Calcium 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
Magnesium	(Mg)	4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis, PDB code: 8q5x:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium 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 Calcium with other atoms in the Ca 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 B:Ca301 b:17.6 occ:1.00 O B:HOH529 2.2 21.0 1.0 OE1 B:GLU69 2.2 19.6 1.0 O B:LYS65 2.3 15.4 1.0 O A:GLU116 2.3 16.8 1.0 O A:HOH577 2.5 19.4 1.0 OD1 B:ASP68 2.7 19.2 1.0 OD2 B:ASP68 2.9 18.9 1.0 CG B:ASP68 3.2 20.9 1.0 CD B:GLU69 3.3 29.5 1.0 C B:LYS65 3.5 16.3 1.0 C A:GLU116 3.6 17.6 1.0 CG B:GLU69 3.8 22.2 1.0 CB B:GLU69 4.0 18.4 1.0 N A:ASP118 4.2 16.2 1.0 CA B:GLY66 4.3 18.4 1.0 N B:GLY66 4.3 18.3 1.0 OE2 B:GLU69 4.3 27.2 1.0 CA A:ASP117 4.4 18.0 1.0 N A:ASP117 4.4 15.6 1.0 CA B:LYS65 4.5 16.4 1.0 CB A:GLU116 4.5 17.7 1.0 CA A:GLU116 4.5 15.8 1.0 N B:GLU69 4.6 16.2 1.0 O A:HOH516 4.6 31.9 1.0 CB B:ASP68 4.7 19.1 1.0 O A:HOH535 4.8 20.4 1.0 C B:GLY66 4.8 17.7 1.0 C A:ASP117 4.9 19.5 1.0 O B:HOH460 5.0 30.1 1.0 O B:GLY66 5.0 16.2 1.0 CA B:GLU69 5.0 19.2 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca302 b:33.7 occ:1.00 OD1 B:ASP145 2.5 17.7 1.0 O B:HOH488 2.6 32.8 1.0 O B:HOH512 2.7 16.7 1.0 O B:HOH677 2.9 40.4 1.0 CG B:ASP145 3.5 21.1 1.0 CB B:ASP145 4.0 12.9 1.0 CA B:ASP145 4.1 15.8 1.0 O B:HOH472 4.2 23.5 1.0 O B:GLY176 4.3 14.5 1.0 OD2 B:ASP145 4.5 16.4 1.0 O B:HOH715 4.5 30.7 1.0 C B:GLY176 4.6 14.2 1.0 O B:ALA144 4.7 14.8 1.0 O B:SER175 4.8 13.6 1.0 CA B:GLY176 4.8 13.3 1.0 O B:HOH603 4.8 31.2 1.0 N B:ASP145 4.9 11.1 1.0 O B:HOH469 5.0 30.6 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca301 b:38.4 occ:1.00 O C:HOH645 2.4 38.1 1.0 O C:HOH657 2.4 47.2 1.0 OD1 C:ASP145 2.5 19.2 1.0 O C:HOH421 2.8 20.9 1.0 O C:HOH427 2.8 29.4 1.0 O C:HOH640 3.0 39.9 1.0 CG C:ASP145 3.6 18.6 1.0 O C:HOH552 4.1 17.9 1.0 CB C:ASP145 4.2 16.6 1.0 O C:GLY176 4.3 15.2 1.0 CA C:ASP145 4.3 16.9 1.0 C C:GLY176 4.6 13.9 1.0 OD2 C:ASP145 4.6 17.6 1.0 O C:SER175 4.7 16.3 1.0 CA C:GLY176 4.7 16.7 1.0 O C:ALA144 4.7 17.5 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca301 b:60.5 occ:1.00 OE2 D:GLU251 2.1 51.9 1.0 CD D:GLU251 3.3 38.0 1.0 OE1 D:GLU251 4.1 37.6 1.0 CG D:GLU251 4.1 32.5 1.0 O D:HOH659 4.6 40.2 1.0 O D:HOH524 4.8 22.8 1.0 O D:GLU249 4.9 14.9 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