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

The structure of Ferredoxin I From C. Reinhardtii, Low X-Ray Dose, PDB code: 6kum 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)	28.74 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	25.878, 32.326, 49.915, 72.38, 78.06, 72.39
R / Rfree (%)	17.1 / 19

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

Iron	(Fe)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Ferredoxin I From C. Reinhardtii, Low X-Ray Dose (pdb code 6kum). 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, Low X-Ray Dose, PDB code: 6kum:

Sodium binding site 1 out of 1 in the Ferredoxin I From C. Reinhardtii, Low 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, Low X-Ray Dose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na106 b:30.7 occ:1.00 O B:HOH215 2.6 21.3 0.7 OE1 B:GLU15 2.7 14.3 1.0 O B:HOH204 2.9 28.4 1.0 O B:ALA0 3.0 12.4 1.0 N B:SCN103 3.3 18.0 1.0 OE2 B:GLU15 3.3 16.5 1.0 C B:SCN103 3.3 19.6 1.0 CG B:LYS2 3.4 40.9 1.0 CD B:GLU15 3.4 15.1 1.0 N B:LYS2 3.4 9.3 1.0 O B:HOH215 3.5 13.5 0.3 C B:ALA0 3.7 12.0 1.0 C B:TYR1 3.8 10.5 1.0 CA B:TYR1 3.9 10.4 1.0 OD1 B:ASP82 4.0 9.7 1.0 N B:TYR1 4.1 10.2 1.0 CB B:LYS2 4.1 39.6 1.0 CA B:LYS2 4.2 9.9 1.0 S B:SCN103 4.5 17.5 1.0 O B:TYR1 4.6 10.5 1.0 OD2 B:ASP82 4.6 10.2 1.0 CA B:ALA0 4.7 11.8 1.0 CG B:ASP82 4.7 10.0 1.0 CB B:ALA0 4.9 11.8 1.0 CG B:GLU15 4.9 15.6 1.0 N B:ALA0 5.0 12.1 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