Zinc in PDB 6s7h: Human CD73 (5'-Nucleotidase) in Complex with PSB12489 (An Aopcp Derivative) in the Closed State

All present enzymatic activity of Human CD73 (5'-Nucleotidase) in Complex with PSB12489 (An Aopcp Derivative) in the Closed State:
3.1.3.5;

The structure of Human CD73 (5'-Nucleotidase) in Complex with PSB12489 (An Aopcp Derivative) in the Closed State, PDB code: 6s7h 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)	29.20 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	53.830, 95.800, 233.590, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 19.9

The structure of Human CD73 (5'-Nucleotidase) in Complex with PSB12489 (An Aopcp Derivative) in the Closed State also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Human CD73 (5'-Nucleotidase) in Complex with PSB12489 (An Aopcp Derivative) in the Closed State (pdb code 6s7h). 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 PSB12489 (An Aopcp Derivative) in the Closed State, PDB code: 6s7h:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human CD73 (5'-Nucleotidase) in Complex with PSB12489 (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 PSB12489 (An Aopcp Derivative) in the Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:35.0 occ:1.00 O A:HOH732 1.9 30.9 1.0 NE2 A:HIS38 2.0 34.9 1.0 OD2 A:ASP36 2.0 33.3 1.0 O3B A:KYW604 2.1 34.2 1.0 OD2 A:ASP85 2.2 35.3 1.0 HB3 A:ASP85 2.9 33.8 1.0 HB3 A:ASP36 2.9 30.3 1.0 CE1 A:HIS38 3.0 36.3 1.0 CD2 A:HIS38 3.1 35.3 1.0 CG A:ASP36 3.1 29.5 1.0 CG A:ASP85 3.1 37.5 1.0 HE1 A:HIS38 3.2 36.6 1.0 PB A:KYW604 3.3 34.1 1.0 HH12 A:ARG395 3.3 39.7 1.0 CB A:ASP85 3.4 33.7 1.0 HD2 A:HIS38 3.4 32.5 1.0 CB A:ASP36 3.4 30.7 1.0 HB2 A:ASP85 3.5 33.8 1.0 HA A:ASP36 3.5 32.5 1.0 HD2 A:HIS118 3.6 41.4 1.0 H3A1 A:KYW604 3.6 28.8 1.0 O1B A:KYW604 3.6 35.6 1.0 HE1 A:HIS220 3.7 33.8 1.0 ZN A:ZN602 3.7 36.4 1.0 HA A:HIS243 3.9 30.9 1.0 C3A A:KYW604 3.9 30.0 1.0 CA A:ASP36 4.1 30.0 1.0 ND1 A:HIS38 4.1 38.5 1.0 NH1 A:ARG395 4.1 40.8 1.0 O2A A:KYW604 4.1 33.1 1.0 CG A:HIS38 4.1 36.4 1.0 OD1 A:ASP36 4.2 32.0 1.0 OD1 A:ASN245 4.2 33.2 1.0 HH11 A:ARG395 4.2 42.1 1.0 CD2 A:HIS118 4.3 43.4 1.0 OD1 A:ASP85 4.3 35.2 1.0 HB2 A:ASP36 4.4 28.6 1.0 O2B A:KYW604 4.5 36.4 1.0 CE1 A:HIS220 4.5 34.6 1.0 HD21 A:ASN245 4.5 59.1 1.0 NE2 A:HIS220 4.6 35.1 1.0 H A:HIS243 4.7 29.6 1.0 PA A:KYW604 4.8 34.9 1.0 CA A:ASP85 4.8 33.9 1.0 NE2 A:HIS118 4.8 43.3 1.0 O A:HIS243 4.9 36.3 1.0 H3A2 A:KYW604 4.9 29.1 1.0 O A:ASP85 4.9 38.3 1.0 CA A:HIS243 4.9 29.9 1.0

Zinc binding site 2 out of 2 in the Human CD73 (5'-Nucleotidase) in Complex with PSB12489 (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 PSB12489 (An Aopcp Derivative) in the Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:36.4 occ:1.00 O1B A:KYW604 2.0 35.6 1.0 OD1 A:ASN117 2.0 37.5 1.0 NE2 A:HIS220 2.1 35.1 1.0 ND1 A:HIS243 2.1 39.8 1.0 OD2 A:ASP85 2.3 35.3 1.0 HD22 A:ASN117 2.8 34.6 1.0 HA A:HIS243 2.9 30.9 1.0 CE1 A:HIS243 3.0 41.2 1.0 CG A:ASN117 3.0 45.7 1.0 HE1 A:HIS243 3.0 41.7 1.0 CD2 A:HIS220 3.0 35.7 1.0 CG A:ASP85 3.1 37.5 1.0 CE1 A:HIS220 3.1 34.6 1.0 HD2 A:HIS118 3.1 41.4 1.0 PB A:KYW604 3.2 34.1 1.0 HD2 A:HIS220 3.3 36.0 1.0 OD1 A:ASP85 3.3 35.2 1.0 ND2 A:ASN117 3.3 37.6 1.0 CG A:HIS243 3.3 37.2 1.0 HE1 A:HIS220 3.4 33.8 1.0 H A:ASN117 3.5 34.4 1.0 H3A1 A:KYW604 3.7 28.8 1.0 HB2 A:HIS243 3.7 30.2 1.0 ZN A:ZN601 3.7 35.0 1.0 O3B A:KYW604 3.8 34.2 1.0 CB A:HIS243 3.8 30.7 1.0 CA A:HIS243 3.8 29.9 1.0 OD2 A:ASP36 3.9 33.3 1.0 C3A A:KYW604 4.0 30.0 1.0 H3A2 A:KYW604 4.1 29.1 1.0 CD2 A:HIS118 4.1 43.4 1.0 H A:HIS118 4.1 39.5 1.0 NE2 A:HIS243 4.2 41.6 1.0 CG A:HIS220 4.2 34.1 1.0 ND1 A:HIS220 4.2 34.4 1.0 HD21 A:ASN117 4.3 39.2 1.0 HB2 A:ASP85 4.3 33.8 1.0 CB A:ASN117 4.3 36.5 1.0 CB A:ASP85 4.3 33.7 1.0 CD2 A:HIS243 4.3 40.9 1.0 N A:ASN117 4.4 36.4 1.0 O A:HIS243 4.4 36.3 1.0 O2B A:KYW604 4.4 36.4 1.0 HB3 A:ASN117 4.6 38.1 1.0 C A:HIS243 4.7 36.2 1.0 H A:HIS243 4.7 29.6 1.0 N A:HIS243 4.8 29.0 1.0 NE2 A:HIS118 4.8 43.3 1.0 HB3 A:ASP85 4.8 33.8 1.0 HD13 A:LEU184 4.8 48.4 1.0 HB3 A:HIS243 4.8 29.9 1.0 CA A:ASN117 4.9 37.6 1.0 O A:HOH835 4.9 35.9 1.0 HA3 A:GLY116 4.9 34.7 1.0 N A:HIS118 5.0 41.0 1.0 HE1 A:HIS38 5.0 36.6 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