Zinc in PDB 7pby: Crystal Structure of CD73 in Complex with 4-Nitrocatechol in the Open Form

All present enzymatic activity of Crystal Structure of CD73 in Complex with 4-Nitrocatechol in the Open Form:
3.1.3.5;

The structure of Crystal Structure of CD73 in Complex with 4-Nitrocatechol in the Open Form, PDB code: 7pby was solved by E.R.Scaletti, N.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.77 / 1.13
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.21, 131.645, 66.348, 90, 90, 90
R / Rfree (%)	12.8 / 14.5

The structure of Crystal Structure of CD73 in Complex with 4-Nitrocatechol in the Open Form also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Crystal Structure of CD73 in Complex with 4-Nitrocatechol in the Open Form (pdb code 7pby). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of CD73 in Complex with 4-Nitrocatechol in the Open Form, PDB code: 7pby:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of CD73 in Complex with 4-Nitrocatechol in the Open Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of CD73 in Complex with 4-Nitrocatechol in the Open Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:8.2 occ:1.00 O A:HOH723 2.0 9.0 1.0 OD1 A:ASP36 2.0 7.4 1.0 NE2 A:HIS38 2.0 7.7 1.0 O A:HOH715 2.1 9.5 1.0 OD2 A:ASP85 2.2 7.9 1.0 CE1 A:HIS38 3.0 8.4 1.0 CD2 A:HIS38 3.0 7.5 1.0 CG A:ASP36 3.1 7.4 1.0 CG A:ASP85 3.2 7.1 1.0 ZN A:ZN602 3.2 8.1 1.0 CB A:ASP85 3.5 7.8 1.0 CB A:ASP36 3.6 7.5 1.0 OD1 A:ASN245 4.0 7.5 0.5 O A:HOH733 4.1 11.1 1.0 O A:HIS243 4.2 9.5 1.0 ND1 A:HIS38 4.2 8.7 1.0 OD2 A:ASP36 4.2 8.2 1.0 CG A:HIS38 4.2 7.6 1.0 O A:HOH813 4.2 13.9 1.0 OD1 A:ASN245 4.2 10.7 0.5 CA A:ASP36 4.2 7.0 1.0 NE2 A:HIS220 4.2 7.5 1.0 CE1 A:HIS220 4.3 7.8 1.0 CD2 A:HIS118 4.3 8.7 1.0 O A:HOH1121 4.4 12.7 1.0 OD1 A:ASP85 4.4 8.5 1.0 CA A:HIS243 4.6 7.9 1.0 ND1 A:HIS243 4.7 9.0 1.0 CB A:SER520 4.8 12.1 1.0 C A:HIS243 4.8 8.7 1.0 OD1 A:ASN117 4.9 8.9 1.0 NE2 A:HIS118 4.9 9.3 1.0 CA A:ASP85 5.0 7.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of CD73 in Complex with 4-Nitrocatechol in the Open Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of CD73 in Complex with 4-Nitrocatechol in the Open Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:8.1 occ:1.00 O A:HOH723 2.0 9.0 1.0 NE2 A:HIS220 2.0 7.5 1.0 OD1 A:ASN117 2.1 8.9 1.0 ND1 A:HIS243 2.1 9.0 1.0 OD2 A:ASP85 2.2 7.9 1.0 CE1 A:HIS243 3.0 9.3 1.0 CD2 A:HIS220 3.0 7.5 1.0 CE1 A:HIS220 3.1 7.8 1.0 CG A:ASP85 3.1 7.1 1.0 CG A:ASN117 3.2 8.6 1.0 CG A:HIS243 3.2 9.0 1.0 O A:HOH733 3.2 11.1 1.0 ZN A:ZN601 3.2 8.2 1.0 OD1 A:ASP85 3.5 8.5 1.0 CA A:HIS243 3.6 7.9 1.0 CB A:HIS243 3.6 8.3 1.0 OD1 A:ASP36 3.7 7.4 1.0 ND2 A:ASN117 3.7 9.6 1.0 O A:HIS243 4.1 9.5 1.0 NE2 A:HIS243 4.2 11.0 1.0 ND1 A:HIS220 4.2 7.7 1.0 CG A:HIS220 4.2 7.7 1.0 CB A:ASP85 4.3 7.8 1.0 CD2 A:HIS243 4.3 10.1 1.0 CD2 A:HIS118 4.4 8.7 1.0 C A:HIS243 4.4 8.7 1.0 N A:ASN117 4.4 8.1 1.0 CB A:ASN117 4.5 8.6 1.0 N A:HIS243 4.6 7.8 1.0 CG A:ASP36 4.8 7.4 1.0 O A:HOH715 4.9 9.5 1.0 NE2 A:HIS38 4.9 7.7 1.0 CA A:ASN117 5.0 8.4 1.0

E.Scaletti, F.U.Huschmann, U.Mueller, M.S.Weiss, N.Strater. Substrate Binding Modes of Purine and Pyrimidine Nucleotides to Human Ecto-5'-Nucleotidase (CD73) and Inhibition By Their Bisphosphonic Acid Derivatives. Purinergic Signal 2021.
ISSN: ISSN 1573-9546
PubMed: 34403084
DOI: 10.1007/S11302-021-09802-W