Zinc in PDB 7xab: Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 22D

All present enzymatic activity of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 22D:
3.1.4.53;

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 22D, PDB code: 7xab was solved by Y.-Y.Huang, X.He, H.-B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.68 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.622, 80.41, 162.952, 90, 90, 90
R / Rfree (%)	19.5 / 24.7

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 22D also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 22D (pdb code 7xab). 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 Catalytic Domain Complexed with Compound 22D, PDB code: 7xab:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 22D


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 Catalytic Domain Complexed with Compound 22D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:15.4 occ:1.00 OD2 A:ASP201 2.1 6.8 1.0 O A:HOH868 2.2 7.1 1.0 NE2 A:HIS164 2.2 8.2 1.0 O A:HOH771 2.2 10.2 1.0 OD1 A:ASP318 2.2 5.5 1.0 NE2 A:HIS200 2.3 5.7 1.0 CG A:ASP318 3.1 7.8 1.0 CD2 A:HIS200 3.1 7.2 1.0 CD2 A:HIS164 3.1 7.9 1.0 CG A:ASP201 3.1 9.0 1.0 CE1 A:HIS164 3.2 8.3 1.0 OD2 A:ASP318 3.3 11.3 1.0 CE1 A:HIS200 3.4 7.9 1.0 OD1 A:ASP201 3.6 9.4 1.0 MG A:MG602 3.7 7.9 1.0 O A:HOH863 3.9 6.9 1.0 O A:HOH795 4.2 9.2 1.0 CD2 A:HIS160 4.2 8.8 1.0 ND1 A:HIS164 4.3 6.8 1.0 CG A:HIS164 4.3 10.1 1.0 CG A:HIS200 4.3 10.1 1.0 CB A:ASP201 4.3 7.7 1.0 ND1 A:HIS200 4.4 11.0 1.0 CB A:ASP318 4.5 6.6 1.0 NE2 A:HIS160 4.5 9.8 1.0 O A:HOH768 4.7 9.4 1.0 C37 A:AWI603 4.7 15.2 1.0 CG2 A:VAL168 4.8 5.2 1.0 N36 A:AWI603 5.0 20.6 1.0 CA A:ASP318 5.0 7.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 22D


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 Catalytic Domain Complexed with Compound 22D within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:18.5 occ:1.00 OD2 B:ASP201 2.1 9.2 1.0 OD1 B:ASP318 2.1 11.5 1.0 O B:HOH781 2.1 12.9 1.0 NE2 B:HIS164 2.2 10.8 1.0 NE2 B:HIS200 2.2 9.4 1.0 O B:HOH798 2.3 9.7 1.0 CD2 B:HIS200 3.1 9.8 1.0 CG B:ASP318 3.1 15.3 1.0 CG B:ASP201 3.1 10.2 1.0 CE1 B:HIS164 3.2 13.4 1.0 CD2 B:HIS164 3.2 11.5 1.0 CE1 B:HIS200 3.3 12.5 1.0 OD2 B:ASP318 3.4 16.0 1.0 OD1 B:ASP201 3.6 10.5 1.0 MG B:MG602 3.7 9.2 1.0 O B:HOH824 4.0 11.1 1.0 CD2 B:HIS160 4.1 10.4 1.0 CG B:HIS200 4.3 11.0 1.0 ND1 B:HIS164 4.3 10.9 1.0 CB B:ASP201 4.3 7.7 1.0 NE2 B:HIS160 4.3 10.9 1.0 ND1 B:HIS200 4.3 10.5 1.0 CG B:HIS164 4.4 11.3 1.0 O B:HOH776 4.4 12.3 1.0 CB B:ASP318 4.5 14.3 1.0 O B:HOH725 4.7 6.7 1.0 CG2 B:VAL168 4.8 13.5 1.0 C37 B:AWI603 4.8 19.7 1.0 CA B:ASP318 5.0 14.8 1.0

H.Liu, Q.Wang, Y.Huang, J.Deng, X.Xie, J.Zhu, Y.Yuan, Y.M.He, Y.Y.Huang, H.B.Luo, X.He. Discovery of Novel PDE4 Inhibitors Targeting the M-Pocket From Natural Mangostanin with Improved Safety For the Treatment of Inflammatory Bowel Diseases. Eur.J.Med.Chem. V. 242 14631 2022.
ISSN: ISSN 0223-5234
PubMed: 35985255
DOI: 10.1016/J.EJMECH.2022.114631