Zinc in PDB 6tve: Unliganded Human CD73 (5'-Nucleotidase) in the Open State

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

The structure of Unliganded Human CD73 (5'-Nucleotidase) in the Open State, PDB code: 6tve 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)	32.84 / 1.05
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.316, 131.380, 66.195, 90.00, 90.00, 90.00
R / Rfree (%)	11.8 / 13.3

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

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Unliganded Human CD73 (5'-Nucleotidase) in the Open State (pdb code 6tve). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Unliganded Human CD73 (5'-Nucleotidase) in the Open State, PDB code: 6tve:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Unliganded Human CD73 (5'-Nucleotidase) 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 Unliganded Human CD73 (5'-Nucleotidase) in the Open State within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn602 b:5.7 occ:1.00 O P:HOH733 2.0 6.4 1.0 NE2 P:HIS220 2.0 5.7 1.0 OD1 P:ASN117 2.1 6.5 1.0 ND1 P:HIS243 2.1 6.6 1.0 OD2 P:ASP85 2.2 5.6 1.0 HA P:HIS243 2.8 6.7 1.0 CE1 P:HIS243 3.0 7.4 1.0 CD2 P:HIS220 3.0 5.7 1.0 CE1 P:HIS220 3.1 5.3 1.0 CG P:ASP85 3.1 5.3 1.0 HE1 P:HIS243 3.1 8.8 1.0 HD2 P:HIS220 3.2 6.9 1.0 CG P:ASN117 3.2 6.0 1.0 O P:HOH727 3.2 8.5 1.0 CG P:HIS243 3.2 6.8 1.0 ZN P:ZN603 3.2 5.8 1.0 HE1 P:HIS220 3.3 6.3 1.0 HD21 P:ASN117 3.4 8.2 1.0 HD2 P:HIS118 3.4 7.7 1.0 HB2 P:HIS243 3.5 7.2 1.0 OD1 P:ASP85 3.5 6.0 1.0 CA P:HIS243 3.6 5.6 1.0 CB P:HIS243 3.6 6.0 1.0 H P:ASN117 3.6 6.8 1.0 OD1 P:ASP36 3.7 5.5 1.0 ND2 P:ASN117 3.7 6.8 1.0 O P:HIS243 4.1 6.8 1.0 ND1 P:HIS220 4.2 5.3 1.0 NE2 P:HIS243 4.2 7.7 1.0 CG P:HIS220 4.2 5.6 1.0 HB2 P:ASP85 4.2 6.6 1.0 CB P:ASP85 4.3 5.5 1.0 CD2 P:HIS243 4.3 7.3 1.0 H P:HIS118 4.3 6.9 1.0 CD2 P:HIS118 4.3 6.4 1.0 C P:HIS243 4.4 6.0 1.0 N P:ASN117 4.4 5.7 1.0 CB P:ASN117 4.4 6.1 1.0 H P:HIS243 4.5 6.4 1.0 HG P:SER520 4.5 9.7 0.2 HD22 P:ASN117 4.6 8.2 1.0 N P:HIS243 4.6 5.3 1.0 HB3 P:ASN117 4.6 7.3 1.0 HB3 P:HIS243 4.6 7.2 1.0 HB3 P:ASP85 4.6 6.6 1.0 CG P:ASP36 4.8 5.5 1.0 HE1 P:HIS38 4.8 7.1 1.0 HA3 P:GLY116 4.9 7.2 1.0 O P:HOH741 4.9 6.7 1.0 NE2 P:HIS38 4.9 5.7 1.0 OG P:SER520 4.9 8.1 0.2 HE2 P:HIS243 4.9 9.2 1.0 HD1 P:HIS220 4.9 6.4 1.0 CA P:ASN117 5.0 5.8 1.0

Zinc binding site 2 out of 2 in the Unliganded Human CD73 (5'-Nucleotidase) 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 Unliganded Human CD73 (5'-Nucleotidase) in the Open State within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn603 b:5.8 occ:1.00 O P:HOH733 2.0 6.4 1.0 OD1 P:ASP36 2.0 5.5 1.0 NE2 P:HIS38 2.1 5.7 1.0 O P:HOH741 2.1 6.7 1.0 OD2 P:ASP85 2.3 5.6 1.0 CE1 P:HIS38 3.0 5.9 1.0 CD2 P:HIS38 3.0 5.4 1.0 HB3 P:ASP85 3.1 6.6 1.0 CG P:ASP36 3.1 5.5 1.0 HB3 P:ASP36 3.2 6.4 1.0 HD2 P:HIS38 3.2 6.5 1.0 HE1 P:HIS38 3.2 7.1 1.0 ZN P:ZN602 3.2 5.7 1.0 CG P:ASP85 3.2 5.3 1.0 CB P:ASP85 3.5 5.5 1.0 HB2 P:ASP85 3.5 6.6 1.0 HD2 P:HIS118 3.6 7.7 1.0 OG P:SER520 3.6 8.1 0.2 CB P:ASP36 3.6 5.4 1.0 HA P:HIS243 3.6 6.7 1.0 HE1 P:HIS220 3.7 6.3 1.0 HG P:SER520 3.7 9.7 0.2 HA P:ASP36 3.7 6.3 1.0 HB2 P:SER520 3.9 9.4 0.8 OD1 P:ASN245 4.1 7.5 1.0 O P:HOH727 4.1 8.5 1.0 ND1 P:HIS38 4.1 6.1 1.0 O P:HIS243 4.2 6.8 1.0 OD2 P:ASP36 4.2 5.9 1.0 CG P:HIS38 4.2 5.4 1.0 O P:HOH794 4.2 10.9 1.0 NE2 P:HIS220 4.2 5.7 1.0 CA P:ASP36 4.2 5.3 1.0 CE1 P:HIS220 4.3 5.3 1.0 CD2 P:HIS118 4.3 6.4 1.0 O P:HOH1276 4.3 9.4 1.0 OD1 P:ASP85 4.4 6.0 1.0 HB2 P:ASP36 4.5 6.4 1.0 CA P:HIS243 4.5 5.6 1.0 HD21 P:ASN245 4.6 12.8 1.0 H P:HIS243 4.6 6.4 1.0 CB P:SER520 4.7 7.8 0.8 C P:HIS243 4.8 6.0 1.0 ND1 P:HIS243 4.8 6.6 1.0 HB3 P:SER520 4.9 9.4 0.8 OD1 P:ASN117 4.9 6.5 1.0 CB P:SER520 4.9 7.7 0.2 NE2 P:HIS118 4.9 6.9 1.0 HD1 P:HIS38 4.9 7.3 1.0 CA P:ASP85 4.9 5.1 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