Sodium in PDB 1v55: Bovine Heart Cytochrome C Oxidase at the Fully Reduced State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State, PDB code: 1v55 was solved by T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	183.060, 206.584, 178.298, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 23

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Reduced 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 at the Fully Reduced State (pdb code 1v55). 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 Reduced State, PDB code: 1v55:
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 Reduced 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 at the Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3519 b:25.2 occ:1.00 O A:HOH3544 2.0 17.1 1.0 O A:GLY45 2.4 28.5 1.0 O A:GLU40 2.4 22.4 1.0 O A:SER441 2.4 24.6 1.0 OE1 A:GLU40 2.5 25.3 1.0 O A:HOH3563 3.4 35.8 1.0 C A:GLU40 3.4 18.9 1.0 CD A:GLU40 3.4 24.6 1.0 C A:GLY45 3.6 26.2 1.0 C A:SER441 3.6 23.5 1.0 CG A:GLU40 3.7 24.3 1.0 CA A:ASP442 3.9 21.9 1.0 O A:GLN43 3.9 23.4 1.0 CB A:ASP442 4.0 23.4 1.0 CG A:ASP442 4.0 24.3 1.0 OD2 A:ASP442 4.1 22.9 1.0 CA A:THR46 4.1 28.6 1.0 N A:ASP442 4.2 21.9 1.0 O A:HOH3568 4.2 32.6 1.0 CA A:LEU41 4.2 15.2 1.0 N A:LEU41 4.2 17.6 1.0 N A:THR46 4.3 27.7 1.0 N A:GLY45 4.4 20.3 1.0 CA A:GLU40 4.4 19.3 1.0 CD2 A:LEU41 4.5 17.1 1.0 OE2 A:GLU40 4.6 25.6 1.0 OD1 A:ASP442 4.6 24.7 1.0 CA A:GLY45 4.6 23.6 1.0 CB A:GLU40 4.6 18.6 1.0 N A:LEU47 4.7 32.1 1.0 CA A:SER441 4.8 22.4 1.0 C A:THR46 4.8 32.1 1.0 C A:PRO44 4.9 21.7 1.0

Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Reduced 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 at the Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ N:Na4519 b:30.9 occ:1.00 O N:HOH1026 2.0 25.6 1.0 O N:GLU40 2.4 26.6 1.0 O N:GLY45 2.4 33.3 1.0 O N:SER441 2.4 31.7 1.0 OE1 N:GLU40 2.5 30.2 1.0 O N:HOH1060 3.3 38.4 1.0 C N:GLU40 3.4 25.8 1.0 CD N:GLU40 3.4 28.4 1.0 C N:GLY45 3.5 30.6 1.0 C N:SER441 3.6 29.6 1.0 CG N:GLU40 3.7 28.1 1.0 CA N:ASP442 3.9 28.0 1.0 O N:GLN43 3.9 28.7 1.0 CB N:ASP442 4.0 29.9 1.0 CA N:THR46 4.0 33.9 1.0 CG N:ASP442 4.1 30.7 1.0 OD2 N:ASP442 4.1 30.5 1.0 O N:HOH1069 4.2 42.6 1.0 N N:ASP442 4.2 28.9 1.0 CA N:LEU41 4.2 26.9 1.0 N N:LEU41 4.2 26.4 1.0 N N:THR46 4.3 32.2 1.0 CA N:GLU40 4.4 25.7 1.0 N N:GLY45 4.4 30.2 1.0 OE2 N:GLU40 4.6 30.2 1.0 CB N:GLU40 4.6 26.7 1.0 CA N:GLY45 4.6 29.4 1.0 N N:LEU47 4.6 37.5 1.0 CD2 N:LEU41 4.6 28.8 1.0 OD1 N:ASP442 4.7 33.4 1.0 C N:THR46 4.7 37.4 1.0 CA N:SER441 4.8 29.3 1.0 C N:PRO44 5.0 30.7 1.0

T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa. The Low-Spin Heme of Cytochrome C Oxidase As the Driving Element of the Proton-Pumping Process. Proc.Natl.Acad.Sci.Usa V. 100 15304 2003.
ISSN: ISSN 0027-8424
PubMed: 14673090
DOI: 10.1073/PNAS.2635097100