Calcium in PDB 7khv: Cpoga in Complex with Ligand 54

All present enzymatic activity of Cpoga in Complex with Ligand 54:
3.2.1.169;

The structure of Cpoga in Complex with Ligand 54, PDB code: 7khv was solved by P.L.Shaffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	203.53 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	149.489, 178.104, 407.054, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 24.7

The structure of Cpoga in Complex with Ligand 54 also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Calcium atom in the Cpoga in Complex with Ligand 54 (pdb code 7khv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Cpoga in Complex with Ligand 54, PDB code: 7khv:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Cpoga in Complex with Ligand 54


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cpoga in Complex with Ligand 54 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:58.0 occ:1.00 O A:HOH1005 2.3 25.1 1.0 O A:HOH1067 2.3 31.5 1.0 OE1 A:GLU108 2.4 40.1 1.0 O A:GLU73 2.4 29.1 1.0 O A:HOH944 2.5 30.6 1.0 OD1 A:ASP111 2.9 35.6 1.0 OD2 A:ASP111 3.0 29.9 1.0 CG A:ASP111 3.3 31.5 1.0 C A:GLU73 3.6 34.5 1.0 HA A:ALA74 3.6 26.7 1.0 CD A:GLU108 3.6 31.1 1.0 HB2 A:GLU108 3.8 27.1 1.0 CA A:ALA74 4.2 26.5 1.0 C A:ALA74 4.3 25.6 1.0 HB3 A:GLU73 4.3 49.2 1.0 N A:ALA74 4.3 28.1 1.0 H A:GLU108 4.3 26.9 1.0 HG2 A:GLU108 4.3 29.8 1.0 CG A:GLU108 4.4 30.8 1.0 N A:ASP75 4.4 25.3 1.0 OE2 A:GLU108 4.4 31.5 1.0 H A:ASP75 4.5 25.0 1.0 HA A:GLU73 4.5 39.0 1.0 CB A:GLU108 4.5 26.1 1.0 CA A:GLU73 4.6 40.0 1.0 HA A:ASP75 4.7 23.4 1.0 O A:ALA74 4.8 30.1 1.0 OD1 A:ASP110 4.8 31.4 1.0 CB A:ASP111 4.8 28.6 1.0 CB A:GLU73 5.0 47.5 1.0

Calcium binding site 2 out of 3 in the Cpoga in Complex with Ligand 54


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cpoga in Complex with Ligand 54 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca702 b:65.5 occ:1.00 O D:HOH851 2.3 34.8 1.0 O D:HOH954 2.3 25.8 1.0 OE1 D:GLU108 2.4 38.6 1.0 O D:HOH998 2.4 35.1 1.0 O D:GLU73 2.4 35.3 1.0 OD1 D:ASP111 2.8 42.1 1.0 OD2 D:ASP111 3.0 36.1 1.0 CG D:ASP111 3.3 38.8 1.0 CD D:GLU108 3.6 35.6 1.0 C D:GLU73 3.6 37.9 1.0 HA D:ALA74 3.7 31.4 1.0 HB2 D:GLU108 3.7 32.4 1.0 H D:GLU108 4.2 29.1 1.0 CA D:ALA74 4.3 31.9 1.0 C D:ALA74 4.3 35.8 1.0 HB3 D:GLU73 4.3 52.1 1.0 HG2 D:GLU108 4.3 34.6 1.0 N D:ALA74 4.4 29.7 1.0 CG D:GLU108 4.4 35.6 1.0 HA D:GLU73 4.5 45.4 1.0 OE2 D:GLU108 4.5 32.6 1.0 CB D:GLU108 4.5 31.2 1.0 N D:ASP75 4.5 34.8 1.0 H D:ASP75 4.6 34.4 1.0 CA D:GLU73 4.6 47.4 1.0 OD1 D:ASP110 4.7 32.0 1.0 O D:ALA74 4.7 33.5 1.0 HA D:ASP75 4.8 31.9 1.0 O D:HOH1005 4.8 39.0 1.0 CB D:ASP111 4.8 34.8 1.0 O D:HOH994 4.8 37.7 1.0 CB D:GLU73 5.0 49.7 1.0

Calcium binding site 3 out of 3 in the Cpoga in Complex with Ligand 54


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cpoga in Complex with Ligand 54 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca702 b:70.0 occ:1.00 OE1 E:GLU108 2.4 42.5 1.0 O E:GLU73 2.4 53.2 1.0 O E:HOH824 2.5 38.2 1.0 O E:HOH951 2.7 26.4 1.0 OD1 E:ASP111 3.0 59.7 1.0 OD2 E:ASP111 3.1 46.8 1.0 CG E:ASP111 3.5 51.2 1.0 C E:GLU73 3.6 55.0 1.0 CD E:GLU108 3.6 30.9 1.0 HA E:ALA74 3.7 40.7 1.0 HB2 E:GLU108 4.0 29.6 1.0 C E:ALA74 4.2 35.8 1.0 CA E:ALA74 4.2 41.9 1.0 N E:ASP75 4.4 35.8 1.0 N E:ALA74 4.4 46.9 1.0 OE2 E:GLU108 4.4 41.1 1.0 HG2 E:GLU108 4.4 27.8 1.0 HA E:GLU73 4.5 50.3 1.0 HB3 E:GLU73 4.5 54.8 1.0 H E:ASP75 4.5 34.8 1.0 CG E:GLU108 4.5 26.1 1.0 HA E:ASP75 4.5 32.0 1.0 H E:GLU108 4.5 33.1 1.0 CA E:GLU73 4.6 51.1 1.0 CB E:GLU108 4.7 29.9 1.0 O E:ALA74 4.7 31.2 1.0 OD1 E:ASP110 4.9 41.2 1.0 CB E:ASP111 5.0 39.8 1.0 CA E:ASP75 5.0 31.0 1.0

C.M.Martinez-Viturro, A.A.Trabanco, J.Royes, E.Fernandez, G.Tresadern, J.A.Vega, A.Del Cerro, F.Delgado, A.Garcia Molina, F.Tovar, P.Shaffer, A.Ebneth, A.Bretteville, L.Mertens, M.Somers, J.M.Alonso, J.M.Bartolome-Nebreda. Diazaspirononane Nonsaccharide Inhibitors of O-Glcnacase (Oga) For the Treatment of Neurodegenerative Disorders. J.Med.Chem. V. 63 14017 2020.
ISSN: ISSN 0022-2623
PubMed: 33197187
DOI: 10.1021/ACS.JMEDCHEM.0C01479