Magnesium in PDB 8boq: A. Vinelandii Fe-Nitrogenase Fefe Protein

All present enzymatic activity of A. Vinelandii Fe-Nitrogenase Fefe Protein:
1.18.6.1;

The structure of A. Vinelandii Fe-Nitrogenase Fefe Protein, PDB code: 8boq was solved by C.Trncik, F.Detemple, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	109.969, 151.048, 158.863, 90, 90, 90
R / Rfree (%)	16.9 / 21.6

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

Iron

(Fe)

32 atoms

The binding sites of Magnesium atom in the A. Vinelandii Fe-Nitrogenase Fefe Protein (pdb code 8boq). 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 Fe-Nitrogenase Fefe Protein, PDB code: 8boq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the A. Vinelandii Fe-Nitrogenase Fefe Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A. Vinelandii Fe-Nitrogenase Fefe Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:17.0 occ:1.00 OE1 B:GLU59 1.9 15.7 1.0 OD2 E:ASP301 2.0 19.8 1.0 O E:HOH813 2.0 13.2 1.0 O E:HOH665 2.1 14.8 1.0 O B:HOH654 2.2 16.9 1.0 O B:HOH810 2.2 18.8 1.0 CG E:ASP301 3.1 19.0 1.0 CD B:GLU59 3.1 14.4 1.0 CG B:GLU59 3.8 13.8 1.0 O B:TYR57 3.9 11.8 1.0 OD1 B:ASP209 3.9 21.6 1.0 CB E:ASP301 3.9 17.6 1.0 OD1 E:ASP301 4.0 17.3 1.0 NZ A:LYS413 4.1 17.3 1.0 OE2 B:GLU59 4.1 15.7 1.0 OD2 E:ASP305 4.2 18.0 1.0 O B:HOH734 4.2 15.7 1.0 O B:SER210 4.3 20.4 1.0 NZ A:LYS414 4.6 20.2 1.0 O B:LYS58 4.6 13.5 1.0 N B:SER210 4.6 19.0 1.0 O E:HOH768 4.7 38.5 1.0 CZ B:PHE424 4.7 17.7 1.0 C E:ASP301 4.8 16.2 1.0 N E:ALA302 4.9 16.2 1.0 CA B:ASP209 4.9 18.8 1.0

Magnesium binding site 2 out of 2 in the A. Vinelandii Fe-Nitrogenase Fefe Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A. Vinelandii Fe-Nitrogenase Fefe Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:15.9 occ:1.00 O E:HOH713 1.9 17.4 1.0 OD2 B:ASP301 2.0 19.9 1.0 OE1 E:GLU59 2.1 18.8 1.0 O B:HOH656 2.1 16.7 1.0 O E:HOH779 2.1 22.9 1.0 O B:HOH862 2.1 19.7 1.0 CD E:GLU59 3.2 20.6 1.0 CG B:ASP301 3.2 19.9 1.0 O E:TYR57 3.8 15.4 1.0 NZ D:LYS413 3.8 21.1 1.0 CG E:GLU59 3.8 19.5 1.0 OD1 B:ASP301 4.0 20.6 1.0 OD1 E:ASP209 4.1 22.4 1.0 OD2 B:ASP305 4.1 18.8 1.0 CB B:ASP301 4.1 18.4 1.0 OE2 E:GLU59 4.1 22.1 1.0 O E:HOH636 4.3 15.9 1.0 O E:SER210 4.4 26.3 1.0 O E:LYS58 4.5 16.1 1.0 NZ D:LYS414 4.6 24.6 1.0 O B:HOH668 4.6 36.8 1.0 N E:SER210 4.7 25.1 1.0 CZ E:PHE424 4.8 18.7 1.0 C B:ASP301 4.8 17.6 1.0 CE D:LYS413 4.9 21.0 1.0 C E:LYS58 4.9 17.1 1.0 O B:ASP301 4.9 18.0 1.0 N B:ALA302 5.0 17.5 1.0

C.Trncik, F.Detemple, O.Einsle. Iron-Only Fe-Nitrogenase Underscores Common Catalytic Principles in Biological Nitrogen Fixation Nat Catal 2023.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-023-00952-1