Calcium in PDB 7jrf: Co-Co-Bound Nitrogenase Mofe-Protein From A. Vinelandii

All present enzymatic activity of Co-Co-Bound Nitrogenase Mofe-Protein From A. Vinelandii:
1.18.6.1;

The structure of Co-Co-Bound Nitrogenase Mofe-Protein From A. Vinelandii, PDB code: 7jrf was solved by T.Spatzal, K.A.Perez, T.M.Buscagan, A.O.Maggiolo, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.63 / 1.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.052, 129.974, 107.223, 90, 109.11, 90
R / Rfree (%)	11.6 / 15

The structure of Co-Co-Bound Nitrogenase Mofe-Protein From A. Vinelandii also contains other interesting chemical elements:

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

The binding sites of Calcium atom in the Co-Co-Bound Nitrogenase Mofe-Protein From A. Vinelandii (pdb code 7jrf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Co-Co-Bound Nitrogenase Mofe-Protein From A. Vinelandii, PDB code: 7jrf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Co-Co-Bound Nitrogenase Mofe-Protein From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Co-Co-Bound Nitrogenase Mofe-Protein From A. Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:9.6 occ:0.60 O B:HOH822 2.1 15.1 1.0 OD2 B:ASP357 2.1 14.1 1.0 O D:ARG108 2.1 10.7 1.0 OD2 B:ASP353 2.1 12.9 1.0 OE2 D:GLU109 2.2 12.9 1.0 O D:HOH962 2.2 12.4 1.0 CG B:ASP357 3.0 12.4 1.0 CG B:ASP353 3.1 12.2 1.0 OD1 B:ASP357 3.3 13.1 1.0 C D:ARG108 3.3 10.0 1.0 CD D:GLU109 3.3 13.3 1.0 OD1 B:ASP353 3.4 13.6 1.0 O B:HOH844 3.8 16.1 1.0 CG D:GLU109 3.9 11.4 1.0 CB D:ARG108 4.0 9.5 1.0 N D:GLU109 4.2 9.8 1.0 CA D:ARG108 4.3 9.7 1.0 NZ C:LYS433 4.3 12.7 1.0 CA D:GLU109 4.3 10.3 1.0 O D:PHE107 4.3 11.2 1.0 OE1 D:GLU109 4.4 15.5 1.0 CB B:ASP357 4.4 10.8 1.0 CD1 C:PHE429 4.5 12.3 1.0 CB B:ASP353 4.5 10.8 1.0 O B:ASP353 4.6 10.8 1.0 O D:HOH998 4.7 12.2 1.0 CB D:GLU109 4.7 10.4 1.0 CE C:LYS433 4.8 13.9 1.0 C B:ASP353 4.9 10.2 1.0 CE1 C:PHE429 4.9 12.2 1.0 CG C:PHE429 5.0 12.0 1.0

Calcium binding site 2 out of 2 in the Co-Co-Bound Nitrogenase Mofe-Protein From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Co-Co-Bound Nitrogenase Mofe-Protein From A. Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca601 b:11.3 occ:0.70 O B:ARG108 2.1 10.2 1.0 OD2 D:ASP357 2.1 13.9 1.0 OD2 D:ASP353 2.1 11.5 1.0 O D:HOH793 2.2 14.1 1.0 OE2 B:GLU109 2.2 12.2 1.0 O B:HOH950 2.2 11.9 1.0 CG D:ASP357 3.0 12.3 1.0 CG D:ASP353 3.1 11.2 1.0 C B:ARG108 3.2 9.1 1.0 CD B:GLU109 3.3 13.6 1.0 OD1 D:ASP357 3.3 13.6 1.0 OD1 D:ASP353 3.5 13.0 1.0 CG B:GLU109 3.8 11.3 1.0 O D:HOH874 3.9 15.1 1.0 CB B:ARG108 4.0 9.5 1.0 N B:GLU109 4.2 10.4 1.0 CA B:ARG108 4.2 9.0 1.0 O B:PHE107 4.3 10.4 1.0 CA B:GLU109 4.3 10.6 1.0 NZ A:LYS433 4.3 12.1 1.0 OE1 B:GLU109 4.4 15.4 1.0 CB D:ASP357 4.4 11.0 1.0 CD1 A:PHE429 4.5 11.8 1.0 CB D:ASP353 4.5 10.4 1.0 O D:ASP353 4.5 9.3 1.0 O B:HOH989 4.7 11.8 1.0 CB B:GLU109 4.7 10.6 1.0 C D:ASP353 4.9 9.3 1.0 CE A:LYS433 4.9 12.7 1.0 CE1 A:PHE429 5.0 11.3 1.0 CG A:PHE429 5.0 11.6 1.0 O B:HOH1014 5.0 12.4 1.0

T.M.Buscagan, K.A.Perez, A.O.Maggiolo, D.C.Rees, T.Spatzal. Structural Characterization of Two Co Molecules Bound to the Nitrogenase Active Site. Angew.Chem.Int.Ed.Engl. V. 60 5704 2021.
ISSN: ESSN 1521-3773
PubMed: 33320413
DOI: 10.1002/ANIE.202015751