Zinc in PDB 6s7f: Human CD73 (5'-Nucleotidase) in Complex with PSB12379 (An Aopcp Derivative) in the Closed State

All present enzymatic activity of Human CD73 (5'-Nucleotidase) in Complex with PSB12379 (An Aopcp Derivative) in the Closed State:
3.1.3.5;

The structure of Human CD73 (5'-Nucleotidase) in Complex with PSB12379 (An Aopcp Derivative) in the Closed State, PDB code: 6s7f was solved by J.Pippel, N.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.97 / 2.05
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	53.910, 95.660, 233.220, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.6

The structure of Human CD73 (5'-Nucleotidase) in Complex with PSB12379 (An Aopcp Derivative) in the Closed State also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Human CD73 (5'-Nucleotidase) in Complex with PSB12379 (An Aopcp Derivative) in the Closed State (pdb code 6s7f). 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 (5'-Nucleotidase) in Complex with PSB12379 (An Aopcp Derivative) in the Closed State, PDB code: 6s7f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human CD73 (5'-Nucleotidase) in Complex with PSB12379 (An Aopcp Derivative) in the Closed 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 (5'-Nucleotidase) in Complex with PSB12379 (An Aopcp Derivative) in the Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:42.9 occ:1.00 O A:HOH741 1.9 37.2 1.0 NE2 A:HIS38 2.0 45.2 1.0 O1B A:KYK604 2.1 46.9 1.0 OD2 A:ASP36 2.1 37.5 1.0 OD2 A:ASP85 2.3 46.2 1.0 HB3 A:ASP85 2.9 43.9 1.0 HB3 A:ASP36 2.9 41.4 1.0 CE1 A:HIS38 3.0 46.4 1.0 CD2 A:HIS38 3.0 46.3 1.0 CG A:ASP36 3.1 39.8 1.0 CG A:ASP85 3.2 45.4 1.0 HE1 A:HIS38 3.2 46.9 1.0 PB A:KYK604 3.3 41.6 1.0 HD2 A:HIS38 3.3 46.1 1.0 HH12 A:ARG395 3.3 53.8 1.0 CB A:ASP85 3.4 42.1 1.0 HB2 A:ASP85 3.4 40.6 1.0 CB A:ASP36 3.4 40.8 1.0 HA A:ASP36 3.6 41.8 1.0 HD2 A:HIS118 3.6 46.8 1.0 O2B A:KYK604 3.6 50.1 1.0 HE1 A:HIS220 3.7 42.3 1.0 ZN A:ZN602 3.8 44.8 1.0 H3A1 A:KYK604 3.9 40.2 1.0 HA A:HIS243 3.9 38.5 1.0 C3A A:KYK604 4.1 40.1 1.0 OD1 A:ASN245 4.1 43.5 1.0 CA A:ASP36 4.1 41.1 1.0 NH1 A:ARG395 4.1 53.6 1.0 ND1 A:HIS38 4.1 48.2 1.0 CG A:HIS38 4.1 46.1 1.0 HD21 A:ASN245 4.2 61.9 1.0 O1A A:KYK604 4.2 41.5 1.0 OD1 A:ASP36 4.3 37.9 1.0 HH11 A:ARG395 4.3 54.9 1.0 OD1 A:ASP85 4.3 47.6 1.0 HB2 A:ASP36 4.4 39.0 1.0 CD2 A:HIS118 4.4 47.8 1.0 CE1 A:HIS220 4.5 43.4 1.0 O3B A:KYK604 4.5 46.5 1.0 NE2 A:HIS220 4.6 44.7 1.0 PA A:KYK604 4.7 45.2 1.0 O A:HIS243 4.7 45.1 1.0 H A:HIS243 4.7 40.5 1.0 CA A:ASP85 4.8 42.9 1.0 HH22 A:ARG395 4.9 54.0 1.0 NE2 A:HIS118 4.9 47.7 1.0 O A:ASP85 4.9 44.2 1.0 CA A:HIS243 4.9 38.1 1.0 C A:ASP36 5.0 44.5 1.0 CG A:ASN245 5.0 55.0 1.0 ND2 A:ASN245 5.0 60.9 1.0

