Calcium in PDB 6op1: Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii

All present enzymatic activity of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii:
1.18.6.1;

The structure of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii, PDB code: 6op1 was solved by R.J.Arias, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.93 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.191, 128.003, 107.633, 90.00, 109.15, 90.00
R / Rfree (%)	13.2 / 16.5

The structure of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii also contains other interesting chemical elements:

Molybdenum	(Mo)	2 atoms
Magnesium	(Mg)	5 atoms
Iron	(Fe)	30 atoms

The binding sites of Calcium atom in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii (pdb code 6op1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii, PDB code: 6op1:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:20.4 occ:1.00 O B:HOH727 2.1 15.1 1.0 OD2 B:ASP357 2.1 12.2 1.0 O D:ARG108 2.1 10.6 1.0 OD2 B:ASP353 2.2 13.4 1.0 OE2 D:GLU109 2.3 14.3 1.0 O D:HOH894 2.3 11.2 1.0 CG B:ASP357 2.9 11.7 1.0 CG B:ASP353 3.1 12.3 1.0 OD1 B:ASP357 3.2 12.8 1.0 C D:ARG108 3.3 10.0 1.0 CD D:GLU109 3.4 13.6 1.0 OD1 B:ASP353 3.4 13.2 1.0 O B:HOH819 3.9 15.2 1.0 CG D:GLU109 3.9 12.9 1.0 CB D:ARG108 4.0 9.6 1.0 N D:GLU109 4.2 9.8 1.0 CA D:ARG108 4.2 9.7 1.0 O D:PHE107 4.3 11.1 1.0 CA D:GLU109 4.3 11.1 1.0 NZ C:LYS433 4.4 15.1 1.0 CB B:ASP357 4.4 11.0 1.0 CD1 C:PHE429 4.4 11.6 1.0 OE1 D:GLU109 4.5 15.9 1.0 CB B:ASP353 4.5 10.4 1.0 O B:ASP353 4.6 10.1 1.0 O D:HOH998 4.7 10.3 1.0 CB D:GLU109 4.7 11.7 1.0 CE C:LYS433 4.8 15.8 1.0 CE1 C:PHE429 4.9 11.6 1.0 C B:ASP353 4.9 10.6 1.0 CG C:PHE429 5.0 11.4 1.0

Calcium binding site 2 out of 2 in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca606 b:19.2 occ:1.00 O D:HOH803 2.0 12.6 1.0 OD2 D:ASP357 2.0 12.3 1.0 O B:ARG108 2.1 9.3 1.0 OD2 D:ASP353 2.2 13.6 1.0 OE2 B:GLU109 2.2 13.9 1.0 O B:HOH962 2.3 10.8 1.0 CG D:ASP357 3.0 12.6 1.0 CG D:ASP353 3.1 12.0 1.0 OD1 D:ASP357 3.2 12.8 1.0 C B:ARG108 3.3 9.4 1.0 CD B:GLU109 3.4 12.6 1.0 OD1 D:ASP353 3.4 11.7 1.0 CG B:GLU109 4.0 11.2 1.0 O D:HOH900 4.0 15.6 1.0 CB B:ARG108 4.1 9.1 1.0 N B:GLU109 4.2 9.5 1.0 CA B:ARG108 4.2 8.9 1.0 CA B:GLU109 4.3 9.7 1.0 O B:PHE107 4.3 9.9 1.0 NZ A:LYS433 4.3 14.7 1.0 CD1 A:PHE429 4.4 11.2 1.0 CB D:ASP357 4.4 10.9 1.0 OE1 B:GLU109 4.4 14.6 1.0 CB D:ASP353 4.5 10.9 1.0 O D:ASP353 4.6 12.4 1.0 CB B:GLU109 4.7 10.4 1.0 O B:HOH996 4.7 9.7 1.0 CE A:LYS433 4.8 13.8 1.0 CE1 A:PHE429 4.8 11.7 1.0 C D:ASP353 4.9 11.0 1.0 CG A:PHE429 4.9 11.1 1.0

J.T.Henthorn, R.J.Arias, S.Koroidov, T.Kroll, D.Sokaras, U.Bergmann, D.C.Rees, S.Debeer. Localized Electronic Structure of Nitrogenase Femoco Revealed By Selenium K-Edge High Resolution X-Ray Absorption Spectroscopy. J.Am.Chem.Soc. V. 141 13676 2019.
ISSN: ESSN 1520-5126
PubMed: 31356071
DOI: 10.1021/JACS.9B06988