Zinc in PDB 7pbb: Crystal Structure of CD73 in Complex with Caffeine in the Open Form

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

The structure of Crystal Structure of CD73 in Complex with Caffeine in the Open Form, PDB code: 7pbb 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)	47.26 / 1.47
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.243, 131.799, 66.316, 90, 90, 90
R / Rfree (%)	17.3 / 19.6

The structure of Crystal Structure of CD73 in Complex with Caffeine 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 Caffeine in the Open Form (pdb code 7pbb). 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 Caffeine in the Open Form, PDB code: 7pbb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of CD73 in Complex with Caffeine 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 Caffeine 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:HOH708 2.0 8.0 1.0 NE2 A:HIS38 2.0 7.6 1.0 OD1 A:ASP36 2.1 8.0 1.0 O A:HOH706 2.1 8.6 1.0 OD2 A:ASP85 2.2 8.3 1.0 CD2 A:HIS38 3.0 7.3 1.0 CE1 A:HIS38 3.1 7.1 1.0 CG A:ASP85 3.2 7.2 1.0 CG A:ASP36 3.2 7.8 1.0 ZN A:ZN602 3.2 8.1 1.0 CB A:ASP85 3.4 6.9 1.0 CB A:ASP36 3.7 7.2 1.0 OG A:SER520 3.8 13.7 0.5 OD1 A:ASN245 4.0 10.1 0.5 O A:HOH780 4.1 12.8 1.0 CG A:HIS38 4.1 7.4 1.0 O A:HIS243 4.2 8.8 1.0 ND1 A:HIS38 4.2 7.3 1.0 OD2 A:ASP36 4.2 8.3 1.0 OD1 A:ASN245 4.2 9.7 0.5 NE2 A:HIS220 4.2 7.7 1.0 CA A:ASP36 4.2 6.7 1.0 O A:HOH759 4.2 14.0 1.0 CD2 A:HIS118 4.3 8.6 1.0 CE1 A:HIS220 4.3 7.5 1.0 OD1 A:ASP85 4.4 7.4 1.0 O A:HOH1002 4.4 14.5 1.0 CA A:HIS243 4.6 8.2 1.0 CB A:SER520 4.7 10.5 0.5 ND1 A:HIS243 4.7 9.4 1.0 C A:HIS243 4.8 8.4 1.0 OD1 A:ASN117 4.9 8.3 1.0 NE2 A:HIS118 4.9 9.1 1.0 CA A:ASP85 4.9 7.0 1.0 CG A:ASN245 5.0 10.1 0.5

Zinc binding site 2 out of 2 in the Crystal Structure of CD73 in Complex with Caffeine 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 Caffeine in the Open Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:8.1 occ:1.00 NE2 A:HIS220 2.0 7.7 1.0 O A:HOH708 2.0 8.0 1.0 OD1 A:ASN117 2.1 8.3 1.0 ND1 A:HIS243 2.1 9.4 1.0 OD2 A:ASP85 2.2 8.3 1.0 CE1 A:HIS243 2.9 10.2 1.0 CD2 A:HIS220 3.0 7.9 1.0 CG A:ASP85 3.1 7.2 1.0 CE1 A:HIS220 3.1 7.5 1.0 CG A:ASN117 3.2 8.3 1.0 O A:HOH780 3.2 12.8 1.0 CG A:HIS243 3.2 8.9 1.0 ZN A:ZN601 3.2 8.2 1.0 OD1 A:ASP85 3.5 7.4 1.0 CA A:HIS243 3.6 8.2 1.0 CB A:HIS243 3.6 8.5 1.0 OD1 A:ASP36 3.7 8.0 1.0 ND2 A:ASN117 3.7 8.8 1.0 O A:HIS243 4.1 8.8 1.0 NE2 A:HIS243 4.1 10.5 1.0 CG A:HIS220 4.1 7.4 1.0 ND1 A:HIS220 4.2 7.1 1.0 CB A:ASP85 4.2 6.9 1.0 CD2 A:HIS243 4.2 10.1 1.0 C A:HIS243 4.4 8.4 1.0 CD2 A:HIS118 4.4 8.6 1.0 N A:ASN117 4.4 8.2 1.0 CB A:ASN117 4.5 8.4 1.0 N A:HIS243 4.6 8.0 1.0 O A:HOH706 4.8 8.6 1.0 NE2 A:HIS38 4.9 7.6 1.0 CG A:ASP36 4.9 7.8 1.0 CA A:ASN117 4.9 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