Iron 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:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the Ferredoxin I From C. Reinhardtii, Low X-Ray Dose, PDB code: 6kum:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Ferredoxin I From C. Reinhardtii, Low X-Ray Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 A:Fe101 b:9.2 occ:1.00 FE1 A:FES101 0.0 9.2 1.0 S2 A:FES101 2.1 9.3 1.0 S1 A:FES101 2.2 9.3 1.0 SG A:CYS42 2.3 10.0 1.0 SG A:CYS37 2.3 11.6 1.0 FE2 A:FES101 2.7 8.0 1.0 CB A:CYS42 3.5 10.5 1.0 CB A:CYS37 3.5 11.7 1.0 N A:CYS42 3.7 11.0 1.0 N A:CYS37 3.7 10.9 1.0 N A:ARG38 3.8 14.1 0.5 N A:ARG38 3.8 14.1 0.5 CA A:CYS42 3.9 10.8 1.0 CA A:CYS37 4.0 11.3 1.0 C A:CYS42 4.0 10.0 1.0 O A:CYS42 4.2 9.7 1.0 N A:ALA41 4.3 12.2 1.0 C A:CYS37 4.3 11.1 1.0 OG A:SER36 4.3 10.1 0.8 SG A:CYS75 4.4 8.5 1.0 N A:GLY40 4.4 10.7 1.0 N A:ALA39 4.5 12.5 1.0 C A:ALA41 4.5 12.8 1.0 N A:SER44 4.6 9.3 1.0 SG A:CYS45 4.6 7.3 1.0 N A:SER43 4.6 11.5 1.0 CA A:ARG38 4.7 14.1 0.5 CA A:ARG38 4.7 14.1 0.5 C A:SER36 4.7 9.8 0.8 CB A:SER44 4.7 9.6 1.0 N A:SER36 4.8 8.7 0.8 C A:SER36 4.8 9.9 0.2 N A:SER36 4.8 8.7 0.2 CA A:GLY40 4.9 10.8 1.0 C A:GLY40 4.9 11.4 1.0

Iron binding site 2 out of 4 in the Ferredoxin I From C. Reinhardtii, Low X-Ray Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ferredoxin I From C. Reinhardtii, Low X-Ray Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:8.0 occ:1.00 FE2 A:FES101 0.0 8.0 1.0 S2 A:FES101 2.1 9.3 1.0 S1 A:FES101 2.2 9.3 1.0 SG A:CYS45 2.3 7.3 1.0 SG A:CYS75 2.3 8.5 1.0 FE1 A:FES101 2.7 9.2 1.0 CB A:CYS75 3.2 8.0 1.0 CB A:CYS45 3.3 6.8 1.0 N A:CYS75 4.2 7.4 1.0 N A:CYS45 4.3 7.6 1.0 N A:ARG38 4.3 14.1 0.5 CA A:CYS75 4.3 8.0 1.0 N A:ARG38 4.3 14.1 0.5 N A:GLY40 4.3 10.7 1.0 SG A:CYS37 4.4 11.6 1.0 CA A:ARG38 4.4 14.1 0.5 CA A:CYS45 4.4 7.1 1.0 CA A:ARG38 4.4 14.1 0.5 CB A:LEU73 4.5 8.3 1.0 SG A:CYS42 4.6 10.0 1.0 CA A:GLY40 4.7 10.8 1.0 N A:ALA39 4.7 12.5 1.0 O A:CYS42 4.9 9.7 1.0 C A:ARG38 4.9 14.1 0.5 C A:ARG38 4.9 14.2 0.5

Iron binding site 3 out of 4 in the Ferredoxin I From C. Reinhardtii, Low X-Ray Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ferredoxin I From C. Reinhardtii, Low X-Ray Dose within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:9.0 occ:1.00 FE1 B:FES101 0.0 9.0 1.0 S2 B:FES101 2.2 9.0 1.0 S1 B:FES101 2.2 8.4 1.0 SG B:CYS42 2.3 9.5 1.0 SG B:CYS37 2.3 10.3 1.0 FE2 B:FES101 2.7 8.1 1.0 CB B:CYS42 3.4 10.0 1.0 CB B:CYS37 3.5 10.2 1.0 N B:CYS37 3.7 9.0 1.0 N B:CYS42 3.7 10.1 1.0 N B:ARG38 3.8 12.1 1.0 CA B:CYS42 3.9 10.2 1.0 CA B:CYS37 4.0 9.8 1.0 C B:CYS42 4.0 9.5 1.0 O B:CYS42 4.1 9.1 1.0 N B:ALA41 4.2 13.0 1.0 C B:CYS37 4.3 9.9 1.0 OG B:SER36 4.3 10.3 1.0 SG B:CYS75 4.4 8.2 1.0 N B:GLY40 4.5 13.5 1.0 N B:ALA39 4.5 13.7 1.0 C B:ALA41 4.5 13.0 1.0 N B:SER44 4.6 8.8 1.0 SG B:CYS45 4.6 7.7 1.0 CA B:ARG38 4.7 12.3 1.0 N B:SER43 4.7 11.7 1.0 C B:SER36 4.7 10.4 1.0 CB B:SER44 4.8 9.0 1.0 N B:SER36 4.8 9.8 1.0 C B:GLY40 5.0 11.6 1.0 CA B:ALA41 5.0 13.2 1.0 CA B:GLY40 5.0 12.2 1.0

Iron binding site 4 out of 4 in the Ferredoxin I From C. Reinhardtii, Low X-Ray Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ferredoxin I From C. Reinhardtii, Low X-Ray Dose within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:8.1 occ:1.00 FE2 B:FES101 0.0 8.1 1.0 S2 B:FES101 2.1 9.0 1.0 S1 B:FES101 2.2 8.4 1.0 SG B:CYS75 2.3 8.2 1.0 SG B:CYS45 2.3 7.7 1.0 FE1 B:FES101 2.7 9.0 1.0 CB B:CYS75 3.2 8.2 1.0 CB B:CYS45 3.3 7.6 1.0 N B:CYS75 4.2 8.3 1.0 N B:CYS45 4.3 8.6 1.0 CA B:CYS75 4.3 8.1 1.0 N B:GLY40 4.3 13.5 1.0 N B:ARG38 4.3 12.1 1.0 SG B:CYS37 4.4 10.3 1.0 CA B:CYS45 4.4 8.0 1.0 CA B:ARG38 4.4 12.3 1.0 CB B:LEU73 4.5 7.5 1.0 SG B:CYS42 4.6 9.5 1.0 CA B:GLY40 4.7 12.2 1.0 N B:ALA39 4.7 13.7 1.0 O B:CYS42 4.9 9.1 1.0 C B:ARG38 4.9 13.0 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