Sodium in PDB 6kv0: Ferredoxin I From C. Reinhardtii, High X-Ray Dose

The structure of Ferredoxin I From C. Reinhardtii, High X-Ray Dose, PDB code: 6kv0 was solved by Y.Onishi, G.Kurisu, H.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.72 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	25.820, 32.300, 49.930, 72.27, 78.09, 72.22
R / Rfree (%)	17.5 / 18.7

The structure of Ferredoxin I From C. Reinhardtii, High X-Ray Dose also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Ferredoxin I From C. Reinhardtii, High X-Ray Dose (pdb code 6kv0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Ferredoxin I From C. Reinhardtii, High X-Ray Dose, PDB code: 6kv0:

Sodium binding site 1 out of 1 in the Ferredoxin I From C. Reinhardtii, High X-Ray Dose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ferredoxin I From C. Reinhardtii, High X-Ray Dose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na105 b:31.9 occ:1.00 OE1 B:GLU15 2.8 16.6 1.0 O B:ALA0 3.0 13.1 1.0 CG B:LYS2 3.2 15.1 1.0 N B:SCN103 3.3 18.2 1.0 N B:LYS2 3.3 11.4 1.0 OE2 B:GLU15 3.4 18.0 1.0 C B:SCN103 3.4 17.2 1.0 CD B:GLU15 3.5 16.8 1.0 C B:ALA0 3.7 12.2 1.0 C B:TYR1 3.7 12.8 1.0 O B:HOH292 3.8 40.7 1.0 CA B:TYR1 3.8 12.6 1.0 OD1 B:ASP82 3.8 12.7 1.0 CD B:LYS2 3.9 16.0 1.0 CB B:LYS2 4.0 15.3 1.0 N B:TYR1 4.1 11.6 1.0 CA B:LYS2 4.1 11.8 1.0 O B:TYR1 4.5 12.0 1.0 OD2 B:ASP82 4.6 13.4 1.0 S B:SCN103 4.6 21.4 1.0 CG B:ASP82 4.6 12.9 1.0 O B:HOH273 4.7 28.4 1.0 CA B:ALA0 4.8 11.2 1.0 CB B:ALA0 5.0 10.7 1.0 CG B:GLU15 5.0 16.6 1.0

Y.Ohnishi, N.Muraki, D.Kiyota, H.Okumura, S.Baba, Y.Kawano, T.Kumasaka, H.Tanaka, G.Kurisu. X-Ray Dose-Dependent Structural Changes of the [2FE-2S] Ferredoxin From Chlamydomonas Reinhardtii. J.Biochem. 2020.
ISSN: ISSN 0021-924X
PubMed: 32282907
DOI: 10.1093/JB/MVAA045