Iron in PDB 9haz: A. Vinelandii Nitrogenase Fe Protein ANC1B

The structure of A. Vinelandii Nitrogenase Fe Protein ANC1B, PDB code: 9haz was solved by F.Detemple, B.Kacar, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.84 / 2.43
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.352, 109.784, 95.213, 90, 118.61, 90
R / Rfree (%)	19.5 / 27.2

The structure of A. Vinelandii Nitrogenase Fe Protein ANC1B also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Iron atom in the A. Vinelandii Nitrogenase Fe Protein ANC1B (pdb code 9haz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the A. Vinelandii Nitrogenase Fe Protein ANC1B, PDB code: 9haz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the A. Vinelandii Nitrogenase Fe Protein ANC1B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of A. Vinelandii Nitrogenase Fe Protein ANC1B within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:17.9 occ:1.00 FE1 A:SF4301 0.0 17.9 1.0 S3 A:SF4301 2.3 19.8 1.0 S2 A:SF4301 2.3 18.4 1.0 S4 A:SF4301 2.3 20.4 1.0 SG D:CYS133 2.5 22.6 1.0 FE2 A:SF4301 2.7 20.3 1.0 FE3 A:SF4301 2.8 20.9 1.0 FE4 A:SF4301 2.8 20.5 1.0 CB D:CYS133 3.1 24.2 1.0 S1 A:SF4301 3.9 19.1 1.0 N D:GLY135 4.0 23.8 1.0 CA D:GLY135 4.1 24.4 1.0 SG A:CYS133 4.5 27.0 1.0 CA D:CYS133 4.5 25.0 1.0 CA A:CYS98 4.6 30.7 1.0 SG A:CYS98 4.6 26.4 1.0 O A:GLY97 4.8 28.5 1.0 N A:ALA99 4.9 33.2 1.0 N D:GLY134 4.9 24.4 1.0 CB A:CYS98 4.9 29.0 1.0 SG D:CYS98 4.9 28.8 1.0 C D:CYS133 4.9 24.6 1.0

Iron binding site 2 out of 8 in the A. Vinelandii Nitrogenase Fe Protein ANC1B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of A. Vinelandii Nitrogenase Fe Protein ANC1B within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:20.3 occ:1.00 FE2 A:SF4301 0.0 20.3 1.0 SG A:CYS133 2.1 27.0 1.0 S4 A:SF4301 2.3 20.4 1.0 S3 A:SF4301 2.3 19.8 1.0 S1 A:SF4301 2.3 19.1 1.0 FE1 A:SF4301 2.7 17.9 1.0 FE3 A:SF4301 2.7 20.9 1.0 FE4 A:SF4301 2.8 20.5 1.0 CB A:CYS133 3.2 26.1 1.0 N A:GLY135 3.8 21.4 1.0 S2 A:SF4301 3.8 18.4 1.0 CA A:GLY135 4.1 21.6 1.0 CA A:CYS133 4.5 26.2 1.0 SG A:CYS98 4.5 26.4 1.0 N A:GLY134 4.6 24.7 1.0 C A:CYS133 4.6 25.4 1.0 SG D:CYS98 4.8 28.8 1.0 CD2 A:PHE136 4.8 19.6 1.0 CA D:CYS98 4.8 28.3 1.0 N D:ALA99 4.8 29.6 1.0 SG D:CYS133 4.9 22.6 1.0 N A:PHE136 4.9 20.7 1.0 O D:GLY97 5.0 29.4 1.0 C A:GLY134 5.0 22.2 1.0

