Sodium in PDB 1v54: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

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

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 1v54 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 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	182.590, 205.140, 178.250, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 22.7

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized 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 Oxidized State (pdb code 1v54). 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, PDB code: 1v54:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3519 b:27.3 occ:1.00 O A:HOH3544 2.0 22.0 1.0 O A:GLY45 2.4 28.3 1.0 O A:SER441 2.4 25.4 1.0 O A:GLU40 2.4 25.0 1.0 OE1 A:GLU40 2.5 25.5 1.0 CD A:GLU40 3.4 27.9 1.0 C A:GLU40 3.4 22.9 1.0 O A:HOH3564 3.5 38.2 1.0 C A:GLY45 3.5 25.5 1.0 C A:SER441 3.6 24.5 1.0 CG A:GLU40 3.7 26.9 1.0 O A:GLN43 3.8 22.4 1.0 CA A:ASP442 3.9 22.0 1.0 OD2 A:ASP442 3.9 24.7 1.0 CB A:ASP442 4.0 23.6 1.0 CG A:ASP442 4.1 25.5 1.0 N A:ASP442 4.2 21.6 1.0 CA A:LEU41 4.2 20.0 1.0 N A:LEU41 4.2 20.7 1.0 CA A:THR46 4.3 26.7 1.0 N A:GLY45 4.3 21.8 1.0 N A:THR46 4.3 25.4 1.0 CA A:GLU40 4.3 24.0 1.0 CD2 A:LEU41 4.5 22.2 1.0 CA A:GLY45 4.5 23.1 1.0 OE2 A:GLU40 4.6 27.5 1.0 CB A:GLU40 4.6 25.3 1.0 N A:LEU47 4.7 30.6 1.0 CA A:SER441 4.7 23.6 1.0 OD1 A:ASP442 4.8 27.9 1.0 C A:PRO44 4.9 24.3 1.0 C A:THR46 4.9 30.6 1.0

Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized 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 Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ N:Na4519 b:31.2 occ:1.00 O N:HOH1026 2.0 29.3 1.0 O N:GLY45 2.3 32.6 1.0 O N:SER441 2.4 27.6 1.0 O N:GLU40 2.4 28.9 1.0 OE1 N:GLU40 2.5 29.9 1.0 C N:GLU40 3.4 26.5 1.0 O N:HOH1060 3.4 42.0 1.0 CD N:GLU40 3.4 29.2 1.0 C N:GLY45 3.5 29.6 1.0 C N:SER441 3.5 26.9 1.0 CG N:GLU40 3.7 29.8 1.0 O N:GLN43 3.9 29.0 1.0 CA N:ASP442 3.9 25.2 1.0 OD2 N:ASP442 4.1 32.1 1.0 CB N:ASP442 4.1 29.2 1.0 CG N:ASP442 4.2 32.5 1.0 CA N:THR46 4.2 30.7 1.0 N N:ASP442 4.2 26.2 1.0 N N:LEU41 4.2 24.8 1.0 CA N:LEU41 4.3 24.4 1.0 N N:THR46 4.3 30.2 1.0 CA N:GLU40 4.3 26.6 1.0 N N:GLY45 4.4 28.2 1.0 CB N:GLU40 4.6 26.6 1.0 CA N:GLY45 4.6 28.7 1.0 OE2 N:GLU40 4.6 30.3 1.0 N N:LEU47 4.6 34.9 1.0 CD2 N:LEU41 4.6 23.1 1.0 CA N:SER441 4.7 28.1 1.0 C N:THR46 4.8 33.2 1.0 OD1 N:ASP442 4.9 35.3 1.0 C N:PRO44 4.9 29.4 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