Zinc in PDB 7qgo: Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4602 (A 3-Methyl- Cmpcp Derivative, Compound 21 in Paper) in the Open State

All present enzymatic activity of Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4602 (A 3-Methyl- Cmpcp Derivative, Compound 21 in Paper) in the Open State:
3.1.3.5;

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4602 (A 3-Methyl- Cmpcp Derivative, Compound 21 in Paper) in the Open State, PDB code: 7qgo was solved by N.S.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.84 / 2.21
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	55.037, 96.833, 232.685, 90, 90, 90
R / Rfree (%)	23.9 / 29.2

The binding sites of Zinc atom in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4602 (A 3-Methyl- Cmpcp Derivative, Compound 21 in Paper) in the Open State (pdb code 7qgo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4602 (A 3-Methyl- Cmpcp Derivative, Compound 21 in Paper) in the Open State, PDB code: 7qgo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4602 (A 3-Methyl- Cmpcp Derivative, Compound 21 in Paper) in the Open State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4602 (A 3-Methyl- Cmpcp Derivative, Compound 21 in Paper) in the Open State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:79.7 occ:1.00 O9 A:BW0603 1.9 64.6 0.9 NE2 A:HIS38 2.0 61.6 1.0 OD1 A:ASP36 2.3 60.0 1.0 OD2 A:ASP85 2.4 64.4 1.0 CE1 A:HIS38 2.8 61.6 1.0 CG A:ASP36 3.1 59.9 1.0 CD2 A:HIS38 3.2 60.8 1.0 CG A:ASP85 3.3 61.8 1.0 P1 A:BW0603 3.4 63.8 0.9 CB A:ASP36 3.4 54.5 1.0 CB A:ASP85 3.5 58.0 1.0 ZN A:ZN602 3.6 69.5 1.0 O10 A:BW0603 3.9 63.5 0.9 OD1 A:ASN245 3.9 67.1 1.0 ND1 A:HIS38 4.0 61.7 1.0 CA A:ASP36 4.1 54.0 1.0 O8 A:BW0603 4.1 64.5 0.9 CD2 A:HIS118 4.1 68.6 1.0 CG A:HIS38 4.2 60.2 1.0 OD2 A:ASP36 4.2 64.7 1.0 H23 A:BW0603 4.2 33.5 0.0 CE1 A:HIS220 4.4 66.5 1.0 C19 A:BW0603 4.5 63.7 0.9 OD1 A:ASP85 4.5 61.4 1.0 NE2 A:HIS220 4.5 67.2 1.0 NE2 A:HIS118 4.6 69.7 1.0 NH1 A:ARG395 4.6 70.2 1.0 O A:HIS243 4.7 66.8 1.0 CA A:HIS243 4.8 64.6 1.0 H24 A:BW0603 4.8 38.1 0.0 CG A:ASN245 4.9 67.4 1.0 CA A:ASP85 5.0 57.6 1.0

Zinc binding site 2 out of 2 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4602 (A 3-Methyl- Cmpcp Derivative, Compound 21 in Paper) in the Open State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4602 (A 3-Methyl- Cmpcp Derivative, Compound 21 in Paper) in the Open State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:69.5 occ:1.00 OD1 A:ASN117 2.1 74.6 1.0 NE2 A:HIS220 2.1 67.2 1.0 ND1 A:HIS243 2.1 67.5 1.0 O10 A:BW0603 2.2 63.5 0.9 OD2 A:ASP85 2.3 64.4 1.0 CE1 A:HIS243 2.9 67.4 1.0 P1 A:BW0603 3.1 63.8 0.9 CE1 A:HIS220 3.1 66.5 1.0 CD2 A:HIS220 3.1 66.2 1.0 CG A:ASP85 3.1 61.8 1.0 CG A:ASN117 3.2 72.0 1.0 O9 A:BW0603 3.2 64.6 0.9 CG A:HIS243 3.3 66.5 1.0 OD1 A:ASP85 3.5 61.4 1.0 H23 A:BW0603 3.6 33.5 0.0 ZN A:ZN601 3.6 79.7 1.0 ND2 A:ASN117 3.8 72.9 1.0 CA A:HIS243 3.8 64.6 1.0 CB A:HIS243 3.8 65.1 1.0 C19 A:BW0603 3.9 63.7 0.9 OD1 A:ASP36 4.0 60.0 1.0 H22 A:BW0603 4.0 35.2 0.0 CD2 A:HIS118 4.1 68.6 1.0 NE2 A:HIS243 4.1 67.6 1.0 CG A:HIS220 4.2 64.7 1.0 ND1 A:HIS220 4.2 66.0 1.0 CD2 A:HIS243 4.3 67.0 1.0 O A:HIS243 4.4 66.8 1.0 CB A:ASP85 4.4 58.0 1.0 N A:ASN117 4.4 64.5 1.0 CB A:ASN117 4.4 67.6 1.0 O8 A:BW0603 4.4 64.5 0.9 C A:HIS243 4.6 65.6 1.0 N A:HIS243 4.7 63.4 1.0 H24 A:BW0603 4.8 38.1 0.0 NE2 A:HIS118 4.8 69.7 1.0 CA A:ASN117 4.9 66.0 1.0 N A:HIS118 5.0 65.0 1.0

M.Scortichini, R.M.Idris, S.Moschutz, A.Keim, V.Salmaso, C.Dobelmann, P.Oliva, K.Losenkova, H.Irjala, S.Vaittinen, J.Sandholm, G.G.Yegutkin, N.Strater, A.Junker, C.E.Muller, K.A.Jacobson. Structure-Activity Relationship of 3-Methylcytidine-5'-Alpha , Beta-Methylenediphosphates As CD73 Inhibitors. J.Med.Chem. V. 65 2409 2022.
ISSN: ISSN 0022-2623
PubMed: 35080883
DOI: 10.1021/ACS.JMEDCHEM.1C01852