Sodium in PDB 8gcq: Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution

All present enzymatic activity of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution:
1.9.3.1;

The structure of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution, PDB code: 8gcq was solved by I.Ishigami, S.-R.Yeh, D.L.Rousseau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.00 / 2.38
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	178.6, 189.5, 211.1, 90, 90, 90
R / Rfree (%)	23.2 / 26.6

The structure of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Copper	(Cu)	6 atoms
Zinc	(Zn)	2 atoms
Iron	(Fe)	4 atoms

The binding sites of Sodium atom in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution (pdb code 8gcq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution, PDB code: 8gcq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:18.6 occ:1.00 O A:HOH740 1.9 8.9 1.0 OE2 A:GLU40 2.2 21.2 1.0 O A:GLU40 2.3 20.8 1.0 O A:GLY45 2.3 14.6 1.0 O A:SER441 2.3 14.0 1.0 CD A:GLU40 3.3 20.8 1.0 O A:HOH761 3.4 29.0 1.0 C A:GLU40 3.4 16.4 1.0 C A:SER441 3.5 10.2 1.0 C A:GLY45 3.5 13.2 1.0 O A:GLN43 3.6 18.1 1.0 CG A:GLU40 3.8 18.9 1.0 CA A:ASP442 3.9 9.4 1.0 OD1 A:ASP442 3.9 6.9 1.0 CB A:ASP442 4.1 8.5 1.0 N A:ASP442 4.1 9.7 1.0 CG A:ASP442 4.2 7.5 1.0 CA A:THR46 4.2 17.1 1.0 CA A:GLU40 4.2 17.2 1.0 N A:LEU41 4.3 13.6 1.0 N A:THR46 4.3 14.9 1.0 CA A:LEU41 4.3 12.6 1.0 OE1 A:GLU40 4.4 23.2 1.0 N A:GLY45 4.5 13.0 1.0 CA A:SER441 4.6 10.1 1.0 CB A:GLU40 4.6 18.1 1.0 CA A:GLY45 4.6 13.1 1.0 C A:PRO44 4.7 12.9 1.0 CE1 A:TYR443 4.7 10.1 1.0 N A:LEU47 4.8 20.8 1.0 C A:GLN43 4.8 17.4 1.0 O A:HOH792 4.8 51.7 1.0 OG1 A:THR46 4.9 14.1 1.0 C A:THR46 4.9 19.6 1.0 CB A:SER441 4.9 9.6 1.0 CD2 A:LEU41 4.9 11.7 1.0 OD2 A:ASP442 5.0 7.6 1.0

Sodium binding site 2 out of 2 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ N:Na603 b:30.8 occ:1.00 O N:GLU40 2.3 39.0 1.0 O N:GLY45 2.3 35.4 1.0 O N:SER441 2.3 28.9 1.0 OE2 N:GLU40 2.9 29.1 1.0 C N:GLU40 3.4 40.8 1.0 O N:GLN43 3.4 34.0 1.0 C N:SER441 3.5 29.8 1.0 O N:HOH746 3.5 9.8 1.0 C N:GLY45 3.6 34.6 1.0 OD1 N:ASP442 3.7 33.6 1.0 CD N:GLU40 3.9 29.2 1.0 CA N:ASP442 3.9 38.3 1.0 CA N:LEU41 3.9 43.8 1.0 CG N:GLU40 4.0 30.2 1.0 CE1 N:TYR443 4.1 34.1 1.0 N N:LEU41 4.1 42.0 1.0 N N:ASP442 4.2 30.9 1.0 CG N:ASP442 4.2 39.3 1.0 N N:GLY45 4.2 39.2 1.0 CB N:ASP442 4.3 40.6 1.0 C N:PRO44 4.4 37.9 1.0 CA N:GLU40 4.5 34.2 1.0 N N:THR46 4.5 33.2 1.0 CA N:GLY45 4.5 34.8 1.0 C N:GLN43 4.6 40.4 1.0 CA N:PRO44 4.6 37.7 1.0 CD1 N:TYR443 4.6 34.6 1.0 CA N:THR46 4.6 35.1 1.0 CA N:SER441 4.7 30.5 1.0 CZ N:TYR443 4.7 37.6 1.0 C N:LEU41 4.7 42.0 1.0 OH N:TYR443 4.8 36.5 1.0 O N:PRO44 4.9 35.4 1.0 CB N:GLU40 4.9 32.0 1.0 CD2 N:LEU41 4.9 48.8 1.0

I.Ishigami, R.G.Sierra, Z.Su, A.Peck, C.Wang, F.Poitevin, S.Lisova, B.Hayes, F.R.Moss 3Rd, S.Boutet, R.E.Sublett, C.H.Yoon, S.R.Yeh, D.L.Rousseau. Structural Insights Into Functional Properties of the Oxidized Form of Cytochrome C Oxidase. Nat Commun V. 14 5752 2023.
ISSN: ESSN 2041-1723
PubMed: 37717031
DOI: 10.1038/S41467-023-41533-X