Zinc in PDB 8wdn: Crystal Structure of PDE4D Complexed with 7B-1

All present enzymatic activity of Crystal Structure of PDE4D Complexed with 7B-1:
3.1.4.53;

The structure of Crystal Structure of PDE4D Complexed with 7B-1, PDB code: 8wdn 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)	36.42 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.965, 80.407, 163.413, 90, 90, 90
R / Rfree (%)	20.8 / 23.1

The structure of Crystal Structure of PDE4D Complexed with 7B-1 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D Complexed with 7B-1 (pdb code 8wdn). 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 7B-1, PDB code: 8wdn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE4D Complexed with 7B-1


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 7B-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:18.8 occ:1.00 OD2 A:ASP201 2.1 15.9 1.0 OD1 A:ASP318 2.1 15.8 1.0 O A:HOH753 2.2 18.2 1.0 NE2 A:HIS164 2.2 16.1 1.0 O A:HOH710 2.2 18.1 1.0 NE2 A:HIS200 2.2 14.8 1.0 CG A:ASP318 3.1 19.9 1.0 CE1 A:HIS164 3.1 16.0 1.0 CG A:ASP201 3.1 14.6 1.0 CD2 A:HIS200 3.1 15.6 1.0 CD2 A:HIS164 3.2 16.9 1.0 CE1 A:HIS200 3.2 17.4 1.0 OD2 A:ASP318 3.3 22.7 1.0 OD1 A:ASP201 3.6 15.3 1.0 MG A:MG601 3.7 16.3 1.0 O A:HOH808 3.8 17.3 1.0 O A:HOH790 4.0 26.9 1.0 O A:HOH801 4.0 33.5 1.0 CD2 A:HIS160 4.2 16.7 1.0 ND1 A:HIS164 4.2 15.6 1.0 CB A:ASP201 4.3 16.3 1.0 CG A:HIS200 4.3 15.7 1.0 CG A:HIS164 4.3 14.7 1.0 ND1 A:HIS200 4.3 15.1 1.0 CB A:ASP318 4.4 15.7 1.0 NE2 A:HIS160 4.6 19.5 1.0 O A:HOH741 4.7 16.4 1.0 CG2 A:VAL168 4.8 17.0 1.0 O4 A:W8E603 4.9 45.0 1.0 CA A:ASP318 5.0 16.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE4D Complexed with 7B-1


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 7B-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:21.8 occ:1.00 OD2 B:ASP201 2.1 19.5 1.0 NE2 B:HIS164 2.1 20.9 1.0 OD1 B:ASP318 2.2 24.8 1.0 O B:HOH709 2.2 19.1 1.0 O B:HOH707 2.2 21.1 1.0 NE2 B:HIS200 2.2 18.0 1.0 CD2 B:HIS200 3.1 19.3 1.0 CG B:ASP318 3.1 28.2 1.0 CD2 B:HIS164 3.1 22.4 1.0 CG B:ASP201 3.1 18.8 1.0 CE1 B:HIS164 3.1 21.0 1.0 CE1 B:HIS200 3.2 19.1 1.0 OD2 B:ASP318 3.3 30.2 1.0 OD1 B:ASP201 3.6 18.5 1.0 MG B:MG601 3.7 17.7 1.0 O B:HOH759 3.8 20.0 1.0 O B:HOH737 4.1 27.4 1.0 CD2 B:HIS160 4.2 18.4 1.0 ND1 B:HIS164 4.2 24.5 1.0 CG B:HIS200 4.3 19.8 1.0 CG B:HIS164 4.3 21.7 1.0 ND1 B:HIS200 4.3 22.1 1.0 CB B:ASP201 4.3 18.2 1.0 CB B:ASP318 4.5 26.6 1.0 NE2 B:HIS160 4.6 21.7 1.0 CG2 B:VAL168 4.7 25.4 1.0 O B:HOH706 4.8 18.6 1.0 O4 B:W8E603 4.8 48.3 1.0 CA B:ASP318 5.0 25.1 1.0

C.Gu, J.Liu, F.Qian, W.Yu, D.Huang, J.Shen, C.Feng, K.Chen, Y.Li, X.Jiang, Y.Xu, L.Zhang. Identification of Dihydrobenzofuran Neolignans As Novel PDE4 Inhibitors and Evaluation of Antiatopic Dermatitis Efficacy in Dncb-Induced Mice Model. J.Med.Chem. V. 67 4855 2024.
ISSN: ISSN 0022-2623
PubMed: 38489246
DOI: 10.1021/ACS.JMEDCHEM.3C02424