Calcium in PDB 7khs: Ogoga in Complex with Ligand 55

All present enzymatic activity of Ogoga in Complex with Ligand 55:
3.2.1.169;

The structure of Ogoga in Complex with Ligand 55, PDB code: 7khs 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)	44.79 / 1.78
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.231, 83.076, 122.964, 90.00, 90.25, 90.00
R / Rfree (%)	27.3 / 29.6

The binding sites of Calcium atom in the Ogoga in Complex with Ligand 55 (pdb code 7khs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Ogoga in Complex with Ligand 55, PDB code: 7khs:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Ogoga in Complex with Ligand 55


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ogoga in Complex with Ligand 55 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:37.3 occ:1.00 O B:HOH630 2.2 30.9 1.0 O B:HOH603 2.2 23.1 1.0 O A:HOH641 2.2 29.1 1.0 O B:HOH635 2.2 33.3 1.0 O B:HOH617 2.3 26.1 1.0 OE1 B:GLU388 2.3 41.7 1.0 H2 B:HOH630 2.7 9.4 1.0 H2 B:HOH603 2.7 8.7 1.0 H2 A:HOH641 2.7 9.2 1.0 H2 B:HOH635 2.8 9.5 1.0 H2 B:HOH617 2.8 9.0 1.0 H1 B:HOH630 2.8 28.9 1.0 H1 B:HOH603 2.8 22.0 1.0 CD B:GLU388 2.9 32.0 1.0 H1 A:HOH641 2.9 27.8 1.0 H1 B:HOH635 2.9 31.5 1.0 H1 B:HOH617 2.9 24.4 1.0 OE2 B:GLU388 3.2 33.8 1.0 O B:HOH612 3.5 28.8 1.0 HB3 B:GLU388 3.6 28.8 1.0 OE1 B:GLU391 3.8 38.5 1.0 OE2 B:GLU392 3.8 31.9 1.0 HA B:GLU388 3.9 29.9 1.0 O A:HOH627 4.0 35.9 1.0 CG B:GLU388 4.0 29.6 1.0 HG2 B:GLU392 4.1 30.9 1.0 CB B:GLU388 4.1 28.0 1.0 HH21 B:ARG230 4.3 33.1 1.0 O A:HOH685 4.4 26.7 1.0 OD1 A:ASP228 4.4 28.3 1.0 HG21 A:ILE229 4.4 31.0 1.0 CA B:GLU388 4.4 29.9 1.0 HA A:ASP228 4.5 27.1 1.0 O B:GLU388 4.5 28.2 1.0 HG3 B:GLU388 4.5 29.5 1.0 O B:HOH608 4.6 31.5 1.0 HE1 B:TYR423 4.6 32.8 1.0 HE B:ARG230 4.6 33.0 1.0 HG2 B:GLU388 4.6 29.6 1.0 CD B:GLU392 4.7 32.2 1.0 CG B:GLU392 4.7 30.8 1.0 H A:ILE229 4.8 28.3 1.0 HB3 B:GLU391 4.8 31.4 1.0 CG A:ASP228 4.8 27.8 1.0 HG3 B:GLU392 4.8 30.5 1.0 C B:GLU388 4.9 29.1 1.0 NH2 B:ARG230 4.9 33.8 1.0 O A:HOH690 4.9 35.9 1.0 OD2 A:ASP228 4.9 30.5 1.0

Calcium binding site 2 out of 2 in the Ogoga in Complex with Ligand 55


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ogoga in Complex with Ligand 55 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca502 b:29.9 occ:1.00 OE1 D:GLU388 2.1 31.8 1.0 O D:HOH606 2.2 20.8 1.0 O D:HOH603 2.2 27.1 1.0 O D:HOH618 2.2 23.6 1.0 O D:HOH652 2.2 27.3 1.0 O D:HOH635 2.3 21.4 1.0 H2 D:HOH603 2.7 9.0 1.0 H2 D:HOH618 2.7 8.7 1.0 H2 D:HOH652 2.8 9.1 1.0 H2 D:HOH635 2.8 8.5 1.0 H1 D:HOH603 2.9 25.1 1.0 H1 D:HOH618 2.9 22.5 1.0 H1 D:HOH652 2.9 25.2 1.0 H1 D:HOH635 2.9 20.3 1.0 CD D:GLU388 3.0 31.0 1.0 OE2 D:GLU388 3.3 29.7 1.0 OE1 D:GLU391 3.7 31.3 1.0 OE2 D:GLU392 3.7 28.0 1.0 O D:HOH630 3.8 27.7 1.0 HB3 D:GLU388 3.9 25.9 1.0 HG2 D:GLU392 3.9 27.9 1.0 HA D:GLU388 3.9 25.1 1.0 CG D:GLU388 4.2 27.4 1.0 HG21 C:ILE229 4.3 28.1 1.0 CB D:GLU388 4.4 25.9 1.0 HE1 D:TYR423 4.4 26.9 1.0 OD1 C:ASP228 4.4 27.6 1.0 HH21 D:ARG230 4.5 24.6 1.0 O D:GLU388 4.5 21.2 1.0 HA C:ASP228 4.5 28.5 1.0 CG D:GLU392 4.5 28.5 1.0 CD D:GLU392 4.5 29.8 1.0 CA D:GLU388 4.5 25.3 1.0 HG3 D:GLU392 4.5 27.6 1.0 H C:ILE229 4.6 28.2 1.0 HB3 D:GLU391 4.6 25.3 1.0 HG3 D:GLU388 4.7 27.8 1.0 CG C:ASP228 4.7 28.3 1.0 HE D:ARG230 4.8 24.2 1.0 OD2 C:ASP228 4.8 28.6 1.0 HG2 D:GLU388 4.8 27.9 1.0 HD1 D:TYR423 4.9 28.0 1.0 C D:GLU388 4.9 22.4 1.0 CD D:GLU391 4.9 31.3 1.0 HG3 C:ARG230 4.9 28.0 1.0 HG22 C:ILE229 5.0 28.0 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