Sodium in PDB 5b1b: Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution, PDB code: 5b1b was solved by N.Yano, K.Muramoto, A.Shimada, S.Takemura, J.Baba, H.Fujisawa, M.Mochizuki, K.Shinzawa-Itoh, 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 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	181.606, 204.140, 177.653, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 18.6

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution 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 the Fully Reduced State at 1.6 Angstrom Resolution (pdb code 5b1b). 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 Reduced State at 1.6 Angstrom Resolution, PDB code: 5b1b:
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 Reduced State at 1.6 Angstrom Resolution


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 Reduced State at 1.6 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:24.1 occ:1.00 O A:GLY45 2.3 26.4 1.0 O A:HOH848 2.3 22.2 1.0 OE1 A:GLU40 2.3 23.6 1.0 O A:SER441 2.3 22.2 1.0 O A:GLU40 2.4 22.5 1.0 CD A:GLU40 3.2 24.4 1.0 C A:GLU40 3.4 21.9 1.0 CG A:GLU40 3.5 24.3 1.0 C A:GLY45 3.5 26.1 1.0 O A:HOH793 3.6 33.4 1.0 C A:SER441 3.6 23.7 1.0 O A:HOH886 3.7 29.7 1.0 CB A:ASP442 3.9 21.8 1.0 CA A:THR46 4.0 27.3 1.0 CA A:ASP442 4.0 21.6 1.0 O A:GLN43 4.0 23.7 1.0 CG A:ASP442 4.1 21.4 1.0 OD1 A:ASP442 4.2 24.5 1.0 N A:THR46 4.2 27.4 1.0 N A:ASP442 4.2 22.0 1.0 CA A:GLU40 4.2 21.2 1.0 CA A:LEU41 4.3 21.0 1.0 N A:LEU41 4.3 20.8 1.0 N A:LEU47 4.3 26.5 1.0 OE2 A:GLU40 4.4 27.7 1.0 CB A:GLU40 4.5 22.2 1.0 N A:GLY45 4.5 23.1 1.0 C A:THR46 4.5 29.5 1.0 CA A:GLY45 4.6 24.7 1.0 CD2 A:LEU41 4.7 22.7 1.0 CA A:SER441 4.7 23.2 1.0 OD2 A:ASP442 4.8 24.0 1.0 O A:HOH759 4.9 32.4 1.0

Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution


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 Reduced State at 1.6 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ N:Na605 b:30.4 occ:1.00 O N:HOH888 2.3 28.4 1.0 OE1 N:GLU40 2.3 32.9 1.0 O N:GLY45 2.3 32.6 1.0 O N:SER441 2.3 28.9 1.0 O N:GLU40 2.4 29.7 1.0 CD N:GLU40 3.2 33.0 1.0 C N:GLU40 3.4 29.6 1.0 CG N:GLU40 3.5 28.5 1.0 O N:HOH784 3.5 41.0 1.0 C N:SER441 3.5 28.5 1.0 C N:GLY45 3.5 34.3 1.0 O N:HOH909 3.8 37.2 1.0 CA N:ASP442 3.9 27.9 1.0 CB N:ASP442 4.0 29.7 1.0 O N:GLN43 4.0 30.8 1.0 CA N:THR46 4.0 34.7 1.0 CG N:ASP442 4.1 30.8 1.0 OD1 N:ASP442 4.2 30.8 1.0 N N:ASP442 4.2 29.2 1.0 CA N:GLU40 4.3 28.7 1.0 N N:LEU41 4.3 26.7 1.0 N N:THR46 4.3 34.5 1.0 CA N:LEU41 4.3 27.6 1.0 N N:GLY45 4.4 31.1 1.0 OE2 N:GLU40 4.4 34.7 1.0 N N:LEU47 4.4 35.1 1.0 CB N:GLU40 4.5 27.7 1.0 C N:THR46 4.6 36.9 1.0 CD2 N:LEU41 4.6 26.7 1.0 CA N:GLY45 4.7 32.9 1.0 CA N:SER441 4.7 28.5 1.0 OD2 N:ASP442 4.8 31.6 1.0

N.Yano, K.Muramoto, A.Shimada, S.Takemura, J.Baba, H.Fujisawa, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, T.Tsukihara, S.Yoshikawa. The MG2+-Containing Water Cluster of Mammalian Cytochrome C Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle. J.Biol.Chem. V. 291 23882 2016.
ISSN: ESSN 1083-351X
PubMed: 27605664
DOI: 10.1074/JBC.M115.711770