Calcium in PDB 1m1n: Nitrogenase Mofe Protein From Azotobacter Vinelandii

All present enzymatic activity of Nitrogenase Mofe Protein From Azotobacter Vinelandii:
1.18.6.1;

The structure of Nitrogenase Mofe Protein From Azotobacter Vinelandii, PDB code: 1m1n was solved by O.Einsle, F.A.Tezcan, S.L.A.Andrade, B.Schmid, M.Yoshida, J.B.Howard, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.16
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.310, 131.630, 159.159, 90.00, 108.37, 90.00
R / Rfree (%)	12.3 / 14.9

The structure of Nitrogenase Mofe Protein From Azotobacter Vinelandii also contains other interesting chemical elements:

Molybdenum	(Mo)	4 atoms
Iron	(Fe)	60 atoms

The binding sites of Calcium atom in the Nitrogenase Mofe Protein From Azotobacter Vinelandii (pdb code 1m1n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Nitrogenase Mofe Protein From Azotobacter Vinelandii, PDB code: 1m1n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Nitrogenase Mofe Protein From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Nitrogenase Mofe Protein From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca7492 b:17.7 occ:1.00 O B:HOH7493 1.8 26.2 1.0 OD2 B:ASP353 2.1 19.8 1.0 O D:ARG108 2.1 12.2 1.0 O B:HOH7584 2.3 16.6 1.0 OE2 D:GLU109 2.3 21.1 1.0 OD2 B:ASP357 2.4 17.3 1.0 O B:HOH8212 2.8 22.5 1.0 CG B:ASP357 3.1 15.3 1.0 OD1 B:ASP357 3.1 16.4 1.0 CG B:ASP353 3.2 15.7 1.0 C D:ARG108 3.3 12.5 1.0 CD D:GLU109 3.4 16.0 1.0 OD1 B:ASP353 3.5 19.1 1.0 CB D:ARG108 4.0 11.4 1.0 O B:HOH7563 4.1 21.9 1.0 CG D:GLU109 4.1 15.1 1.0 CA D:ARG108 4.2 11.3 1.0 N D:GLU109 4.3 11.9 1.0 NZ C:LYS433 4.3 15.7 1.0 OE1 D:GLU109 4.3 19.9 1.0 O D:PHE107 4.4 11.0 1.0 CA D:GLU109 4.4 12.1 1.0 CD1 C:PHE429 4.5 13.2 1.0 CB B:ASP353 4.5 12.6 1.0 CB B:ASP357 4.5 12.8 1.0 O B:ASP353 4.6 11.9 1.0 O D:HOH7583 4.8 14.9 1.0 O D:HOH7581 4.8 18.8 1.0 C B:ASP353 4.8 11.3 1.0 CB D:GLU109 4.8 13.2 1.0 O D:HOH7518 4.9 16.2 1.0 CE C:LYS433 4.9 15.8 1.0 CE1 C:PHE429 4.9 13.7 1.0

Calcium binding site 2 out of 4 in the Nitrogenase Mofe Protein From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Nitrogenase Mofe Protein From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca6492 b:18.9 occ:1.00 O D:HOH7499 1.6 27.2 1.0 O B:ARG108 2.1 12.8 1.0 OD2 D:ASP353 2.1 18.8 1.0 OE2 B:GLU109 2.2 22.4 1.0 O D:HOH7568 2.3 17.7 1.0 OD2 D:ASP357 2.3 18.8 1.0 O D:HOH8199 2.7 24.6 1.0 OD1 D:ASP357 3.1 18.0 1.0 CG D:ASP357 3.1 15.4 1.0 CG D:ASP353 3.1 15.4 1.0 C B:ARG108 3.3 13.0 1.0 CD B:GLU109 3.3 20.1 1.0 OD1 D:ASP353 3.6 19.3 1.0 CB B:ARG108 4.0 12.8 1.0 CG B:GLU109 4.0 15.2 1.0 O D:HOH7606 4.1 22.6 1.0 N B:GLU109 4.2 12.3 1.0 CA B:ARG108 4.3 12.5 1.0 NZ A:LYS433 4.3 16.5 1.0 OE1 B:GLU109 4.3 20.6 1.0 CA B:GLU109 4.3 12.8 1.0 O B:PHE107 4.4 12.5 1.0 CD1 A:PHE429 4.5 13.3 1.0 CB D:ASP353 4.5 13.6 1.0 CB D:ASP357 4.6 13.3 1.0 O D:ASP353 4.6 12.6 1.0 O B:HOH7519 4.8 15.7 1.0 CB B:GLU109 4.8 14.5 1.0 O B:HOH7516 4.8 19.9 1.0 C D:ASP353 4.9 12.7 1.0 O B:HOH7565 4.9 16.8 1.0 CE1 A:PHE429 5.0 14.5 1.0 CE A:LYS433 5.0 17.6 1.0

