Zinc in PDB 6f6u: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 7B

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 7B:
3.1.4.53;

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 7B, PDB code: 6f6u 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)	45.71 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.827, 98.936, 119.532, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 7B also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 7B (pdb code 6f6u). 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- 7B, PDB code: 6f6u:
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- 7B


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- 7B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:19.0 occ:1.00 O A:HOH783 2.1 13.7 1.0 OD2 A:ASP367 2.1 12.5 1.0 NE2 A:HIS366 2.2 11.1 1.0 OD1 A:ASP484 2.2 13.5 1.0 NE2 A:HIS330 2.2 12.3 1.0 O A:HOH877 2.3 19.8 1.0 CG A:ASP484 3.0 16.3 1.0 CD2 A:HIS366 3.1 15.1 1.0 CG A:ASP367 3.1 17.2 1.0 CD2 A:HIS330 3.2 12.4 1.0 CE1 A:HIS366 3.2 16.7 1.0 CE1 A:HIS330 3.2 16.4 1.0 OD2 A:ASP484 3.3 24.6 1.0 OD1 A:ASP367 3.6 13.4 1.0 MG A:MG601 3.7 13.2 1.0 O A:HOH875 4.0 16.3 1.0 O A:HOH847 4.1 21.0 1.0 CD2 A:HIS326 4.2 18.2 1.0 CG A:HIS366 4.2 13.2 1.0 ND1 A:HIS366 4.3 10.2 1.0 CG A:HIS330 4.3 14.0 1.0 ND1 A:HIS330 4.3 11.6 1.0 CB A:ASP367 4.3 13.2 1.0 CB A:ASP484 4.4 12.1 1.0 O A:HOH717 4.4 35.0 1.0 NE2 A:HIS326 4.5 17.2 1.0 CG2 A:VAL334 4.6 14.6 1.0 O A:HOH934 4.7 35.1 1.0 O A:HOH799 4.8 15.6 1.0 CA A:ASP484 4.9 13.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 7B


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- 7B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:19.9 occ:1.00 O B:HOH780 2.1 13.7 1.0 OD2 B:ASP367 2.1 14.6 1.0 O B:HOH851 2.2 19.9 1.0 NE2 B:HIS330 2.2 13.0 1.0 NE2 B:HIS366 2.2 13.5 1.0 OD1 B:ASP484 2.2 16.2 1.0 CD2 B:HIS366 3.1 14.8 1.0 CD2 B:HIS330 3.1 15.8 1.0 CG B:ASP484 3.1 21.7 1.0 CG B:ASP367 3.1 15.1 1.0 CE1 B:HIS366 3.3 16.4 1.0 CE1 B:HIS330 3.3 21.1 1.0 OD2 B:ASP484 3.3 24.5 1.0 OD1 B:ASP367 3.6 13.3 1.0 MG B:MG601 3.6 13.1 1.0 O B:HOH857 3.8 15.6 1.0 O B:HOH704 3.9 22.1 0.8 O B:HOH850 4.0 22.2 1.0 CD2 B:HIS326 4.1 12.9 1.0 CG B:HIS366 4.2 15.2 1.0 CG B:HIS330 4.3 15.7 1.0 O B:HOH874 4.3 31.7 1.0 ND1 B:HIS366 4.3 14.0 1.0 ND1 B:HIS330 4.3 15.8 1.0 CB B:ASP367 4.4 14.7 1.0 NE2 B:HIS326 4.4 17.2 1.0 CB B:ASP484 4.4 14.1 1.0 O B:HOH767 4.7 13.0 1.0 CG2 B:VAL334 4.8 14.7 1.0 O B:HOH835 4.9 20.6 1.0 CA B:ASP484 5.0 15.9 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