP442 4.3 24.9 1.0 CB A:ASP442 4.3 29.7 1.0 N A:THR46 4.3 43.7 1.0 OE2 A:GLU40 4.3 36.8 1.0 OD2 A:ASP442 4.3 29.7 1.0 CA A:LEU41 4.4 20.6 1.0 N A:LEU47 4.4 50.5 1.0 CB A:GLU40 4.4 28.5 1.0 CG A:ASP442 4.4 30.2 1.0 N A:GLY45 4.5 29.5 1.0 CA A:SER441 4.7 30.1 1.0 CD2 A:LEU41 4.7 21.9 1.0 CA A:GLY45 4.7 33.1 1.0 C A:THR46 4.7 51.6 1.0

Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


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 Modified By Dccd within 5.0Å range: probe atom residue distance (Å) B Occ N:Na603 b:50.5 occ:1.00 OE1 N:GLU40 2.2 49.5 1.0 O N:GLU40 2.3 43.8 1.0 O N:SER441 2.3 35.5 1.0 O N:GLY45 2.4 49.2 1.0 O N:HOH718 2.6 46.5 1.0 CD N:GLU40 3.1 45.4 1.0 CG N:GLU40 3.3 44.6 1.0 C N:GLU40 3.3 40.2 1.0 O N:HOH738 3.5 63.4 1.0 C N:SER441 3.6 35.2 1.0 C N:GLY45 3.6 46.0 1.0 O N:GLN43 4.0 35.0 1.0 CA N:THR46 4.0 50.8 1.0 CA N:GLU40 4.1 39.2 1.0 CA N:ASP442 4.2 28.9 1.0 OE2 N:GLU40 4.3 50.8 1.0 N N:LEU41 4.3 37.4 1.0 N N:THR46 4.3 48.6 1.0 CB N:GLU40 4.3 40.4 1.0 N N:LEU47 4.3 55.4 1.0 N N:ASP442 4.3 31.0 1.0 CB N:ASP442 4.3 37.1 1.0 CG N:ASP442 4.4 42.1 1.0 CA N:LEU41 4.4 37.6 1.0 OD2 N:ASP442 4.5 44.3 1.0 N N:GLY45 4.5 40.3 1.0 C N:THR46 4.6 56.0 1.0 CA N:SER441 4.7 35.2 1.0 CA N:GLY45 4.7 40.7 1.0 CD2 N:LEU41 4.8 32.5 1.0 OD1 N:ASP442 4.8 42.7 1.0

K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, H.Terada, T.Kurauchi, Y.Tadehara, A.Yamasaki, T.Sugimura, S.Kurono, K.Tsujimoto, T.Mizushima, E.Yamashita, T.Tsukihara, S.Yoshikawa. Structures and Physiological Roles of 13 Integral Lipids of Bovine Heart Cytochrome C Oxidase Embo J. V. 26 1713 2007.
ISSN: ISSN 0261-4189
PubMed: 17332748
DOI: 10.1038/SJ.EMBOJ.7601618