Calcium in PDB 7jv8: Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35

All present enzymatic activity of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35:
3.1.3.5;

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35, PDB code: 7jv8 was solved by P.Gibbons, X.Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	126.17 / 2.46
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.876, 102.354, 129.609, 90.00, 103.22, 90.00
R / Rfree (%)	22 / 27.9

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 also contains other interesting chemical elements:

Zinc	(Zn)	8 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Calcium atom in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 (pdb code 7jv8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35, PDB code: 7jv8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:32.0 occ:0.70 O A:ASN213 2.2 31.3 1.0 O A:HOH745 2.3 23.0 1.0 O A:GLY298 2.4 37.4 1.0 OD2 A:ASP237 2.4 39.0 1.0 OD1 A:ASP237 2.4 41.2 1.0 O A:HOH786 2.5 36.1 1.0 CG A:ASP237 2.8 36.4 1.0 C A:GLY298 3.3 43.6 1.0 C A:ASN213 3.5 37.5 1.0 CA A:GLY298 4.0 47.1 1.0 O A:GLY235 4.0 48.8 1.0 N A:ASN299 4.1 42.7 1.0 CB A:ASP237 4.3 33.5 1.0 O A:ARG297 4.3 39.0 1.0 CA A:ASN213 4.4 42.2 1.0 O A:HOH770 4.4 50.6 1.0 N A:LYS214 4.4 34.7 1.0 CA A:ASN299 4.4 40.9 1.0 OD1 A:ASN299 4.5 48.2 1.0 CA A:LYS214 4.6 39.2 1.0 CB A:ASN213 4.7 42.8 1.0 O A:HOH871 4.8 39.0 1.0 N A:ILE215 4.9 31.7 1.0 C A:GLY235 5.0 48.3 1.0

Calcium binding site 2 out of 4 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:64.9 occ:0.70 O B:ASN213 2.3 63.1 1.0 O B:GLY298 2.4 75.2 1.0 OD2 B:ASP237 2.4 76.0 1.0 OD1 B:ASP237 2.5 79.0 1.0 CG B:ASP237 2.8 77.5 1.0 C B:GLY298 3.4 86.4 1.0 C B:ASN213 3.5 62.4 1.0 O B:GLY235 4.1 48.2 1.0 CA B:GLY298 4.2 81.0 1.0 NH2 B:ARG273 4.2 93.5 1.0 O B:HOH703 4.3 52.0 1.0 N B:ASN299 4.3 80.1 1.0 CB B:ASP237 4.3 69.2 1.0 CA B:ASN213 4.4 58.6 1.0 N B:LYS214 4.4 58.0 1.0 O B:ARG297 4.5 78.1 1.0 CA B:LYS214 4.6 53.8 1.0 CA B:ASN299 4.6 79.4 1.0 OD1 B:ASN299 4.6 70.4 1.0 CB B:ASN213 4.8 55.3 1.0 N B:ILE215 4.9 56.2 1.0

Calcium binding site 3 out of 4 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca603 b:28.4 occ:0.70 O C:HOH722 2.2 35.8 1.0 O C:ASN213 2.3 45.7 1.0 O C:GLY298 2.4 36.2 1.0 OD2 C:ASP237 2.4 35.8 1.0 OD1 C:ASP237 2.5 42.1 1.0 CG C:ASP237 2.8 39.5 1.0 C C:GLY298 3.4 39.2 1.0 C C:ASN213 3.5 39.6 1.0 O C:GLY235 4.0 67.7 1.0 CA C:GLY298 4.2 41.1 1.0 CB C:ASP237 4.3 39.1 1.0 N C:ASN299 4.3 40.0 1.0 N C:LYS214 4.4 37.5 1.0 CA C:ASN213 4.4 38.2 1.0 CA C:LYS214 4.5 35.1 1.0 CA C:ASN299 4.6 40.9 1.0 O C:ARG297 4.7 36.7 1.0 CB C:ASN213 4.8 35.5 1.0 N C:ILE215 4.8 41.0 1.0 O C:HOH744 4.9 24.8 1.0 OD1 C:ASN299 4.9 36.7 1.0 C C:GLY235 5.0 47.8 1.0

Calcium binding site 4 out of 4 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca603 b:36.1 occ:0.70 O D:ASN213 2.3 41.1 1.0 O D:GLY298 2.4 40.2 1.0 OD2 D:ASP237 2.4 29.2 1.0 O D:HOH734 2.4 24.7 1.0 OD1 D:ASP237 2.5 35.9 1.0 O D:HOH791 2.6 30.8 1.0 CG D:ASP237 2.8 30.8 1.0 O D:HOH835 2.9 42.7 1.0 C D:GLY298 3.3 41.4 1.0 C D:ASN213 3.5 35.5 1.0 CA D:GLY298 4.0 39.0 1.0 N D:ASN299 4.1 35.8 1.0 O D:GLY235 4.1 42.4 1.0 O D:HOH715 4.2 36.0 1.0 O D:ARG297 4.3 48.8 1.0 CB D:ASP237 4.3 29.1 1.0 OD1 D:ASN299 4.4 41.9 1.0 CA D:ASN213 4.4 36.8 1.0 N D:LYS214 4.4 33.2 1.0 CA D:ASN299 4.4 37.2 1.0 CA D:LYS214 4.5 34.2 1.0 O D:HOH766 4.6 34.3 1.0 O D:HOH760 4.7 34.8 1.0 CB D:ASN213 4.7 35.2 1.0 N D:ILE215 4.9 27.4 1.0

X.Du, J.Moore, B.R.Blank, J.Eksterowicz, D.Sutimantanapi, N.Yuen, T.Metzger, B.Chan, T.Huang, X.Chen, Y.Chen, F.Duong, W.Kong, J.H.Chang, J.Sun, T.Zavorotinskaya, Q.Ye, M.R.Junttila, C.Ndubaku, L.S.Friedman, V.R.Fantin, D.Sun. Orally Bioavailable Small-Molecule CD73 Inhibitor (Op-5244) Reverses Immunosuppression Through Blockade of Adenosine Production. J.Med.Chem. V. 63 10433 2020.
ISSN: ISSN 0022-2623
PubMed: 32865411
DOI: 10.1021/ACS.JMEDCHEM.0C01086