Zinc in PDB 6tvg: Human CD73 (Ecto 5'-Nucleotidase) in Complex with Ampcp in the Open State

All present enzymatic activity of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Ampcp in the Open State:
3.1.3.5;

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Ampcp in the Open State, PDB code: 6tvg was solved by E.Scaletti, N.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.19 / 1.48
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.259, 131.268, 66.213, 90.00, 90.00, 90.00
R / Rfree (%)	12.8 / 16.7

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Ampcp in the Open State also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Ampcp in the Open State (pdb code 6tvg). 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 Ampcp in the Open State, PDB code: 6tvg:
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 Ampcp 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 Ampcp in the Open State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:8.7 occ:1.00 O A:HOH926 2.0 9.4 1.0 NE2 A:HIS220 2.0 7.1 1.0 OD1 A:ASN117 2.0 7.8 1.0 ND1 A:HIS243 2.1 8.6 1.0 OD2 A:ASP85 2.2 7.3 1.0 HA A:HIS243 2.8 8.4 1.0 CD2 A:HIS220 3.0 6.7 1.0 CE1 A:HIS243 3.0 10.4 1.0 CE1 A:HIS220 3.0 8.3 1.0 HE1 A:HIS243 3.1 12.4 1.0 CG A:ASP85 3.1 7.6 1.0 HD2 A:HIS220 3.1 8.0 1.0 CG A:ASN117 3.1 7.8 1.0 O A:HOH705 3.2 12.4 1.0 CG A:HIS243 3.2 8.6 1.0 ZN A:ZN602 3.2 8.3 1.0 HE1 A:HIS220 3.2 10.0 1.0 HD21 A:ASN117 3.3 10.0 1.0 HD2 A:HIS118 3.5 10.2 1.0 HB2 A:HIS243 3.5 9.0 1.0 OD1 A:ASP85 3.5 7.7 1.0 CA A:HIS243 3.6 7.0 1.0 H A:ASN117 3.6 7.3 1.0 CB A:HIS243 3.6 7.5 1.0 OD1 A:ASP36 3.6 7.0 1.0 ND2 A:ASN117 3.6 8.4 1.0 O A:HIS243 4.1 9.0 1.0 ND1 A:HIS220 4.1 8.1 1.0 CG A:HIS220 4.1 6.1 1.0 NE2 A:HIS243 4.2 11.9 1.0 HB2 A:ASP85 4.2 7.9 1.0 CB A:ASP85 4.3 6.6 1.0 CD2 A:HIS243 4.3 11.2 1.0 H A:HIS118 4.3 8.7 1.0 C A:HIS243 4.4 8.3 1.0 CD2 A:HIS118 4.4 8.5 1.0 N A:ASN117 4.4 6.1 1.0 CB A:ASN117 4.4 7.2 1.0 HD22 A:ASN117 4.5 10.0 1.0 H A:HIS243 4.5 8.1 1.0 HB3 A:ASN117 4.6 8.6 1.0 N A:HIS243 4.6 6.8 1.0 HB3 A:HIS243 4.6 9.0 1.0 HB3 A:ASP85 4.6 7.9 1.0 HG A:SER520 4.6 17.1 0.6 HA3 A:GLY116 4.8 8.3 1.0 CG A:ASP36 4.8 6.7 1.0 HE1 A:HIS38 4.8 9.6 1.0 O A:HOH927 4.9 9.4 1.0 HE2 A:HIS243 4.9 14.2 1.0 HD1 A:HIS220 4.9 9.7 1.0 NE2 A:HIS38 4.9 6.8 1.0 CA A:ASN117 4.9 6.7 1.0 OG A:SER520 5.0 14.3 0.6

Zinc binding site 2 out of 2 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Ampcp 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 Ampcp in the Open State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:8.3 occ:1.00 O A:HOH926 2.0 9.4 1.0 OD1 A:ASP36 2.0 7.0 1.0 NE2 A:HIS38 2.1 6.8 1.0 O A:HOH927 2.2 9.4 1.0 OD2 A:ASP85 2.2 7.3 1.0 CE1 A:HIS38 3.0 8.0 1.0 HB3 A:ASP85 3.0 7.9 1.0 CD2 A:HIS38 3.1 7.1 1.0 CG A:ASP36 3.1 6.7 1.0 HB3 A:ASP36 3.2 9.3 1.0 HE1 A:HIS38 3.2 9.6 1.0 CG A:ASP85 3.2 7.6 1.0 ZN A:ZN601 3.2 8.7 1.0 HD2 A:HIS38 3.3 8.5 1.0 CB A:ASP85 3.4 6.6 1.0 HB2 A:ASP85 3.5 7.9 1.0 HD2 A:HIS118 3.6 10.2 1.0 OG A:SER520 3.6 14.3 0.6 CB A:ASP36 3.6 7.8 1.0 HE1 A:HIS220 3.6 10.0 1.0 HA A:HIS243 3.7 8.4 1.0 HG A:SER520 3.7 17.1 0.6 HA A:ASP36 3.8 8.3 1.0 HB2 A:SER520 3.9 10.9 0.5 O A:HOH705 4.1 12.4 1.0 ND1 A:HIS38 4.1 7.5 1.0 O A:HIS243 4.1 9.0 1.0 OD1 A:ASN245 4.2 12.3 1.0 CG A:HIS38 4.2 7.4 1.0 OD2 A:ASP36 4.2 7.3 1.0 NE2 A:HIS220 4.2 7.1 1.0 CE1 A:HIS220 4.2 8.3 1.0 O A:HOH741 4.3 16.3 1.0 CA A:ASP36 4.3 6.9 1.0 CD2 A:HIS118 4.3 8.5 1.0 O A:HOH776 4.4 20.0 1.0 OD1 A:ASP85 4.4 7.7 1.0 HB2 A:ASP36 4.4 9.3 1.0 CA A:HIS243 4.6 7.0 1.0 H A:HIS243 4.7 8.1 1.0 CB A:SER520 4.8 9.1 0.5 C A:HIS243 4.8 8.3 1.0 ND1 A:HIS243 4.8 8.6 1.0 HB3 A:SER520 4.8 10.9 0.5 OD1 A:ASN117 4.9 7.8 1.0 NE2 A:HIS118 4.9 9.7 1.0 HD1 A:HIS38 4.9 9.0 1.0 CB A:SER520 4.9 11.5 0.6 HD21 A:ASN245 4.9 23.3 1.0 CA A:ASP85 4.9 5.8 1.0

S.Bhattarai, J.Pippel, E.R.Scaletti, R.Idris, M.Freundlieb, G.Rolshoven, C.Renn, S.Y.Lee, A.Abdelrahman, H.Zimmermann, A.El-Tayeb, C.E.Muller, N.Strater. 2-Substituted Alpha , Beta Methylene-Adp Derivatives: Potent Competitive Ecto-5'-Nucleotidase (CD73) Inhibitors with Variable Binding Modes. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32045236
DOI: 10.1021/ACS.JMEDCHEM.9B01611