Zinc in PDB 6f8r: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 54

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 54:
3.1.4.53;

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 54, PDB code: 6f8r 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)	49.27 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.671, 98.303, 120.091, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 54 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- 54 (pdb code 6f8r). 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- 54, PDB code: 6f8r:
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- 54


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- 54 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:15.4 occ:0.99 OD2 A:ASP367 2.1 8.6 1.0 O A:HOH726 2.1 10.4 1.0 OD1 A:ASP484 2.1 9.2 1.0 NE2 A:HIS366 2.2 8.9 1.0 O A:HOH864 2.2 14.2 1.0 NE2 A:HIS330 2.2 9.8 1.0 CG A:ASP484 3.0 12.9 1.0 CD2 A:HIS366 3.1 14.2 1.0 CG A:ASP367 3.1 15.6 1.0 CD2 A:HIS330 3.2 9.9 1.0 CE1 A:HIS366 3.2 14.9 1.0 OD2 A:ASP484 3.2 19.7 1.0 CE1 A:HIS330 3.2 13.7 1.0 OD1 A:ASP367 3.7 9.5 1.0 MG A:MG602 3.7 9.5 1.0 O A:HOH906 4.0 11.8 1.0 O A:HOH790 4.1 16.8 1.0 CD2 A:HIS326 4.2 13.0 1.0 CG A:HIS366 4.3 10.9 1.0 ND1 A:HIS366 4.3 9.5 1.0 CB A:ASP367 4.3 11.3 1.0 CG A:HIS330 4.3 12.3 1.0 ND1 A:HIS330 4.3 11.0 1.0 NE2 A:HIS326 4.4 17.1 1.0 CB A:ASP484 4.4 12.8 1.0 CG2 A:VAL334 4.7 9.4 1.0 O A:HOH781 4.7 10.8 1.0 CA A:ASP484 4.9 13.8 1.0 H31 A:CZK601 4.9 33.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 54


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- 54 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:17.7 occ:1.00 O B:HOH722 2.1 14.7 1.0 O B:HOH863 2.1 16.5 1.0 OD2 B:ASP367 2.2 13.9 1.0 OD1 B:ASP484 2.2 11.1 1.0 NE2 B:HIS330 2.2 13.5 1.0 NE2 B:HIS366 2.2 12.7 1.0 CG B:ASP484 3.1 20.1 1.0 CD2 B:HIS366 3.1 13.5 1.0 CG B:ASP367 3.1 13.7 1.0 CE1 B:HIS330 3.2 15.6 1.0 CD2 B:HIS330 3.2 15.2 1.0 CE1 B:HIS366 3.3 13.1 1.0 OD2 B:ASP484 3.3 19.6 1.0 OD1 B:ASP367 3.5 13.7 1.0 MG B:MG602 3.6 10.5 1.0 O B:HOH701 3.8 22.1 1.0 O B:HOH858 3.9 14.2 1.0 O B:HOH820 4.0 19.3 1.0 CD2 B:HIS326 4.2 13.5 1.0 CG B:HIS366 4.3 15.1 1.0 O B:HOH902 4.3 30.1 1.0 ND1 B:HIS330 4.3 16.5 1.0 ND1 B:HIS366 4.3 15.3 1.0 CB B:ASP367 4.3 14.0 1.0 CG B:HIS330 4.3 15.3 1.0 NE2 B:HIS326 4.3 15.4 1.0 CB B:ASP484 4.4 13.7 1.0 CG2 B:VAL334 4.7 12.7 1.0 O B:HOH760 4.8 13.6 1.0 O B:HOH831 5.0 14.3 1.0 CA B:ASP484 5.0 12.8 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