Calcium binding site 3 out of 4 in the Nitrogenase Mofe Protein From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Nitrogenase Mofe Protein From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca9492 b:19.0 occ:1.00 O F:HOH2543 1.9 27.7 1.0 O H:ARG108 2.1 13.3 1.0 OD2 F:ASP353 2.1 19.7 1.0 OE2 H:GLU109 2.2 23.4 1.0 O H:HOH2870 2.2 18.1 1.0 OD2 F:ASP357 2.4 19.4 1.0 O F:HOH5006 2.7 23.6 1.0 CG F:ASP357 3.1 15.9 1.0 OD1 F:ASP357 3.1 16.7 1.0 CG F:ASP353 3.2 16.2 1.0 C H:ARG108 3.3 12.1 1.0 CD H:GLU109 3.4 18.1 1.0 OD1 F:ASP353 3.6 19.9 1.0 CG H:GLU109 4.0 15.5 1.0 O F:HOH2799 4.0 22.5 1.0 CB H:ARG108 4.0 12.8 1.0 N H:GLU109 4.2 12.8 1.0 CA H:ARG108 4.2 12.4 1.0 NZ G:LYS433 4.3 16.5 1.0 OE1 H:GLU109 4.3 20.6 1.0 O H:PHE107 4.4 12.2 1.0 CA H:GLU109 4.4 13.4 1.0 CD1 G:PHE429 4.4 14.3 1.0 CB F:ASP353 4.5 14.2 1.0 CB F:ASP357 4.5 13.8 1.0 O F:ASP353 4.6 12.4 1.0 O H:HOH2842 4.8 15.7 1.0 O H:HOH2840 4.8 20.2 1.0 CB H:GLU109 4.8 14.8 1.0 C F:ASP353 4.9 12.9 1.0 O H:HOH2614 4.9 16.4 1.0 CE G:LYS433 4.9 16.5 1.0 CE1 G:PHE429 5.0 14.5 1.0

Calcium binding site 4 out of 4 in the Nitrogenase Mofe Protein From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Nitrogenase Mofe Protein From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca8492 b:18.9 occ:1.00 O H:HOH2542 1.8 27.1 1.0 OD2 H:ASP353 2.1 19.9 1.0 O F:ARG108 2.1 13.3 1.0 OE2 F:GLU109 2.2 22.3 1.0 O H:HOH2778 2.3 17.6 1.0 OD2 H:ASP357 2.3 18.9 1.0 O H:HOH5005 2.7 22.4 1.0 OD1 H:ASP357 3.1 18.3 1.0 CG H:ASP357 3.1 17.1 1.0 CG H:ASP353 3.2 17.1 1.0 C F:ARG108 3.3 13.0 1.0 CD F:GLU109 3.4 17.7 1.0 OD1 H:ASP353 3.6 21.0 1.0 CG F:GLU109 4.0 16.2 1.0 CB F:ARG108 4.0 13.3 1.0 O H:HOH2924 4.1 22.3 1.0 CA F:ARG108 4.2 13.0 1.0 N F:GLU109 4.3 12.3 1.0 NZ E:LYS433 4.3 16.8 1.0 OE1 F:GLU109 4.4 20.5 1.0 O F:PHE107 4.4 12.6 1.0 CA F:GLU109 4.4 13.5 1.0 CD1 E:PHE429 4.4 15.1 1.0 CB H:ASP353 4.5 13.4 1.0 CB H:ASP357 4.5 13.7 1.0 O H:ASP353 4.6 12.6 1.0 O F:HOH2635 4.8 15.3 1.0 C H:ASP353 4.8 12.7 1.0 CB F:GLU109 4.9 14.0 1.0 O F:HOH2629 4.9 21.0 1.0 O F:HOH2805 4.9 16.2 1.0 CE E:LYS433 4.9 17.2 1.0 CE1 E:PHE429 5.0 15.5 1.0

O.Einsle, F.A.Tezcan, S.L.Andrade, B.Schmid, M.Yoshida, J.B.Howard, D.C.Rees. Nitrogenase Mofe-Protein at 1.16 A Resolution: A Central Ligand in the Femo-Cofactor. Science V. 297 1696 2002.
ISSN: ISSN 0036-8075
PubMed: 12215645
DOI: 10.1126/SCIENCE.1073877