Iron in PDB 6lk1: Ultrahigh Resolution X-Ray Structure of Ferredoxin I From C. Reinhardtii

The structure of Ultrahigh Resolution X-Ray Structure of Ferredoxin I From C. Reinhardtii, PDB code: 6lk1 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)	37.96 / 0.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	25.955, 60.090, 50.085, 90.00, 102.40, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Iron atom in the Ultrahigh Resolution X-Ray Structure of Ferredoxin I From C. Reinhardtii (pdb code 6lk1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Ultrahigh Resolution X-Ray Structure of Ferredoxin I From C. Reinhardtii, PDB code: 6lk1:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Ultrahigh Resolution X-Ray Structure of Ferredoxin I From C. Reinhardtii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ultrahigh Resolution X-Ray Structure of Ferredoxin I From C. Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:7.5 occ:1.00 FE1 A:FES101 0.0 7.5 1.0 S2 A:FES101 2.2 7.5 1.0 S1 A:FES101 2.2 7.2 1.0 SG A:CYS43 2.3 8.4 1.0 SG A:CYS38 2.3 8.5 1.0 FE2 A:FES101 2.7 6.5 1.0 CB A:CYS43 3.4 9.3 1.0 CB A:CYS38 3.5 10.9 1.0 N A:CYS38 3.6 9.4 1.0 N A:CYS43 3.6 8.1 1.0 N A:ARG39 3.8 7.8 1.0 CA A:CYS43 3.8 8.2 1.0 CA A:CYS38 3.9 9.8 1.0 C A:CYS43 4.0 8.1 1.0 O A:CYS43 4.2 9.8 1.0 C A:CYS38 4.3 9.5 1.0 N A:ALA42 4.3 8.4 1.0 OG A:SER37 4.3 6.1 0.4 SG A:CYS76 4.4 7.0 1.0 N A:GLY41 4.4 7.7 1.0 C A:ALA42 4.5 8.9 1.0 N A:ALA40 4.5 8.7 1.0 N A:SER45 4.5 7.3 1.0 SG A:CYS46 4.6 6.2 1.0 C A:SER37 4.7 9.1 1.0 N A:SER44 4.7 8.6 1.0 CA A:ARG39 4.7 8.6 0.5 CB A:SER45 4.7 9.3 1.0 CA A:ARG39 4.7 8.2 0.5 N A:SER37 4.7 7.8 1.0 C A:GLY41 5.0 7.8 1.0 CA A:ALA42 5.0 8.6 1.0 CA A:GLY41 5.0 7.5 1.0

Iron binding site 2 out of 4 in the Ultrahigh Resolution X-Ray Structure of Ferredoxin I From C. Reinhardtii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ultrahigh Resolution X-Ray Structure of Ferredoxin I From C. Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:6.5 occ:1.00 FE2 A:FES101 0.0 6.5 1.0 S2 A:FES101 2.2 7.5 1.0 S1 A:FES101 2.2 7.2 1.0 SG A:CYS46 2.3 6.2 1.0 SG A:CYS76 2.3 7.0 1.0 FE1 A:FES101 2.7 7.5 1.0 CB A:CYS76 3.2 7.2 1.0 CB A:CYS46 3.3 6.4 1.0 N A:CYS76 4.2 5.7 1.0 N A:CYS46 4.2 6.8 1.0 N A:GLY41 4.3 7.7 1.0 CA A:CYS76 4.3 6.2 1.0 N A:ARG39 4.3 7.8 1.0 CA A:CYS46 4.4 6.2 1.0 SG A:CYS38 4.4 8.5 1.0 CA A:ARG39 4.4 8.6 0.5 CA A:ARG39 4.4 8.2 0.5 CB A:LEU74 4.5 6.5 1.0 SG A:CYS43 4.6 8.4 1.0 CA A:GLY41 4.7 7.5 1.0 N A:ALA40 4.7 8.7 1.0 O A:CYS43 4.9 9.8 1.0 C A:ARG39 4.9 8.6 1.0

Iron binding site 3 out of 4 in the Ultrahigh Resolution X-Ray Structure of Ferredoxin I From C. Reinhardtii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ultrahigh Resolution X-Ray Structure of Ferredoxin I From C. Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:7.8 occ:1.00 FE1 B:FES101 0.0 7.8 1.0 S2 B:FES101 2.2 7.8 1.0 S1 B:FES101 2.3 7.4 1.0 SG B:CYS43 2.3 8.5 1.0 SG B:CYS38 2.3 9.3 1.0 FE2 B:FES101 2.8 6.9 1.0 CB B:CYS43 3.4 9.0 1.0 CB B:CYS38 3.5 10.5 1.0 N B:CYS43 3.6 8.9 1.0 N B:CYS38 3.6 9.2 1.0 N B:ARG39 3.8 9.3 1.0 CA B:CYS43 3.8 8.4 1.0 CA B:CYS38 4.0 9.9 1.0 C B:CYS43 4.1 8.2 1.0 O B:CYS43 4.2 10.2 1.0 OG B:SER37 4.2 5.0 0.4 N B:ALA42 4.2 9.3 1.0 C B:CYS38 4.3 10.5 1.0 SG B:CYS76 4.4 7.8 1.0 N B:ALA40 4.5 9.3 1.0 N B:GLY41 4.5 8.9 1.0 C B:ALA42 4.5 9.1 1.0 N B:SER45 4.5 7.4 1.0 SG B:CYS46 4.6 6.8 1.0 N B:SER44 4.6 8.2 1.0 C B:SER37 4.7 9.0 1.0 CA B:ARG39 4.7 8.8 1.0 CB B:SER45 4.7 8.4 1.0 N B:SER37 4.7 7.9 1.0 CA B:ALA42 4.9 9.8 1.0 C B:GLY41 5.0 9.6 1.0 CA B:GLY41 5.0 9.8 1.0 N B:CYS46 5.0 6.8 1.0

Iron binding site 4 out of 4 in the Ultrahigh Resolution X-Ray Structure of Ferredoxin I From C. Reinhardtii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ultrahigh Resolution X-Ray Structure of Ferredoxin I From C. Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:6.9 occ:1.00 FE2 B:FES101 0.0 6.9 1.0 S2 B:FES101 2.2 7.8 1.0 S1 B:FES101 2.2 7.4 1.0 SG B:CYS46 2.3 6.8 1.0 SG B:CYS76 2.3 7.8 1.0 FE1 B:FES101 2.8 7.8 1.0 CB B:CYS76 3.2 7.9 1.0 CB B:CYS46 3.3 6.7 1.0 N B:CYS76 4.2 7.2 1.0 N B:CYS46 4.2 6.8 1.0 CA B:CYS76 4.3 7.2 1.0 N B:ARG39 4.3 9.3 1.0 N B:GLY41 4.3 8.9 1.0 CA B:CYS46 4.4 6.3 1.0 SG B:CYS38 4.4 9.3 1.0 CA B:ARG39 4.4 8.8 1.0 CB B:LEU74 4.5 6.2 1.0 SG B:CYS43 4.6 8.5 1.0 N B:ALA40 4.6 9.3 1.0 CA B:GLY41 4.7 9.8 1.0 C B:ARG39 4.8 9.0 1.0 O B:CYS43 4.9 10.2 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