Zinc binding site 2 out of 2 in the Human CD73 (5'-Nucleotidase) in Complex with PSB12379 (An Aopcp Derivative) in the Closed 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 (5'-Nucleotidase) in Complex with PSB12379 (An Aopcp Derivative) in the Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:44.8 occ:1.00 O2B A:KYK604 2.0 50.1 1.0 NE2 A:HIS220 2.1 44.7 1.0 ND1 A:HIS243 2.1 47.6 1.0 OD1 A:ASN117 2.1 43.9 1.0 OD2 A:ASP85 2.3 46.2 1.0 CE1 A:HIS243 2.9 49.1 1.0 HD21 A:ASN117 2.9 49.1 1.0 HE1 A:HIS243 2.9 50.1 1.0 CD2 A:HIS220 3.0 45.4 1.0 HA A:HIS243 3.0 38.5 1.0 CG A:ASN117 3.0 55.1 1.0 CG A:ASP85 3.1 45.4 1.0 CE1 A:HIS220 3.1 43.4 1.0 HD2 A:HIS220 3.2 46.5 1.0 PB A:KYK604 3.3 41.6 1.0 CG A:HIS243 3.3 44.4 1.0 OD1 A:ASP85 3.3 47.6 1.0 HD2 A:HIS118 3.3 46.8 1.0 ND2 A:ASN117 3.3 50.0 1.0 H A:ASN117 3.4 42.3 1.0 HE1 A:HIS220 3.5 42.3 1.0 H3A1 A:KYK604 3.7 40.2 1.0 HB2 A:HIS243 3.8 38.7 1.0 O1B A:KYK604 3.8 46.9 1.0 CB A:HIS243 3.8 38.8 1.0 ZN A:ZN601 3.8 42.9 1.0 CA A:HIS243 3.9 38.1 1.0 C3A A:KYK604 4.0 40.1 1.0 OD2 A:ASP36 4.0 37.5 1.0 NE2 A:HIS243 4.1 49.7 1.0 CG A:HIS220 4.1 43.4 1.0 H A:HIS118 4.2 43.3 1.0 ND1 A:HIS220 4.2 44.6 1.0 H3A2 A:KYK604 4.2 39.1 1.0 CD2 A:HIS118 4.3 47.8 1.0 CD2 A:HIS243 4.3 47.8 1.0 HD22 A:ASN117 4.3 52.3 1.0 HB2 A:ASP85 4.3 40.6 1.0 N A:ASN117 4.3 42.6 1.0 CB A:ASP85 4.3 42.1 1.0 CB A:ASN117 4.4 45.5 1.0 O3B A:KYK604 4.4 46.5 1.0 O A:HIS243 4.4 45.1 1.0 C A:HIS243 4.7 44.8 1.0 HB3 A:ASN117 4.7 45.8 1.0 H A:HIS243 4.7 40.5 1.0 HB3 A:ASP85 4.8 43.9 1.0 N A:HIS243 4.8 39.4 1.0 HB3 A:HIS243 4.9 39.0 1.0 HA3 A:GLY116 4.9 45.2 1.0 HD12 A:LEU184 4.9 61.0 1.0 CA A:ASN117 4.9 43.8 1.0 NE2 A:HIS118 4.9 47.7 1.0 HE2 A:HIS243 5.0 51.4 1.0

S.Bhattarai, J.Pippel, A.Meyer, M.Freundlieb, C.Schmies, A.Abdelrahman, A.Fiene, S.Y.Lee, H.Zimmermann, A.El-Tayeb, G.G.Yegutkin, N.Strater, C.E.Muller. X-Ray Co-Crystal Structure Guides the Way to Subnanomolar Competitive Ecto-5'-Nucleotidase (CD73) Inhibitors For Cancer Immunotherapy Adv Ther 2019.
DOI: 10.1002/ADTP.201900075