Iron binding site 3 out of 8 in the A. Vinelandii Nitrogenase Fe Protein ANC1B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of A. Vinelandii Nitrogenase Fe Protein ANC1B within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:20.9 occ:1.00 FE3 A:SF4301 0.0 20.9 1.0 SG A:CYS98 2.1 26.4 1.0 S1 A:SF4301 2.3 19.1 1.0 S4 A:SF4301 2.3 20.4 1.0 S2 A:SF4301 2.3 18.4 1.0 FE2 A:SF4301 2.7 20.3 1.0 FE4 A:SF4301 2.7 20.5 1.0 FE1 A:SF4301 2.8 17.9 1.0 CB A:CYS98 3.1 29.0 1.0 CA A:CYS98 3.6 30.7 1.0 S3 A:SF4301 3.9 19.8 1.0 N A:ALA99 4.0 33.2 1.0 CA A:GLY135 4.0 21.6 1.0 C A:CYS98 4.3 32.0 1.0 N A:GLY135 4.3 21.4 1.0 SG A:CYS133 4.6 27.0 1.0 SG D:CYS98 4.7 28.8 1.0 N A:CYS98 4.8 30.4 1.0 N A:GLY100 4.9 38.8 1.0

Iron binding site 4 out of 8 in the A. Vinelandii Nitrogenase Fe Protein ANC1B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of A. Vinelandii Nitrogenase Fe Protein ANC1B within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:20.5 occ:1.00 FE4 A:SF4301 0.0 20.5 1.0 S2 A:SF4301 2.3 18.4 1.0 S1 A:SF4301 2.3 19.1 1.0 SG D:CYS98 2.3 28.8 1.0 S3 A:SF4301 2.3 19.8 1.0 FE3 A:SF4301 2.7 20.9 1.0 FE2 A:SF4301 2.8 20.3 1.0 FE1 A:SF4301 2.8 17.9 1.0 CB D:CYS98 3.4 28.3 1.0 CA D:CYS98 3.7 28.3 1.0 N D:ALA99 3.9 29.6 1.0 S4 A:SF4301 3.9 20.4 1.0 CA D:GLY135 3.9 24.4 1.0 C D:CYS98 4.2 27.9 1.0 N D:GLY135 4.3 23.8 1.0 SG D:CYS133 4.7 22.6 1.0 SG A:CYS133 4.7 27.0 1.0 SG A:CYS98 4.7 26.4 1.0 N D:GLY100 4.8 31.2 1.0

Iron binding site 5 out of 8 in the A. Vinelandii Nitrogenase Fe Protein ANC1B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of A. Vinelandii Nitrogenase Fe Protein ANC1B within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:19.3 occ:1.00 FE1 B:SF4301 0.0 19.3 1.0 S3 B:SF4301 2.2 18.4 1.0 S2 B:SF4301 2.2 22.7 1.0 S4 B:SF4301 2.3 20.0 1.0 SG B:CYS133 2.4 23.4 1.0 FE2 B:SF4301 2.7 20.0 1.0 FE3 B:SF4301 2.7 18.8 1.0 FE4 B:SF4301 2.7 19.5 1.0 CB B:CYS133 3.1 25.2 1.0 S1 B:SF4301 3.9 22.2 1.0 N B:GLY135 4.0 22.6 1.0 CA B:GLY135 4.2 22.5 1.0 CA B:CYS133 4.5 25.7 1.0 SG C:CYS133 4.6 28.7 1.0 SG C:CYS98 4.6 22.3 1.0 CA C:CYS98 4.7 23.5 1.0 N B:PHE136 4.8 21.3 1.0 CD2 B:PHE136 4.8 17.9 1.0 N B:GLY134 4.9 25.1 1.0 N C:ALA99 4.9 26.2 1.0 C B:CYS133 4.9 26.4 1.0 SG B:CYS98 4.9 22.1 1.0 CB C:CYS98 5.0 22.8 1.0 C B:GLY135 5.0 22.2 1.0

