Sodium in PDB 6nkn: Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature

All present enzymatic activity of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature:
1.9.3.1;

The structure of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature, PDB code: 6nkn 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)	10.50 / 2.50
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 / 21.7

The structure of Time-Resolved Sfx Structure of the Pr Intermediate of 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 Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature (pdb code 6nkn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature, PDB code: 6nkn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Time-Resolved Sfx Structure of the Pr Intermediate of 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 Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:45.4 occ:1.00 O A:HOH818 2.2 36.9 1.0 OE1 A:GLU40 2.2 45.7 1.0 O A:GLY45 2.2 53.2 1.0 O A:SER441 2.2 42.8 1.0 O A:GLU40 2.3 45.5 1.0 CD A:GLU40 3.2 48.0 1.0 C A:GLU40 3.3 38.6 1.0 O A:HOH772 3.4 56.2 1.0 C A:GLY45 3.4 47.0 1.0 C A:SER441 3.4 43.3 1.0 CG A:GLU40 3.5 46.4 1.0 CA A:ASP442 3.9 41.6 1.0 O A:GLN43 4.1 46.3 1.0 CB A:ASP442 4.1 44.2 1.0 N A:ASP442 4.1 41.0 1.0 CA A:THR46 4.1 53.1 1.0 N A:THR46 4.2 46.1 1.0 CA A:GLU40 4.2 41.2 1.0 N A:LEU41 4.2 39.9 1.0 CG A:ASP442 4.3 45.8 1.0 CA A:LEU41 4.3 40.7 1.0 OD1 A:ASP442 4.4 42.8 1.0 OE2 A:GLU40 4.4 52.2 1.0 N A:GLY45 4.4 47.0 1.0 CB A:GLU40 4.4 44.0 1.0 CD2 A:LEU41 4.4 47.2 1.0 N A:LEU47 4.5 57.8 1.0 CA A:GLY45 4.5 50.4 1.0 CA A:SER441 4.6 44.4 1.0 C A:THR46 4.7 57.4 1.0 CB A:SER441 5.0 46.8 1.0 OD2 A:ASP442 5.0 51.6 1.0

Sodium binding site 2 out of 2 in the Time-Resolved Sfx Structure of the Pr Intermediate of 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 Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ N:Na604 b:62.2 occ:1.00 O N:HOH769 2.2 57.2 1.0 OE1 N:GLU40 2.3 63.4 1.0 O N:SER441 2.3 55.4 1.0 O N:GLY45 2.3 71.2 1.0 O N:GLU40 2.3 59.1 1.0 CD N:GLU40 3.3 70.3 1.0 C N:GLY45 3.4 72.6 1.0 C N:GLU40 3.4 63.0 1.0 C N:SER441 3.4 58.5 1.0 CG N:GLU40 3.6 70.8 1.0 CB N:ASP442 3.8 76.7 1.0 CA N:ASP442 3.9 63.0 1.0 O N:GLN43 3.9 69.7 1.0 N N:THR46 4.0 73.7 1.0 CA N:THR46 4.0 71.7 1.0 N N:ASP442 4.1 55.0 1.0 CG N:ASP442 4.1 74.8 1.0 OD1 N:ASP442 4.2 72.5 1.0 CA N:GLU40 4.3 66.0 1.0 N N:LEU41 4.3 67.1 1.0 CA N:LEU41 4.4 73.0 1.0 OE2 N:GLU40 4.4 80.5 1.0 CD2 N:LEU41 4.5 66.5 1.0 N N:GLY45 4.6 76.0 1.0 CB N:GLU40 4.6 71.2 1.0 CA N:GLY45 4.6 74.4 1.0 CA N:SER441 4.6 62.9 1.0 C N:PRO44 4.7 68.3 1.0 C N:THR46 4.8 74.0 1.0 OD2 N:ASP442 4.8 76.1 1.0 N N:LEU47 4.9 73.8 1.0 O N:PRO44 5.0 70.2 1.0 CB N:SER441 5.0 66.7 1.0 CE2 N:TYR443 5.0 57.8 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