Zinc in PDB 6f8u: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B:
3.1.4.53;

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B, PDB code: 6f8u 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)	49.33 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.672, 98.669, 119.644, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 21.9

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Magnesium	(Mg)	5 atoms

The binding sites of Zinc atom in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B (pdb code 6f8u). 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- 20B, PDB code: 6f8u:
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- 20B


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- 20B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:19.2 occ:1.00 OD2 A:ASP367 2.1 12.5 1.0 O A:HOH769 2.1 13.8 1.0 NE2 A:HIS366 2.2 8.9 1.0 NE2 A:HIS330 2.2 10.8 1.0 O A:HOH871 2.2 19.0 1.0 OD1 A:ASP484 2.3 18.1 1.0 CD2 A:HIS366 3.1 11.2 1.0 CG A:ASP484 3.1 19.4 1.0 CG A:ASP367 3.1 17.3 1.0 CE1 A:HIS330 3.1 10.3 1.0 CD2 A:HIS330 3.2 9.8 1.0 CE1 A:HIS366 3.2 13.8 1.0 OD2 A:ASP484 3.3 22.4 1.0 OD1 A:ASP367 3.6 12.5 1.0 MG A:MG602 3.7 10.2 1.0 O A:HOH890 3.9 12.2 1.0 O A:HOH703 3.9 25.9 1.0 O A:HOH763 4.0 20.5 1.0 CD2 A:HIS326 4.2 14.1 1.0 CG A:HIS366 4.2 12.2 1.0 ND1 A:HIS366 4.3 10.2 1.0 ND1 A:HIS330 4.3 14.7 1.0 CG A:HIS330 4.3 12.9 1.0 CB A:ASP367 4.3 10.4 1.0 CB A:ASP484 4.5 15.7 1.0 NE2 A:HIS326 4.5 16.4 1.0 O A:HOH796 4.7 12.6 1.0 CG2 A:VAL334 4.7 11.9 1.0 CA A:ASP484 5.0 15.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B


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- 20B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:20.1 occ:1.00 OD2 B:ASP367 2.1 15.4 1.0 OD1 B:ASP484 2.2 14.6 1.0 O B:HOH787 2.2 17.6 1.0 NE2 B:HIS330 2.2 15.2 1.0 NE2 B:HIS366 2.3 12.7 1.0 O B:HOH753 2.3 15.7 1.0 CG B:ASP484 3.0 22.7 1.0 CD2 B:HIS366 3.1 13.9 1.0 CG B:ASP367 3.1 16.7 1.0 OD2 B:ASP484 3.1 27.1 1.0 CD2 B:HIS330 3.2 13.2 1.0 CE1 B:HIS330 3.2 14.7 1.0 CE1 B:HIS366 3.3 9.9 1.0 OD1 B:ASP367 3.5 14.0 1.0 MG B:MG602 3.7 10.9 1.0 O B:HOH800 3.8 14.7 1.0 O B:HOH809 4.0 22.6 1.0 CD2 B:HIS326 4.1 15.2 1.0 O B:HOH837 4.1 28.4 1.0 O B:HOH708 4.2 26.1 1.0 CG B:HIS366 4.3 16.7 1.0 NE2 B:HIS326 4.3 20.2 1.0 CG B:HIS330 4.3 14.0 1.0 ND1 B:HIS330 4.3 14.0 1.0 CB B:ASP367 4.4 13.9 1.0 ND1 B:HIS366 4.4 11.2 1.0 CB B:ASP484 4.4 14.7 1.0 O B:HOH765 4.6 15.1 1.0 CG2 B:VAL334 4.7 10.4 1.0 CA B:ASP484 5.0 14.9 1.0 O B:HOH777 5.0 15.1 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