Calcium in PDB 1m1y: Chemical Crosslink of Nitrogenase Mofe Protein and Fe Protein

All present enzymatic activity of Chemical Crosslink of Nitrogenase Mofe Protein and Fe Protein:
1.18.6.1;

The structure of Chemical Crosslink of Nitrogenase Mofe Protein and Fe Protein, PDB code: 1m1y was solved by B.Schmid, O.Einsle, H.J.Chiu, A.Willing, 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 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	113.267, 214.937, 320.466, 90.00, 90.00, 90.00
R / Rfree (%)	27.9 / 32.9

The structure of Chemical Crosslink of Nitrogenase Mofe Protein and Fe Protein also contains other interesting chemical elements:

Molybdenum	(Mo)	4 atoms
Iron	(Fe)	76 atoms

The binding sites of Calcium atom in the Chemical Crosslink of Nitrogenase Mofe Protein and Fe Protein (pdb code 1m1y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Chemical Crosslink of Nitrogenase Mofe Protein and Fe Protein, PDB code: 1m1y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Chemical Crosslink of Nitrogenase Mofe Protein and Fe Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Chemical Crosslink of Nitrogenase Mofe Protein and Fe Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca7492 b:20.0 occ:1.00 O D:ARG108 1.9 63.9 1.0 OE2 D:GLU109 2.1 55.4 1.0 OD2 B:ASP357 2.3 52.1 1.0 OD2 B:ASP353 2.5 74.7 1.0 OD1 B:ASP353 2.9 74.7 1.0 CD D:GLU109 2.9 55.4 1.0 CG B:ASP357 3.0 52.1 1.0 OD1 B:ASP357 3.0 52.1 1.0 C D:ARG108 3.0 63.9 1.0 CG B:ASP353 3.0 74.7 1.0 OE1 D:GLU109 3.6 55.4 1.0 CG D:GLU109 3.7 55.4 1.0 N D:GLU109 3.8 57.5 1.0 CA D:GLU109 3.9 57.5 1.0 NZ C:LYS433 4.0 51.5 1.0 CD1 C:PHE429 4.0 75.0 1.0 CB D:ARG108 4.1 39.4 1.0 CA D:ARG108 4.1 63.9 1.0 CE1 C:PHE429 4.3 75.0 1.0 O D:PHE107 4.3 45.3 1.0 CB D:GLU109 4.3 55.4 1.0 CB B:ASP357 4.4 52.1 1.0 CB B:ASP353 4.6 74.7 1.0 CG C:PHE429 4.8 75.0 1.0 CE C:LYS433 4.9 51.5 1.0

Calcium binding site 2 out of 4 in the Chemical Crosslink of Nitrogenase Mofe Protein and Fe Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Chemical Crosslink of Nitrogenase Mofe Protein and Fe Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca6492 b:20.0 occ:1.00 O B:ARG108 2.0 42.2 1.0 OE2 B:GLU109 2.1 80.0 1.0 OD2 D:ASP357 2.2 46.0 1.0 OD2 D:ASP353 2.5 68.0 1.0 CD B:GLU109 2.8 80.0 1.0 OD1 D:ASP353 2.9 68.0 1.0 CG D:ASP357 2.9 46.0 1.0 OD1 D:ASP357 3.0 46.0 1.0 CG D:ASP353 3.1 68.0 1.0 C B:ARG108 3.1 42.2 1.0 OE1 B:GLU109 3.5 80.0 1.0 CG B:GLU109 3.7 80.0 1.0 N B:GLU109 3.9 27.3 1.0 CA B:GLU109 3.9 27.3 1.0 NZ A:LYS433 3.9 58.5 1.0 CD1 A:PHE429 4.1 55.8 1.0 CB B:ARG108 4.2 53.7 1.0 CA B:ARG108 4.2 42.2 1.0 CB B:GLU109 4.4 80.0 1.0 O B:PHE107 4.4 46.0 1.0 CB D:ASP357 4.4 46.0 1.0 CE1 A:PHE429 4.4 55.8 1.0 CB D:ASP353 4.6 68.0 1.0 CE A:LYS433 4.8 58.5 1.0 CG A:PHE429 4.9 55.8 1.0

