Sodium in PDB 6jy3: Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

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

The structure of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 6jy3 was solved by K.Shinzawa-Itoh, K.Muramoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	149.529, 152.131, 174.083, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 19.2

The structure of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	1 atom
Iron	(Fe)	2 atoms
Copper	(Cu)	3 atoms

The binding sites of Sodium atom in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State (pdb code 6jy3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 6jy3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in 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 Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:35.7 occ:1.00 O A:GLY45 2.3 39.8 1.0 OE1 A:GLU40 2.3 38.2 1.0 O A:SER441 2.3 32.3 1.0 O A:GLU40 2.3 35.5 1.0 O A:HOH844 2.3 34.7 1.0 CD A:GLU40 3.2 36.5 1.0 O A:HOH816 3.3 46.2 1.0 C A:GLU40 3.3 33.3 1.0 CG A:GLU40 3.4 32.6 1.0 C A:GLY45 3.4 42.3 1.0 C A:SER441 3.5 32.7 1.0 CA A:ASP442 4.0 34.8 1.0 CB A:ASP442 4.1 32.6 1.0 O A:GLN43 4.1 38.3 1.0 OD2 A:ASP442 4.1 38.9 1.0 CA A:THR46 4.1 41.4 1.0 CG A:ASP442 4.2 32.5 1.0 CA A:GLU40 4.2 32.6 1.0 N A:THR46 4.2 41.0 1.0 N A:ASP442 4.2 32.6 1.0 N A:LEU41 4.2 33.1 1.0 N A:LEU47 4.3 37.1 1.0 OE2 A:GLU40 4.3 35.2 1.0 CB A:GLU40 4.4 33.8 1.0 CA A:LEU41 4.4 34.2 1.0 N A:GLY45 4.4 37.1 1.0 CA A:GLY45 4.5 36.4 1.0 CA A:SER441 4.6 31.3 1.0 CD2 A:LEU41 4.7 33.6 1.0 C A:THR46 4.7 40.4 1.0 CB A:SER441 4.9 28.4 1.0 OD1 A:ASP442 4.9 39.0 1.0

Sodium binding site 2 out of 2 in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in 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 Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:64.4 occ:1.00 OE1 C:GLU236 2.2 83.6 1.0 NE2 C:HIS148 2.3 58.5 1.0 NE2 C:HIS232 2.3 45.1 1.0 CD C:GLU236 2.9 61.4 1.0 CD2 C:HIS232 3.0 39.2 1.0 CE1 C:HIS148 3.1 51.4 1.0 CD2 C:HIS148 3.3 46.5 1.0 CG C:GLU236 3.3 42.2 1.0 CE1 C:HIS232 3.4 44.5 1.0 OE2 C:GLU236 3.6 43.2 1.0 CG C:MET152 4.2 49.1 1.0 SD C:MET152 4.2 58.6 1.0 CG C:HIS232 4.3 37.7 1.0 ND1 C:HIS148 4.3 54.4 1.0 ND1 C:HIS232 4.4 40.3 1.0 CG C:HIS148 4.4 39.1 1.0 O C:HOH440 4.7 53.4 1.0 O C:HOH420 4.8 39.1 1.0 CB C:GLU236 4.8 36.1 1.0

K.Shinzawa-Itoh, T.Sugimura, T.Misaki, Y.Tadehara, S.Yamamoto, M.Hanada, N.Yano, T.Nakagawa, S.Uene, T.Yamada, H.Aoyama, E.Yamashita, T.Tsukihara, S.Yoshikawa, K.Muramoto. Monomeric Structure of An Active Form of Bovine Cytochromecoxidase. Proc.Natl.Acad.Sci.Usa V. 116 19945 2019.
ISSN: ESSN 1091-6490
PubMed: 31533957
DOI: 10.1073/PNAS.1907183116