Zinc in PDB 8w4r: Crystal Structure of PDE4D Complexed with Cvt-313

All present enzymatic activity of Crystal Structure of PDE4D Complexed with Cvt-313:
3.1.4.53;

The structure of Crystal Structure of PDE4D Complexed with Cvt-313, PDB code: 8w4r 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)	30.33 / 1.37
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.63, 80.71, 163.67, 90, 90, 90
R / Rfree (%)	20.7 / 21.5

The structure of Crystal Structure of PDE4D Complexed with Cvt-313 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D Complexed with Cvt-313 (pdb code 8w4r). 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 PDE4D Complexed with Cvt-313, PDB code: 8w4r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE4D Complexed 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 PDE4D Complexed with Cvt-313 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:20.3 occ:1.00 OD2 A:ASP201 2.0 16.1 1.0 O A:HOH602 2.1 17.7 1.0 OD2 A:ASP318 2.1 16.4 1.0 O A:HOH669 2.2 19.0 1.0 NE2 A:HIS164 2.2 16.1 1.0 NE2 A:HIS200 2.2 16.8 1.0 CG A:ASP318 3.1 18.6 1.0 CD2 A:HIS200 3.1 16.4 1.0 CG A:ASP201 3.1 17.2 1.0 CD2 A:HIS164 3.2 16.2 1.0 CE1 A:HIS164 3.2 17.0 1.0 CE1 A:HIS200 3.3 17.8 1.0 OD1 A:ASP318 3.3 23.6 1.0 OD1 A:ASP201 3.6 16.9 1.0 MG A:MG502 3.8 14.9 1.0 O A:HOH694 3.9 19.4 1.0 O A:HOH643 4.1 21.6 1.0 CD2 A:HIS160 4.2 17.3 1.0 CB A:ASP201 4.3 15.1 1.0 CG A:HIS200 4.3 16.2 1.0 ND1 A:HIS164 4.3 15.2 1.0 CG A:HIS164 4.3 15.9 1.0 ND1 A:HIS200 4.3 16.4 1.0 NE2 A:HIS160 4.3 18.5 1.0 CB A:ASP318 4.5 16.8 1.0 O A:HOH619 4.7 17.9 1.0 CG2 A:VAL168 4.8 17.2 1.0 CA A:ASP318 4.9 16.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE4D Complexed with Cvt-313


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 PDE4D Complexed with Cvt-313 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:23.1 occ:1.00 OD2 B:ASP201 2.1 18.4 1.0 O B:HOH601 2.1 19.9 1.0 OD1 B:ASP318 2.1 19.6 1.0 O B:HOH648 2.2 22.1 1.0 NE2 B:HIS164 2.2 21.0 1.0 NE2 B:HIS200 2.2 19.2 1.0 CG B:ASP318 3.1 21.9 1.0 CD2 B:HIS200 3.1 18.6 1.0 CG B:ASP201 3.1 18.0 1.0 CE1 B:HIS164 3.1 20.2 1.0 CD2 B:HIS164 3.2 19.9 1.0 CE1 B:HIS200 3.2 19.6 1.0 OD2 B:ASP318 3.3 26.9 1.0 OD1 B:ASP201 3.6 19.4 1.0 MG B:MG502 3.8 18.6 1.0 O B:HOH661 4.0 20.1 1.0 O B:HOH632 4.1 23.0 1.0 CD2 B:HIS160 4.1 18.5 1.0 CG B:HIS200 4.3 18.9 1.0 ND1 B:HIS164 4.3 20.7 1.0 ND1 B:HIS200 4.3 19.6 1.0 CG B:HIS164 4.3 20.5 1.0 CB B:ASP201 4.3 18.3 1.0 NE2 B:HIS160 4.4 21.7 1.0 CB B:ASP318 4.5 20.0 1.0 CG2 B:VAL168 4.7 21.7 1.0 O B:HOH613 4.7 18.2 1.0 CA B:ASP318 4.9 20.7 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