Zinc in PDB 7ay6: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B:
3.1.4.53;

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B, PDB code: 7ay6 was solved by A.Torretta, S.Abbate, E.Parisini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.33 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.838, 98.66, 120.239, 90, 90, 90
R / Rfree (%)	18.2 / 21.4

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B (pdb code 7ay6). 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 the PDE4D Catalytic Domain in Complex with Gebr- 41B, PDB code: 7ay6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B


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 the PDE4D Catalytic Domain in Complex with Gebr- 41B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:14.0 occ:1.00 OD2 A:ASP201 2.0 9.4 1.0 O A:HOH621 2.1 11.6 1.0 OD1 A:ASP318 2.1 10.7 1.0 NE2 A:HIS200 2.2 9.7 1.0 NE2 A:HIS164 2.2 8.8 1.0 O A:HOH767 2.2 12.5 1.0 CG A:ASP318 3.1 13.0 1.0 CD2 A:HIS200 3.1 10.5 1.0 CG A:ASP201 3.1 12.2 1.0 CE1 A:HIS164 3.1 9.2 1.0 CD2 A:HIS164 3.2 10.0 1.0 CE1 A:HIS200 3.2 10.2 1.0 OD2 A:ASP318 3.3 22.1 1.0 OD1 A:ASP201 3.6 11.0 1.0 MG A:MG503 3.7 8.7 1.0 O A:HOH820 4.0 10.7 1.0 O A:HOH671 4.1 14.2 1.0 CD2 A:HIS160 4.2 11.3 1.0 CG A:HIS200 4.2 8.6 1.0 ND1 A:HIS200 4.3 10.8 1.0 ND1 A:HIS164 4.3 9.6 1.0 O A:HOH888 4.3 28.7 1.0 CB A:ASP201 4.3 7.2 1.0 CG A:HIS164 4.3 11.5 1.0 NE2 A:HIS160 4.4 14.4 1.0 CB A:ASP318 4.5 13.3 1.0 CG2 A:VAL168 4.7 11.2 1.0 O A:HOH715 4.7 10.5 1.0 CA A:ASP318 5.0 10.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B


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 the PDE4D Catalytic Domain in Complex with Gebr- 41B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:14.8 occ:1.00 OD2 B:ASP201 2.0 11.5 1.0 OD1 B:ASP318 2.1 12.4 1.0 O B:HOH646 2.2 13.2 1.0 NE2 B:HIS200 2.2 13.2 1.0 O B:HOH755 2.2 16.2 1.0 NE2 B:HIS164 2.2 9.4 1.0 CG B:ASP318 3.0 17.4 1.0 CD2 B:HIS200 3.0 13.3 1.0 CG B:ASP201 3.1 13.3 1.0 CD2 B:HIS164 3.1 12.5 1.0 CE1 B:HIS164 3.2 14.6 1.0 CE1 B:HIS200 3.2 12.9 1.0 OD2 B:ASP318 3.3 23.7 1.0 OD1 B:ASP201 3.6 12.2 1.0 MG B:MG503 3.8 9.2 1.0 O B:HOH813 4.0 12.0 1.0 CD2 B:HIS160 4.2 11.0 1.0 O B:HOH687 4.2 14.5 1.0 CG B:HIS200 4.2 12.6 1.0 O B:HOH843 4.2 30.4 1.0 ND1 B:HIS200 4.3 12.6 1.0 ND1 B:HIS164 4.3 12.4 1.0 CG B:HIS164 4.3 13.9 1.0 CB B:ASP201 4.3 11.0 1.0 NE2 B:HIS160 4.3 16.5 1.0 CB B:ASP318 4.4 11.2 1.0 O B:HOH699 4.7 10.3 1.0 CG2 B:VAL168 4.7 14.2 1.0 CA B:ASP318 5.0 10.4 1.0

C.Brullo, F.Rapetti, S.Abbate, T.Prosdocimi, A.Torretta, M.Semrau, M.Massa, S.Alfei, P.Storici, E.Parisini, O.Bruno. Design, Synthesis, Biological Evaluation and Structural Characterization of Novel Gebr Library PDE4D Inhibitors Eur.J.Med.Chem. 2021.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2021.113638