Zinc in PDB 6fdc: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A:
3.1.4.53;

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A, PDB code: 6fdc 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)	49.32 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.692, 98.608, 120.165, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 19.9

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Magnesium	(Mg)	5 atoms

The binding sites of Zinc atom in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A (pdb code 6fdc). 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- 32A, PDB code: 6fdc:
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- 32A


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- 32A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:13.8 occ:1.00 OD2 A:ASP367 2.1 10.7 1.0 OD1 A:ASP484 2.1 11.6 1.0 O A:HOH839 2.1 13.3 1.0 NE2 A:HIS330 2.2 11.0 1.0 NE2 A:HIS366 2.2 10.2 1.0 O A:HOH725 2.2 13.4 1.0 CG A:ASP484 3.0 13.7 1.0 CD2 A:HIS366 3.1 10.2 1.0 CG A:ASP367 3.1 11.0 1.0 CE1 A:HIS330 3.1 12.0 1.0 CD2 A:HIS330 3.2 11.3 1.0 CE1 A:HIS366 3.2 10.7 1.0 OD2 A:ASP484 3.3 21.0 1.0 OD1 A:ASP367 3.6 10.9 1.0 O A:HOH701 3.7 15.6 1.0 MG A:MG602 3.8 8.8 1.0 O A:HOH895 4.0 12.8 1.0 O A:HOH795 4.1 16.2 1.0 CD2 A:HIS326 4.1 12.6 1.0 ND1 A:HIS330 4.2 12.2 1.0 CG A:HIS366 4.3 10.2 1.0 ND1 A:HIS366 4.3 10.8 1.0 CB A:ASP367 4.3 11.3 1.0 NE2 A:HIS326 4.3 14.2 1.0 CG A:HIS330 4.3 11.6 1.0 CB A:ASP484 4.4 12.0 1.0 CG2 A:VAL334 4.7 12.5 1.0 O A:HOH769 4.7 12.3 1.0 H28 A:DD5606 4.8 24.6 0.7 CA A:ASP484 4.9 13.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A


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- 32A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:15.0 occ:1.00 OD2 B:ASP367 2.0 12.8 1.0 OD1 B:ASP484 2.1 11.9 1.0 NE2 B:HIS330 2.2 12.9 1.0 O B:HOH838 2.2 16.2 1.0 O B:HOH720 2.2 14.3 1.0 NE2 B:HIS366 2.2 13.7 1.0 CG B:ASP484 3.1 14.9 1.0 CD2 B:HIS366 3.1 11.8 1.0 CG B:ASP367 3.1 13.8 1.0 CE1 B:HIS330 3.1 13.8 1.0 CD2 B:HIS330 3.1 13.6 1.0 CE1 B:HIS366 3.2 12.8 1.0 OD2 B:ASP484 3.3 23.6 1.0 OD1 B:ASP367 3.6 13.2 1.0 O B:HOH705 3.8 14.8 1.0 MG B:MG602 3.8 9.9 1.0 O B:HOH871 3.9 14.1 1.0 O B:HOH791 4.1 18.6 1.0 CD2 B:HIS326 4.2 15.2 1.0 O B:HOH890 4.2 27.7 1.0 ND1 B:HIS330 4.3 14.4 1.0 CG B:HIS366 4.3 12.4 1.0 CG B:HIS330 4.3 13.4 1.0 CB B:ASP367 4.3 13.3 1.0 ND1 B:HIS366 4.3 12.9 1.0 NE2 B:HIS326 4.4 16.4 1.0 CB B:ASP484 4.4 11.9 1.0 CG2 B:VAL334 4.7 13.6 1.0 O B:HOH762 4.8 13.2 1.0 CA B:ASP484 5.0 12.1 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