Zinc in PDB 8w4q: Crystal Structure of PDE4D Complexed with Cx-4945

All present enzymatic activity of Crystal Structure of PDE4D Complexed with Cx-4945:
3.1.4.53;

The structure of Crystal Structure of PDE4D Complexed with Cx-4945, PDB code: 8w4q 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)	28.32 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.509, 79.99, 162.723, 90, 90, 90
R / Rfree (%)	22.6 / 24

The structure of Crystal Structure of PDE4D Complexed with Cx-4945 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D Complexed with Cx-4945 (pdb code 8w4q). 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 Cx-4945, PDB code: 8w4q:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE4D Complexed with Cx-4945


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 Cx-4945 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:20.4 occ:1.00 OD2 A:ASP201 2.1 33.9 1.0 OD1 A:ASP318 2.1 27.8 1.0 NE2 A:HIS164 2.1 27.0 1.0 O A:HOH602 2.2 20.8 1.0 NE2 A:HIS200 2.2 28.7 1.0 O A:HOH615 2.2 24.2 1.0 CG A:ASP318 3.1 25.5 1.0 CD2 A:HIS200 3.1 26.5 1.0 CG A:ASP201 3.1 31.1 1.0 CE1 A:HIS164 3.1 25.1 1.0 CD2 A:HIS164 3.2 25.6 1.0 CE1 A:HIS200 3.2 27.7 1.0 OD2 A:ASP318 3.3 26.3 1.0 OD1 A:ASP201 3.6 32.4 1.0 MG A:MG501 3.8 20.0 1.0 O A:HOH621 4.0 20.8 1.0 CD2 A:HIS160 4.2 22.0 1.0 O A:HOH629 4.2 29.1 1.0 ND1 A:HIS164 4.2 25.4 1.0 CB A:ASP201 4.3 27.2 1.0 CG A:HIS200 4.3 25.7 1.0 CG A:HIS164 4.3 24.7 1.0 ND1 A:HIS200 4.3 27.3 1.0 CB A:ASP318 4.4 22.8 1.0 NE2 A:HIS160 4.6 21.9 1.0 O A:HOH622 4.7 18.9 1.0 CG2 A:VAL168 4.7 19.4 1.0 O24 A:3NG503 4.7 40.4 1.0 CA A:ASP318 4.9 20.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE4D Complexed with Cx-4945


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 Cx-4945 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:27.0 occ:1.00 O B:HOH605 2.1 25.3 1.0 OD2 B:ASP201 2.1 45.1 1.0 NE2 B:HIS164 2.1 50.9 1.0 OD1 B:ASP318 2.1 51.2 1.0 O B:HOH602 2.2 25.8 1.0 NE2 B:HIS200 2.2 27.4 1.0 CG B:ASP318 3.0 46.3 1.0 CD2 B:HIS164 3.1 48.6 1.0 CD2 B:HIS200 3.1 26.8 1.0 CG B:ASP201 3.1 40.8 1.0 CE1 B:HIS164 3.2 51.0 1.0 OD2 B:ASP318 3.2 47.0 1.0 CE1 B:HIS200 3.3 29.3 1.0 OD1 B:ASP201 3.6 41.6 1.0 MG B:MG501 3.8 23.1 1.0 O B:HOH615 3.8 23.7 1.0 O B:HOH613 4.2 36.4 1.0 CD2 B:HIS160 4.2 29.2 1.0 CG B:HIS164 4.2 45.0 1.0 ND1 B:HIS164 4.3 33.7 1.0 CG B:HIS200 4.3 27.2 1.0 ND1 B:HIS200 4.3 29.4 1.0 CB B:ASP201 4.4 36.5 1.0 CB B:ASP318 4.5 44.0 1.0 O25 B:3NG503 4.5 44.7 1.0 CG2 B:VAL168 4.7 39.4 1.0 NE2 B:HIS160 4.7 28.1 1.0 O B:HOH608 4.7 23.9 1.0 CA B:ASP318 4.9 41.4 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