Iron in PDB 6n4k: Dithionite-Reduced Nucleotide-Free Form of the Nitrogenase Fe-Protein From A. Vinelandii

All present enzymatic activity of Dithionite-Reduced Nucleotide-Free Form of the Nitrogenase Fe-Protein From A. Vinelandii:
1.18.6.1;

The structure of Dithionite-Reduced Nucleotide-Free Form of the Nitrogenase Fe-Protein From A. Vinelandii, PDB code: 6n4k was solved by B.B.Wenke, T.Spatzal, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.29 / 1.76
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.620, 45.199, 108.772, 90.00, 96.58, 90.00
R / Rfree (%)	17.1 / 21.3

The binding sites of Iron atom in the Dithionite-Reduced Nucleotide-Free Form of the Nitrogenase Fe-Protein From A. Vinelandii (pdb code 6n4k). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Dithionite-Reduced Nucleotide-Free Form of the Nitrogenase Fe-Protein From A. Vinelandii, PDB code: 6n4k:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Dithionite-Reduced Nucleotide-Free Form of the Nitrogenase Fe-Protein From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dithionite-Reduced Nucleotide-Free Form of the Nitrogenase Fe-Protein From A. Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:18.3 occ:1.00 FE1 A:SF4301 0.0 18.3 1.0 S2 A:SF4301 2.2 18.5 1.0 S3 A:SF4301 2.2 18.3 1.0 S4 A:SF4301 2.3 18.7 1.0 SG A:CYS97 2.4 22.4 1.0 FE2 A:SF4301 2.6 17.9 1.0 FE4 A:SF4301 2.7 18.3 1.0 FE3 A:SF4301 2.7 19.1 1.0 CB A:CYS97 3.2 24.3 1.0 CA A:CYS97 3.6 24.2 1.0 S1 A:SF4301 3.8 19.1 1.0 N A:ALA98 4.0 21.6 1.0 CA A:GLY134 4.2 20.0 1.0 C A:CYS97 4.2 22.5 1.0 N A:GLY134 4.5 20.9 1.0 SG A:CYS132 4.6 18.9 1.0 SG B:CYS97 4.8 22.2 1.0 SG B:CYS132 4.8 19.9 1.0 N A:GLY99 4.8 22.0 1.0 CB B:CYS132 4.9 19.7 1.0 N A:CYS97 4.9 26.4 1.0

Iron binding site 2 out of 4 in the Dithionite-Reduced Nucleotide-Free Form of the Nitrogenase Fe-Protein From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dithionite-Reduced Nucleotide-Free Form of the Nitrogenase Fe-Protein From A. Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:17.9 occ:1.00 FE2 A:SF4301 0.0 17.9 1.0 S1 A:SF4301 2.2 19.1 1.0 S4 A:SF4301 2.2 18.7 1.0 S3 A:SF4301 2.2 18.3 1.0 SG A:CYS132 2.3 18.9 1.0 FE1 A:SF4301 2.6 18.3 1.0 FE4 A:SF4301 2.6 18.3 1.0 FE3 A:SF4301 2.7 19.1 1.0 CB A:CYS132 3.1 19.9 1.0 S2 A:SF4301 3.8 18.5 1.0 N A:GLY134 4.1 20.9 1.0 CA A:GLY134 4.2 20.0 1.0 CA A:CYS132 4.5 19.9 1.0 SG A:CYS97 4.7 22.4 1.0 SG B:CYS132 4.8 19.9 1.0 CD2 A:PHE135 4.8 20.1 1.0 C A:CYS132 4.8 20.3 1.0 CA B:CYS97 4.8 22.8 1.0 SG B:CYS97 4.9 22.2 1.0 N A:GLY133 4.9 21.6 1.0 O B:GLY96 5.0 24.4 1.0 CG1 A:VAL130 5.0 26.7 1.0

Iron binding site 3 out of 4 in the Dithionite-Reduced Nucleotide-Free Form of the Nitrogenase Fe-Protein From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dithionite-Reduced Nucleotide-Free Form of the Nitrogenase Fe-Protein From A. Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:19.1 occ:1.00 FE3 A:SF4301 0.0 19.1 1.0 S4 A:SF4301 2.2 18.7 1.0 S1 A:SF4301 2.2 19.1 1.0 S2 A:SF4301 2.2 18.5 1.0 SG B:CYS97 2.4 22.2 1.0 FE4 A:SF4301 2.6 18.3 1.0 FE1 A:SF4301 2.7 18.3 1.0 FE2 A:SF4301 2.7 17.9 1.0 CB B:CYS97 3.3 23.4 1.0 CA B:CYS97 3.6 22.8 1.0 S3 A:SF4301 3.8 18.3 1.0 N B:ALA98 4.0 21.9 1.0 CA B:GLY134 4.1 19.4 1.0 C B:CYS97 4.2 23.0 1.0 N B:GLY134 4.5 18.6 1.0 SG B:CYS132 4.7 19.9 1.0 SG A:CYS97 4.8 22.4 1.0 SG A:CYS132 4.8 18.9 1.0 CB A:CYS132 4.8 19.9 1.0 N B:GLY99 4.9 23.8 1.0 N B:CYS97 5.0 25.0 1.0

Iron binding site 4 out of 4 in the Dithionite-Reduced Nucleotide-Free Form of the Nitrogenase Fe-Protein From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dithionite-Reduced Nucleotide-Free Form of the Nitrogenase Fe-Protein From A. Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:18.3 occ:1.00 FE4 A:SF4301 0.0 18.3 1.0 S3 A:SF4301 2.2 18.3 1.0 S1 A:SF4301 2.2 19.1 1.0 S2 A:SF4301 2.3 18.5 1.0 SG B:CYS132 2.4 19.9 1.0 FE3 A:SF4301 2.6 19.1 1.0 FE2 A:SF4301 2.6 17.9 1.0 FE1 A:SF4301 2.7 18.3 1.0 CB B:CYS132 3.1 19.7 1.0 S4 A:SF4301 3.8 18.7 1.0 N B:GLY134 4.1 18.6 1.0 CA B:GLY134 4.2 19.4 1.0 CA B:CYS132 4.5 20.4 1.0 SG B:CYS97 4.7 22.2 1.0 SG A:CYS132 4.7 18.9 1.0 CA A:CYS97 4.8 24.2 1.0 CD2 B:PHE135 4.8 17.8 1.0 CG1 B:VAL130 4.8 23.7 1.0 SG A:CYS97 4.8 22.4 1.0 C B:CYS132 4.9 20.1 1.0 N B:GLY133 4.9 20.8 1.0 O A:GLY96 5.0 24.9 1.0 N A:ALA98 5.0 21.6 1.0

B.B.Wenke, T.Spatzal, D.C.Rees. Site-Specific Oxidation State Assignments of the Iron Atoms in the [4FE:4S]2+/1+/0STATES of the Nitrogenase Fe-Protein. Angew. Chem. Int. Ed. Engl. V. 58 3894 2019.
ISSN: ESSN 1521-3773
PubMed: 30698901
DOI: 10.1002/ANIE.201813966