Calcium binding site 3 out of 4 in the Chemical Crosslink of Nitrogenase Mofe Protein and Fe Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Chemical Crosslink of Nitrogenase Mofe Protein and Fe Protein within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca9492 b:20.0 occ:1.00 OE2 L:GLU109 2.1 67.7 1.0 O L:ARG108 2.1 37.4 1.0 OD2 J:ASP357 2.4 50.7 1.0 OD2 J:ASP353 2.5 55.8 1.0 CD L:GLU109 2.7 67.7 1.0 OD1 J:ASP353 2.9 55.8 1.0 CG J:ASP353 3.0 55.8 1.0 C L:ARG108 3.1 37.4 1.0 CG J:ASP357 3.2 50.7 1.0 OD1 J:ASP357 3.2 50.7 1.0 OE1 L:GLU109 3.3 67.7 1.0 CG L:GLU109 3.6 67.7 1.0 CA L:GLU109 3.8 39.8 1.0 N L:GLU109 3.8 39.8 1.0 NZ K:LYS433 3.8 41.0 1.0 CD1 K:PHE429 4.1 61.7 1.0 CB L:GLU109 4.3 67.7 1.0 CA L:ARG108 4.3 37.4 1.0 CB L:ARG108 4.3 56.6 1.0 O L:PHE107 4.4 33.4 1.0 CE1 K:PHE429 4.5 61.7 1.0 CB J:ASP353 4.5 55.8 1.0 CB J:ASP357 4.6 50.7 1.0 CE K:LYS433 4.7 41.0 1.0 CG K:PHE429 4.9 61.7 1.0

Calcium binding site 4 out of 4 in the Chemical Crosslink of Nitrogenase Mofe Protein and Fe Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Chemical Crosslink of Nitrogenase Mofe Protein and Fe Protein within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca8492 b:20.0 occ:1.00 O J:ARG108 2.0 36.3 1.0 OE2 J:GLU109 2.1 46.5 1.0 OD2 L:ASP357 2.4 47.2 1.0 OD2 L:ASP353 2.5 58.3 1.0 OD1 L:ASP353 2.8 58.3 1.0 CD J:GLU109 2.8 46.5 1.0 CG L:ASP353 3.0 58.3 1.0 CG L:ASP357 3.1 47.2 1.0 C J:ARG108 3.1 36.3 1.0 OD1 L:ASP357 3.1 47.2 1.0 OE1 J:GLU109 3.5 46.5 1.0 CG J:GLU109 3.7 46.5 1.0 N J:GLU109 3.8 35.2 1.0 CA J:GLU109 3.8 35.2 1.0 NZ I:LYS433 3.9 41.1 1.0 CD1 I:PHE429 4.1 39.6 1.0 CA J:ARG108 4.2 36.3 1.0 CB J:ARG108 4.2 48.5 1.0 CB J:GLU109 4.3 46.5 1.0 O J:PHE107 4.4 43.9 1.0 CE1 I:PHE429 4.4 39.6 1.0 CB L:ASP353 4.5 58.3 1.0 CB L:ASP357 4.5 47.2 1.0 CE I:LYS433 4.8 41.1 1.0 CG I:PHE429 4.9 39.6 1.0

B.Schmid, O.Einsle, H.J.Chiu, A.Willing, M.Yoshida, J.B.Howard, D.C.Rees. Biochemical and Structural Characterization of the Crosslinked Complex of Nitrogenase: Comparison to the Adp-ALF4- Stabilized Structure Biochemistry V. 41 15557 2002.
ISSN: ISSN 0006-2960
PubMed: 12501184
DOI: 10.1021/BI026642B