Magnesium in PDB 9hb9: A. Vinelandii Nitrogenase Mofe Protein ANC1A

All present enzymatic activity of A. Vinelandii Nitrogenase Mofe Protein ANC1A:
1.18.6.1;

The structure of A. Vinelandii Nitrogenase Mofe Protein ANC1A, PDB code: 9hb9 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)	19.88 / 2.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.29, 138.615, 208.581, 90, 90, 90
R / Rfree (%)	16.9 / 22

The structure of A. Vinelandii Nitrogenase Mofe Protein ANC1A also contains other interesting chemical elements:

Molybdenum	(Mo)	2 atoms
Iron	(Fe)	30 atoms

The binding sites of Magnesium atom in the A. Vinelandii Nitrogenase Mofe Protein ANC1A (pdb code 9hb9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the A. Vinelandii Nitrogenase Mofe Protein ANC1A, PDB code: 9hb9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the A. Vinelandii Nitrogenase Mofe Protein ANC1A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A. Vinelandii Nitrogenase Mofe Protein ANC1A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:21.9 occ:1.00 OD2 B:ASP357 2.1 53.2 1.0 OE2 D:GLU109 2.3 40.8 1.0 O D:ARG108 2.4 39.7 1.0 OD2 B:ASP353 2.4 48.1 1.0 O B:HOH706 2.7 17.6 1.0 O D:HOH732 3.1 28.1 1.0 CD D:GLU109 3.3 43.5 1.0 CG B:ASP357 3.3 48.8 1.0 C D:ARG108 3.4 37.9 1.0 CG B:ASP353 3.5 44.2 1.0 O D:PHE107 3.6 36.0 1.0 CG D:GLU109 3.7 43.0 1.0 CB D:ARG108 3.8 37.1 1.0 OD1 B:ASP353 3.9 44.2 1.0 OD1 B:ASP357 3.9 50.8 1.0 CA D:ARG108 4.2 36.3 1.0 N D:GLU109 4.3 39.6 1.0 OE1 D:GLU109 4.4 42.0 1.0 CB B:ASP357 4.5 43.1 1.0 C D:PHE107 4.6 33.9 1.0 CA D:GLU109 4.6 39.6 1.0 CE1 D:HIS478 4.7 29.7 1.0 CB D:GLU109 4.8 40.8 1.0 CB B:ASP353 4.8 38.6 1.0 O B:ASP353 4.9 27.9 1.0 N D:ARG108 4.9 34.9 1.0 NE2 D:HIS480 4.9 37.9 1.0 CE1 D:HIS480 4.9 38.6 1.0 ND1 D:HIS478 5.0 29.2 1.0

Magnesium binding site 2 out of 2 in the A. Vinelandii Nitrogenase Mofe Protein ANC1A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A. Vinelandii Nitrogenase Mofe Protein ANC1A within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:19.2 occ:1.00 OE2 B:GLU109 1.9 42.0 1.0 O D:HOH712 2.0 32.5 1.0 O B:ARG108 2.2 43.0 1.0 OD2 D:ASP357 2.2 38.3 1.0 OD2 D:ASP353 2.2 38.2 1.0 O D:HOH703 2.5 39.8 1.0 CG D:ASP353 3.0 38.1 1.0 CD B:GLU109 3.0 45.8 1.0 OD1 D:ASP353 3.0 37.4 1.0 CG D:ASP357 3.1 37.0 1.0 OD1 D:ASP357 3.3 41.2 1.0 C B:ARG108 3.4 42.5 1.0 CG B:GLU109 3.7 46.6 1.0 OE1 B:GLU109 4.0 46.3 1.0 N B:GLU109 4.2 42.1 1.0 CA B:GLU109 4.2 43.2 1.0 CB B:ARG108 4.3 43.6 1.0 CA B:ARG108 4.4 42.7 1.0 O B:PHE107 4.4 35.7 1.0 NZ A:LYS433 4.4 60.1 1.0 CB D:ASP353 4.4 37.0 1.0 CD1 A:TYR429 4.4 46.2 1.0 CB D:ASP357 4.5 33.3 1.0 O D:ASP353 4.5 38.2 1.0 CB B:GLU109 4.6 45.0 1.0 CE A:LYS433 4.7 58.0 1.0 C D:ASP353 4.9 35.8 1.0 CG A:TYR429 4.9 46.7 1.0 CB A:TYR429 5.0 49.4 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