Iron binding site 6 out of 8 in the A. Vinelandii Nitrogenase Fe Protein ANC1B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of A. Vinelandii Nitrogenase Fe Protein ANC1B within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:20.0 occ:1.00 FE2 B:SF4301 0.0 20.0 1.0 S3 B:SF4301 2.2 18.4 1.0 S4 B:SF4301 2.3 20.0 1.0 S1 B:SF4301 2.3 22.2 1.0 SG B:CYS98 2.4 22.1 1.0 FE4 B:SF4301 2.7 19.5 1.0 FE1 B:SF4301 2.7 19.3 1.0 FE3 B:SF4301 2.7 18.8 1.0 CB B:CYS98 3.4 22.9 1.0 CA B:CYS98 3.7 24.0 1.0 S2 B:SF4301 3.8 22.7 1.0 N B:ALA99 3.9 27.8 1.0 CA B:GLY135 4.1 22.5 1.0 C B:CYS98 4.2 25.1 1.0 N B:GLY135 4.5 22.6 1.0 N B:GLY100 4.7 34.6 1.0 SG C:CYS133 4.7 28.7 1.0 SG C:CYS98 4.7 22.3 1.0 SG B:CYS133 4.7 23.4 1.0 CA B:ALA99 5.0 29.5 1.0

Iron binding site 7 out of 8 in the A. Vinelandii Nitrogenase Fe Protein ANC1B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of A. Vinelandii Nitrogenase Fe Protein ANC1B within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:18.8 occ:1.00 FE3 B:SF4301 0.0 18.8 1.0 SG C:CYS133 2.1 28.7 1.0 S1 B:SF4301 2.2 22.2 1.0 S2 B:SF4301 2.3 22.7 1.0 S4 B:SF4301 2.3 20.0 1.0 FE4 B:SF4301 2.7 19.5 1.0 FE1 B:SF4301 2.7 19.3 1.0 FE2 B:SF4301 2.7 20.0 1.0 CB C:CYS133 3.1 28.0 1.0 N C:GLY135 3.6 23.8 1.0 S3 B:SF4301 3.8 18.4 1.0 CA C:GLY135 4.0 23.7 1.0 N C:GLY134 4.3 25.4 1.0 CA C:CYS133 4.4 27.6 1.0 SG C:CYS98 4.6 22.3 1.0 C C:CYS133 4.6 26.1 1.0 C C:GLY134 4.8 24.1 1.0 SG B:CYS133 4.8 23.4 1.0 CD2 C:PHE136 4.8 20.4 1.0 SG B:CYS98 4.8 22.1 1.0 CA B:CYS98 4.9 24.0 1.0 O B:GLY97 4.9 25.3 1.0 N C:PHE136 4.9 20.8 1.0 N B:ALA99 4.9 27.8 1.0

Iron binding site 8 out of 8 in the A. Vinelandii Nitrogenase Fe Protein ANC1B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of A. Vinelandii Nitrogenase Fe Protein ANC1B within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:19.5 occ:1.00 FE4 B:SF4301 0.0 19.5 1.0 SG C:CYS98 2.2 22.3 1.0 S1 B:SF4301 2.3 22.2 1.0 S2 B:SF4301 2.3 22.7 1.0 S3 B:SF4301 2.3 18.4 1.0 FE3 B:SF4301 2.7 18.8 1.0 FE2 B:SF4301 2.7 20.0 1.0 FE1 B:SF4301 2.7 19.3 1.0 CB C:CYS98 3.2 22.8 1.0 CA C:CYS98 3.7 23.5 1.0 CA C:GLY135 3.8 23.7 1.0 S4 B:SF4301 3.8 20.0 1.0 N C:GLY135 4.0 23.8 1.0 N C:ALA99 4.2 26.2 1.0 C C:CYS98 4.3 24.2 1.0 SG C:CYS133 4.5 28.7 1.0 SG B:CYS98 4.7 22.1 1.0 N C:GLY100 4.8 26.9 1.0 SG B:CYS133 5.0 23.4 1.0

B.Cuevas-Zuviria, F.Detemple, K.Amritkar, A.K.Garcia, L.C.Seefeldt, O.Einsle, B.Kacar. Structural Evolution of Nitrogenase Enzymes Over Geologic Time Elife 2025.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.105613.3