Zinc in PDB 8w4s: Crystal Structure of PDE5A in Complex with Cvt-313

All present enzymatic activity of Crystal Structure of PDE5A in Complex with Cvt-313:
3.1.4.35;

The structure of Crystal Structure of PDE5A in Complex with Cvt-313, PDB code: 8w4s was solved by J.Y.Liu, M.J.Li, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.05 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.335, 74.335, 131.822, 90, 90, 120
R / Rfree (%)	20.9 / 24.5

The structure of Crystal Structure of PDE5A in Complex with Cvt-313 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of PDE5A in Complex with Cvt-313 (pdb code 8w4s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of PDE5A in Complex with Cvt-313, PDB code: 8w4s:

Zinc binding site 1 out of 1 in the Crystal Structure of PDE5A in Complex with Cvt-313


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 PDE5A in Complex with Cvt-313 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:27.1 occ:0.00 OD2 A:ASP654 1.7 33.8 1.0 OD1 A:ASP764 1.9 30.9 1.0 NE2 A:HIS617 2.0 24.9 1.0 NE2 A:HIS653 2.2 26.2 1.0 O A:HOH1007 2.5 23.9 1.0 O A:HOH1001 2.6 22.4 1.0 CG A:ASP764 2.8 30.5 1.0 CE1 A:HIS617 3.0 27.6 1.0 CD2 A:HIS653 3.0 20.8 1.0 CG A:ASP654 3.0 20.4 1.0 CD2 A:HIS617 3.1 23.1 1.0 OD2 A:ASP764 3.1 32.7 1.0 CE1 A:HIS653 3.2 26.6 1.0 OD1 A:ASP654 3.8 28.2 1.0 O A:HOH1048 4.0 38.8 1.0 ND1 A:HIS617 4.1 26.0 1.0 CB A:ASP764 4.2 26.9 1.0 CG A:HIS617 4.2 25.5 1.0 CG A:HIS653 4.2 22.9 1.0 CD2 A:HIS613 4.3 32.7 1.0 ND1 A:HIS653 4.3 22.1 1.0 O A:HOH1064 4.3 30.6 1.0 MG A:MG901 4.4 28.3 0.0 CB A:ASP654 4.4 22.3 1.0 NE2 A:HIS613 4.5 35.9 1.0 O A:ASP764 4.6 26.5 1.0 CA A:ASP764 4.6 23.4 1.0 OG1 A:THR621 4.7 24.5 1.0

J.Liu, X.Zhang, G.Chen, Q.Shao, Y.Zou, Z.Li, H.Su, M.Li, Y.Xu. Drug Repurposing and Structure-Based Discovery of New PDE4 and PDE5 Inhibitors. Eur.J.Med.Chem. V. 262 15893 2023.
ISSN: ISSN 0223-5234
PubMed: 37918035
DOI: 10.1016/J.EJMECH.2023.115893