Zinc in PDB 6f8x: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 26G

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 26G:
3.1.4.53;

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 26G, PDB code: 6f8x 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)	49.21 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.547, 119.820, 64.502, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.5

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 26G 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- 26G (pdb code 6f8x). 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- 26G, PDB code: 6f8x:
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- 26G


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- 26G within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:11.4 occ:0.83 OD2 A:ASP367 2.1 11.4 1.0 O A:HOH725 2.1 12.6 1.0 O A:HOH835 2.1 16.3 1.0 NE2 A:HIS366 2.2 9.1 1.0 OD1 A:ASP484 2.2 11.4 1.0 NE2 A:HIS330 2.2 10.2 1.0 CD2 A:HIS366 3.0 9.6 1.0 CG A:ASP484 3.0 14.5 1.0 CE1 A:HIS330 3.1 11.5 1.0 CG A:ASP367 3.1 12.7 1.0 CD2 A:HIS330 3.2 9.3 1.0 CE1 A:HIS366 3.2 10.4 1.0 OD2 A:ASP484 3.3 18.2 1.0 OD1 A:ASP367 3.6 12.3 1.0 O A:HOH702 3.6 16.2 1.0 MG A:MG602 3.7 8.7 1.0 O A:HOH735 3.8 30.9 1.0 O A:HOH860 4.0 11.2 1.0 O A:HOH787 4.1 14.4 1.0 CD2 A:HIS326 4.2 13.5 1.0 CG A:HIS366 4.2 9.1 1.0 ND1 A:HIS330 4.2 11.4 1.0 ND1 A:HIS366 4.3 9.6 1.0 CB A:ASP367 4.3 8.1 1.0 CG A:HIS330 4.3 13.9 1.0 NE2 A:HIS326 4.4 14.8 1.0 CB A:ASP484 4.4 11.2 1.0 CG2 A:VAL334 4.6 11.6 1.0 O A:HOH801 4.7 10.0 1.0 CA A:ASP484 4.9 12.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 26G


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- 26G within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:17.3 occ:1.00 O B:HOH786 2.1 18.3 1.0 OD2 B:ASP367 2.1 14.0 1.0 OD1 B:ASP484 2.1 10.8 1.0 NE2 B:HIS330 2.2 11.4 1.0 O B:HOH758 2.2 15.3 1.0 NE2 B:HIS366 2.3 16.0 1.0 CG B:ASP484 3.1 19.5 1.0 CD2 B:HIS330 3.1 14.3 1.0 CG B:ASP367 3.1 12.0 1.0 CD2 B:HIS366 3.1 12.0 1.0 CE1 B:HIS330 3.2 15.4 1.0 CE1 B:HIS366 3.3 12.1 1.0 OD2 B:ASP484 3.4 25.0 1.0 O B:HOH705 3.5 17.6 1.0 OD1 B:ASP367 3.5 11.9 1.0 MG B:MG602 3.7 9.0 1.0 O B:HOH731 3.9 30.3 1.0 O B:HOH837 4.0 12.5 1.0 O B:HOH774 4.1 14.9 1.0 CD2 B:HIS326 4.2 12.1 1.0 CG B:HIS330 4.3 11.5 1.0 CG B:HIS366 4.3 15.3 1.0 ND1 B:HIS330 4.3 9.9 1.0 CB B:ASP367 4.3 15.3 1.0 ND1 B:HIS366 4.4 10.9 1.0 CB B:ASP484 4.4 14.6 1.0 NE2 B:HIS326 4.5 13.5 1.0 CG2 B:VAL334 4.7 11.1 1.0 O B:HOH765 4.7 11.3 1.0 CA B:ASP484 5.0 17.9 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