Calcium in PDB 7mci: Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor

All present enzymatic activity of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor:
1.18.6.1;

The structure of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor, PDB code: 7mci was solved by W.Kang, C.Lee, Y.Hu, M.W.Ribbe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.22 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	166.834, 73.995, 208.766, 90, 103.05, 90
R / Rfree (%)	17.2 / 19.5

The structure of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor also contains other interesting chemical elements:

Iron	(Fe)	30 atoms
Molybdenum	(Mo)	8 atoms

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

Calcium binding site 1 out of 2 in the Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca607 b:24.6 occ:0.56 O B:HOH806 2.2 26.2 1.0 O D:ARG108 2.2 21.8 1.0 O D:HOH771 2.3 21.6 1.0 OE1 D:GLU109 2.3 32.0 1.0 OD2 B:ASP353 2.3 24.4 1.0 OD2 B:ASP357 2.4 25.4 1.0 CG B:ASP357 3.1 23.9 1.0 OD1 B:ASP357 3.1 24.4 1.0 C D:ARG108 3.4 20.8 1.0 CG B:ASP353 3.4 25.1 1.0 CD D:GLU109 3.4 25.8 1.0 OD1 B:ASP353 3.7 26.6 1.0 O B:HOH751 3.8 27.8 1.0 CB D:ARG108 4.0 19.9 1.0 CG D:GLU109 4.1 20.2 1.0 NZ C:LYS433 4.1 20.8 1.0 N D:GLU109 4.3 20.0 1.0 CA D:ARG108 4.3 19.5 1.0 O D:PHE107 4.3 19.5 1.0 CA D:GLU109 4.4 19.8 1.0 OE2 D:GLU109 4.4 28.3 1.0 CD1 C:PHE429 4.5 22.2 1.0 CB B:ASP357 4.6 22.7 1.0 O B:ASP353 4.7 21.5 1.0 CB B:ASP353 4.7 22.0 1.0 O D:HOH914 4.7 24.1 1.0 O D:HOH895 4.8 24.4 1.0 CE C:LYS433 4.8 25.1 1.0 O D:HOH825 4.8 29.4 1.0 CB D:GLU109 4.9 20.8 1.0 CE1 C:PHE429 4.9 20.9 1.0 C B:ASP353 5.0 20.8 1.0

Calcium binding site 2 out of 2 in the Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca601 b:25.7 occ:0.55 O D:HOH828 2.1 27.8 1.0 O B:ARG108 2.2 21.2 1.0 O B:HOH851 2.2 22.0 1.0 OE2 B:GLU109 2.2 32.6 1.0 OD2 D:ASP353 2.4 27.8 1.0 OD2 D:ASP357 2.4 26.9 1.0 CG D:ASP357 3.1 24.5 1.0 OD1 D:ASP357 3.2 24.8 1.0 CD B:GLU109 3.3 29.4 1.0 C B:ARG108 3.3 22.4 1.0 CG D:ASP353 3.4 26.5 1.0 OD1 D:ASP353 3.8 28.4 1.0 O D:HOH802 3.8 27.1 1.0 CG B:GLU109 3.9 22.5 1.0 CB B:ARG108 3.9 19.5 1.0 O B:PHE107 4.2 21.1 1.0 NZ A:LYS433 4.2 26.3 1.0 CA B:ARG108 4.2 21.5 1.0 N B:GLU109 4.3 21.4 1.0 OE1 B:GLU109 4.3 30.7 1.0 CA B:GLU109 4.4 20.5 1.0 CD1 A:PHE429 4.5 22.5 1.0 CB D:ASP357 4.6 23.0 1.0 O B:HOH935 4.6 22.5 1.0 O B:HOH940 4.7 22.6 1.0 CB D:ASP353 4.7 25.8 1.0 O D:ASP353 4.8 22.1 1.0 CB B:GLU109 4.8 23.1 1.0 O B:HOH870 4.9 29.5 1.0 CE A:LYS433 4.9 24.8 1.0 CE1 A:PHE429 4.9 21.7 1.0

C.C.Lee, W.Kang, A.J.Jasniewski, M.T.Stiebritz, K.Tanifuji, M.W.Ribbe, Y.Hu. Evidence of Substrate Binding and Product Release Via Belt-Sulfur Mobilization of the Nitrogenase Cofactor Nat Catal V. 5 443 2022.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-022-00782-7