Zinc in PDB 6f8v: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B:
3.1.4.53;

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B, PDB code: 6f8v was solved by T.Prosdocimi, S.Donini, E.Parisini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.49 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.558, 98.314, 120.089, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 25.4

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B (pdb code 6f8v). 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- 18B, PDB code: 6f8v:
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- 18B


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- 18B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:18.5 occ:1.00 OD2 A:ASP367 2.1 11.6 1.0 OD1 A:ASP484 2.2 12.4 1.0 NE2 A:HIS366 2.2 11.7 1.0 NE2 A:HIS330 2.2 9.9 1.0 O A:HOH731 2.3 15.0 1.0 O A:HOH814 2.4 18.5 1.0 CG A:ASP484 3.0 12.5 1.0 CD2 A:HIS366 3.0 11.6 1.0 CG A:ASP367 3.1 15.8 1.0 CD2 A:HIS330 3.2 11.7 1.0 OD2 A:ASP484 3.2 18.8 1.0 CE1 A:HIS330 3.2 10.1 1.0 CE1 A:HIS366 3.2 16.7 1.0 OD1 A:ASP367 3.6 14.1 1.0 MG A:MG602 3.8 12.5 1.0 H19 A:D0B605 3.9 20.4 1.0 O A:HOH737 4.1 15.4 1.0 O A:HOH906 4.1 14.1 1.0 CD2 A:HIS326 4.2 11.3 1.0 CG A:HIS366 4.2 12.7 1.0 ND1 A:HIS366 4.3 9.3 1.0 ND1 A:HIS330 4.3 12.5 1.0 CB A:ASP367 4.3 12.2 1.0 CG A:HIS330 4.3 16.6 1.0 H01 A:D0B605 4.4 20.4 1.0 CB A:ASP484 4.4 13.8 1.0 NE2 A:HIS326 4.4 13.2 1.0 CG2 A:VAL334 4.6 11.3 1.0 C15 A:D0B605 4.6 17.0 1.0 O A:HOH748 4.7 12.8 1.0 CA A:ASP484 4.9 15.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B


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- 18B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:19.1 occ:1.00 OD2 B:ASP367 2.1 14.5 1.0 NE2 B:HIS366 2.2 14.6 1.0 OD1 B:ASP484 2.2 11.9 1.0 NE2 B:HIS330 2.2 11.8 1.0 O B:HOH712 2.3 16.8 1.0 O B:HOH753 2.4 13.2 1.0 CG B:ASP484 3.0 16.9 1.0 CD2 B:HIS366 3.1 15.0 1.0 CG B:ASP367 3.1 10.4 1.0 CD2 B:HIS330 3.2 14.7 1.0 CE1 B:HIS366 3.2 15.7 1.0 CE1 B:HIS330 3.2 14.6 1.0 OD2 B:ASP484 3.2 19.5 1.0 OD1 B:ASP367 3.6 11.4 1.0 MG B:MG602 3.7 10.5 1.0 H19 B:D0B603 3.9 23.8 1.0 O B:HOH812 4.0 18.5 1.0 O B:HOH801 4.0 12.5 1.0 CD2 B:HIS326 4.1 11.7 1.0 CG B:HIS366 4.2 13.6 1.0 ND1 B:HIS366 4.2 10.2 1.0 NE2 B:HIS326 4.2 14.8 1.0 ND1 B:HIS330 4.3 12.1 1.0 H01 B:D0B603 4.3 23.8 1.0 CG B:HIS330 4.3 13.7 1.0 CB B:ASP367 4.3 14.4 1.0 CB B:ASP484 4.4 10.1 1.0 C15 B:D0B603 4.6 19.8 1.0 CG2 B:VAL334 4.7 12.9 1.0 O B:HOH751 4.8 13.5 1.0 CA B:ASP484 4.9 14.1 1.0

T.Prosdocimi, L.Mollica, S.Donini, M.S.Semrau, A.P.Lucarelli, E.Aiolfi, A.Cavalli, P.Storici, S.Alfei, C.Brullo, O.Bruno, E.Parisini. Molecular Bases of PDE4D Inhibition By Memory-Enhancing Gebr Library Compounds. Biochemistry V. 57 2876 2018.
ISSN: ISSN 1520-4995
PubMed: 29652483
DOI: 10.1021/ACS.BIOCHEM.8B00288