Sodium in PDB 6nmf: Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature

All present enzymatic activity of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature:
1.9.3.1;

The structure of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature, PDB code: 6nmf was solved by D.L.Rousseau, S.-R.Yeh, I.Ishigami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	178.700, 189.800, 211.300, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 23.2

The structure of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature 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 Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature (pdb code 6nmf). 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 Reduced Cytochrome C Oxidase at Room Temperature, PDB code: 6nmf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature


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 Reduced Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:55.0 occ:1.00 O A:HOH784 2.2 46.6 1.0 OE1 A:GLU40 2.2 55.3 1.0 O A:GLU40 2.2 55.5 1.0 O A:SER441 2.3 52.5 1.0 O A:GLY45 2.3 63.6 1.0 C A:GLU40 3.3 50.6 1.0 CD A:GLU40 3.3 55.4 1.0 C A:GLY45 3.5 58.0 1.0 C A:SER441 3.5 53.6 1.0 CG A:GLU40 3.6 55.4 1.0 CA A:ASP442 4.0 49.5 1.0 O A:GLN43 4.0 51.3 1.0 N A:LEU41 4.1 48.1 1.0 CA A:THR46 4.1 56.5 1.0 CA A:LEU41 4.1 49.2 1.0 CB A:ASP442 4.2 52.5 1.0 CA A:GLU40 4.2 49.1 1.0 N A:ASP442 4.2 50.6 1.0 N A:THR46 4.3 55.7 1.0 N A:GLY45 4.3 55.4 1.0 CG A:ASP442 4.4 53.3 1.0 CD2 A:LEU41 4.4 57.3 1.0 OE2 A:GLU40 4.4 54.5 1.0 OD1 A:ASP442 4.4 49.8 1.0 CB A:GLU40 4.4 51.9 1.0 CA A:GLY45 4.5 59.3 1.0 CA A:SER441 4.7 52.0 1.0 OG1 A:THR46 4.8 59.7 1.0 C A:THR46 4.8 64.3 1.0 N A:LEU47 4.9 64.5 1.0 C A:LEU41 5.0 51.3 1.0 C A:PRO44 5.0 53.8 1.0

Sodium binding site 2 out of 2 in the Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature


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 Reduced Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ N:Na605 b:82.0 occ:1.00 O N:HOH774 2.2 64.5 1.0 OE1 N:GLU40 2.2 75.5 1.0 O N:GLU40 2.3 72.3 1.0 O N:SER441 2.3 70.5 1.0 O N:GLY45 2.3 91.1 1.0 CD N:GLU40 3.3 83.9 1.0 C N:GLU40 3.4 78.0 1.0 C N:GLY45 3.5 88.1 1.0 C N:SER441 3.5 65.4 1.0 CG N:GLU40 3.9 85.8 1.0 O N:HOH715 3.9 64.4 1.0 CA N:ASP442 4.0 75.7 1.0 CA N:THR46 4.0 86.6 1.0 CB N:ASP442 4.0 86.6 1.0 OD1 N:ASP442 4.1 82.4 1.0 N N:THR46 4.1 86.8 1.0 O N:GLN43 4.2 76.4 1.0 N N:ASP442 4.2 64.1 1.0 N N:LEU41 4.2 79.8 1.0 CG N:ASP442 4.2 85.0 1.0 CA N:LEU41 4.3 83.0 1.0 OE2 N:GLU40 4.4 80.2 1.0 CA N:GLU40 4.4 80.9 1.0 N N:LEU47 4.5 82.3 1.0 CD2 N:LEU41 4.6 82.1 1.0 CA N:SER441 4.6 70.3 1.0 CA N:GLY45 4.6 88.0 1.0 N N:GLY45 4.7 86.5 1.0 CB N:GLU40 4.7 84.9 1.0 C N:THR46 4.8 83.4 1.0 C N:PRO44 4.9 82.7 1.0 CB N:SER441 4.9 69.6 1.0

I.Ishigami, A.Lewis-Ballester, A.Echelmeier, G.Brehm, N.A.Zatsepin, T.D.Grant, J.D.Coe, S.Lisova, G.Nelson, S.Zhang, Z.F.Dobson, S.Boutet, R.G.Sierra, A.Batyuk, P.Fromme, R.Fromme, J.C.H.Spence, A.Ros, S.R.Yeh, D.L.Rousseau. Snapshot of An Oxygen Intermediate in the Catalytic Reaction of Cytochromecoxidase. Proc. Natl. Acad. Sci. V. 116 3572 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30808749
DOI: 10.1073/PNAS.1814526116