Magnesium in PDB 8q5x: Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis

The structure of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis, PDB code: 8q5x was solved by N.Maslac, T.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.89 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.546, 111.094, 78.82, 90, 90.01, 90
R / Rfree (%)	16 / 18.6

The structure of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis also contains other interesting chemical elements:

Iron	(Fe)	8 atoms
Calcium	(Ca)	4 atoms

The binding sites of Magnesium atom in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis (pdb code 8q5x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis, PDB code: 8q5x:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:7.1 occ:1.00 OG A:SER16 2.0 10.8 1.0 O A:HOH416 2.0 8.8 1.0 O3B A:ADP301 2.1 13.6 1.0 O A:HOH437 2.1 13.2 1.0 O A:HOH424 2.2 11.3 1.0 O A:HOH474 2.2 13.3 1.0 CB A:SER16 3.1 9.8 1.0 PB A:ADP301 3.3 10.6 1.0 O2B A:ADP301 3.5 8.6 1.0 OD1 A:ASP44 3.8 23.6 1.0 OD2 A:ASP40 3.9 19.1 1.0 N A:SER16 3.9 13.7 1.0 OD2 A:ASP125 4.0 13.5 1.0 CA A:SER16 4.1 11.4 1.0 O2A A:ADP301 4.2 12.9 1.0 OG A:SER45 4.2 17.2 1.0 O1B A:ADP301 4.3 8.2 1.0 OD1 A:ASP125 4.4 10.5 1.0 O3A A:ADP301 4.4 11.3 1.0 O1A A:ADP301 4.5 11.5 1.0 CG A:ASP40 4.6 13.5 1.0 CG A:ASP125 4.6 10.3 1.0 PA A:ADP301 4.6 11.4 1.0 CB A:LYS15 4.8 10.9 1.0 O A:HOH549 4.8 14.4 1.0 CG A:ASP44 4.9 24.1 1.0 CB A:ASP40 4.9 11.1 1.0 C A:LYS15 4.9 9.8 1.0

Magnesium binding site 2 out of 4 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:9.9 occ:1.00 OG B:SER16 2.0 9.6 1.0 O B:HOH487 2.1 10.9 1.0 O B:HOH475 2.1 12.7 1.0 O3B B:ADP303 2.1 11.5 1.0 O B:HOH513 2.2 14.2 1.0 O B:HOH434 2.2 11.6 1.0 CB B:SER16 3.1 10.1 1.0 PB B:ADP303 3.3 11.0 1.0 O1B B:ADP303 3.4 10.5 1.0 OD1 B:ASP44 3.8 20.1 1.0 OD2 B:ASP40 3.9 16.0 1.0 N B:SER16 3.9 11.3 1.0 O1A B:ADP303 4.0 15.1 1.0 OD2 B:ASP125 4.1 14.9 1.0 CA B:SER16 4.1 9.3 1.0 OG B:SER45 4.3 14.6 1.0 O2B B:ADP303 4.3 11.2 1.0 O3A B:ADP303 4.4 13.8 1.0 OD1 B:ASP125 4.4 13.2 1.0 CG B:ASP40 4.5 13.2 1.0 PA B:ADP303 4.6 12.5 1.0 O2A B:ADP303 4.6 12.3 1.0 CG B:ASP125 4.6 14.1 1.0 O B:HOH546 4.8 13.1 1.0 CB B:ASP40 4.9 11.3 1.0 CB B:LYS15 5.0 8.7 1.0 CG B:ASP44 5.0 20.4 1.0

Magnesium binding site 3 out of 4 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:7.9 occ:1.00 OG C:SER16 2.0 9.8 1.0 O3B C:ADP302 2.1 11.4 1.0 O C:HOH494 2.1 14.9 1.0 O C:HOH547 2.2 15.3 1.0 O C:HOH484 2.2 12.3 1.0 O C:HOH436 2.3 12.1 1.0 CB C:SER16 3.2 15.7 1.0 PB C:ADP302 3.3 11.4 1.0 O1B C:ADP302 3.4 10.9 1.0 OD2 C:ASP40 3.8 16.8 1.0 N C:SER16 3.9 12.5 1.0 OD2 C:ASP125 4.0 15.0 1.0 O1A C:ADP302 4.1 15.9 1.0 CA C:SER16 4.1 13.5 1.0 OD1 C:ASP44 4.1 19.1 1.0 O2B C:ADP302 4.2 11.3 1.0 OG C:SER45 4.3 14.5 1.0 OD1 C:ASP125 4.3 13.7 1.0 O3A C:ADP302 4.4 8.9 1.0 CG C:ASP40 4.6 16.3 1.0 O2A C:ADP302 4.6 10.2 1.0 PA C:ADP302 4.6 14.8 1.0 CG C:ASP125 4.6 14.5 1.0 O C:HOH539 4.8 17.1 1.0 CB C:LYS15 4.8 16.3 1.0 CB C:ASP40 4.9 13.7 1.0 NZ C:LYS15 4.9 11.7 1.0 C C:LYS15 5.0 11.3 1.0

Magnesium binding site 4 out of 4 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg304 b:9.1 occ:1.00 O D:HOH442 2.0 14.6 1.0 O D:HOH444 2.0 10.7 1.0 O3B D:ADP303 2.1 12.6 1.0 O D:HOH460 2.1 16.6 1.0 O D:HOH469 2.2 13.7 1.0 OG D:SER16 2.2 10.1 1.0 CB D:SER16 3.2 9.1 1.0 PB D:ADP303 3.2 9.1 1.0 O2B D:ADP303 3.4 10.9 1.0 OD2 D:ASP40 3.7 14.9 1.0 OD1 D:ASP44 3.9 22.8 1.0 N D:SER16 4.0 8.8 1.0 O2A D:ADP303 4.1 9.9 1.0 OD2 D:ASP125 4.1 15.1 1.0 CA D:SER16 4.2 9.6 1.0 O1B D:ADP303 4.2 10.7 1.0 OG D:SER45 4.3 18.8 1.0 O3A D:ADP303 4.4 9.1 1.0 OD1 D:ASP125 4.4 10.9 1.0 CG D:ASP40 4.5 13.8 1.0 PA D:ADP303 4.6 9.5 1.0 O D:HOH482 4.6 9.3 1.0 O1A D:ADP303 4.6 11.4 1.0 CG D:ASP125 4.7 11.8 1.0 CB D:ASP40 4.8 13.7 1.0 CB D:LYS15 4.9 9.3 1.0 O D:HOH458 4.9 17.1 1.0 CE D:LYS15 4.9 13.6 1.0

N.Maslac, C.Cadoux, P.Bolte, F.Murken, W.Gu, R.D.Milton, T.Wagner. Structural Comparison of (Hyper-)Thermophilic Nitrogenase Reductases From Three Marine Methanococcales. Febs J. 2024.
ISSN: ISSN 1742-464X
PubMed: 38696373
DOI: 10.1111/FEBS.17148