Zinc in PDB 6f8t: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 4A

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 4A:
3.1.4.53;

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 4A, PDB code: 6f8t 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)	45.63 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.531, 98.717, 119.623, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 21.2

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 4A also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Zinc atom in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 4A (pdb code 6f8t). 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- 4A, PDB code: 6f8t:
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- 4A


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- 4A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:15.1 occ:1.00 O A:HOH756 2.1 10.9 1.0 OD2 A:ASP367 2.1 8.5 1.0 OD1 A:ASP484 2.1 10.5 1.0 NE2 A:HIS330 2.2 7.7 1.0 NE2 A:HIS366 2.2 9.0 1.0 O A:HOH840 2.2 15.1 1.0 CG A:ASP484 3.1 13.6 1.0 CD2 A:HIS366 3.1 9.7 1.0 CG A:ASP367 3.1 13.6 1.0 CD2 A:HIS330 3.1 7.9 1.0 CE1 A:HIS330 3.2 10.2 1.0 CE1 A:HIS366 3.2 10.2 1.0 OD2 A:ASP484 3.3 19.6 1.0 OD1 A:ASP367 3.6 11.2 1.0 MG A:MG602 3.7 9.9 1.0 O A:HOH707 3.9 29.4 1.0 O A:HOH933 3.9 10.1 1.0 O A:HOH818 4.1 17.1 1.0 CD2 A:HIS326 4.1 11.7 1.0 CG A:HIS366 4.2 8.5 1.0 ND1 A:HIS330 4.3 8.8 1.0 ND1 A:HIS366 4.3 8.0 1.0 CG A:HIS330 4.3 10.6 1.0 CB A:ASP367 4.3 9.4 1.0 NE2 A:HIS326 4.3 13.5 1.0 CB A:ASP484 4.4 12.2 1.0 O A:HOH966 4.5 29.6 1.0 CG2 A:VAL334 4.6 9.9 1.0 O A:HOH803 4.7 11.2 1.0 CA A:ASP484 4.9 11.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 4A


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- 4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:16.5 occ:1.00 OD2 B:ASP367 2.1 12.6 1.0 O B:HOH726 2.1 12.6 1.0 OD1 B:ASP484 2.2 10.9 1.0 NE2 B:HIS330 2.2 8.5 1.0 NE2 B:HIS366 2.2 11.0 1.0 O B:HOH838 2.3 17.8 1.0 CG B:ASP484 3.0 16.5 1.0 CD2 B:HIS366 3.1 12.4 1.0 CG B:ASP367 3.1 15.9 1.0 CD2 B:HIS330 3.1 10.7 1.0 CE1 B:HIS330 3.1 15.7 1.0 CE1 B:HIS366 3.3 10.2 1.0 OD2 B:ASP484 3.3 20.4 1.0 OD1 B:ASP367 3.6 11.0 1.0 MG B:MG602 3.7 11.3 1.0 O B:HOH868 3.9 12.2 1.0 O B:HOH809 4.0 19.2 1.0 CD2 B:HIS326 4.1 13.9 1.0 O B:HOH929 4.2 27.8 1.0 ND1 B:HIS330 4.2 9.8 1.0 CG B:HIS330 4.3 11.2 1.0 CG B:HIS366 4.3 10.9 1.0 CB B:ASP367 4.3 12.3 1.0 ND1 B:HIS366 4.3 11.1 1.0 NE2 B:HIS326 4.3 17.6 1.0 CB B:ASP484 4.4 11.0 1.0 CG2 B:VAL334 4.7 11.3 1.0 O B:HOH758 4.7 11.6 1.0 CA B:ASP484 4.9 12.3 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