Zinc in PDB 6f8w: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18A

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18A:
3.1.4.53;

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18A, PDB code: 6f8w 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)	45.69 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.039, 98.717, 120.765, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 21.9

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18A 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- 18A (pdb code 6f8w). 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- 18A, PDB code: 6f8w:
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- 18A


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- 18A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:21.2 occ:1.00 OD2 A:ASP367 2.1 18.3 1.0 O A:HOH850 2.1 19.3 1.0 OD1 A:ASP484 2.2 18.3 1.0 NE2 A:HIS366 2.2 18.0 1.0 NE2 A:HIS330 2.2 15.8 1.0 O A:HOH749 2.2 18.9 1.0 CD2 A:HIS366 3.0 15.8 1.0 CG A:ASP484 3.1 20.9 1.0 CG A:ASP367 3.1 20.6 1.0 CD2 A:HIS330 3.1 18.4 1.0 CE1 A:HIS330 3.2 20.1 1.0 CE1 A:HIS366 3.2 17.6 1.0 OD2 A:ASP484 3.3 23.6 1.0 OD1 A:ASP367 3.6 17.2 1.0 O A:HOH701 3.7 28.6 1.0 MG A:MG602 3.8 15.1 1.0 H19 A:D0E605 3.9 20.9 0.8 O A:HOH872 4.0 17.6 1.0 O A:HOH802 4.0 22.8 1.0 CD2 A:HIS326 4.2 17.1 1.0 CG A:HIS366 4.2 18.0 1.0 ND1 A:HIS366 4.3 18.1 1.0 CB A:ASP367 4.3 18.3 1.0 ND1 A:HIS330 4.3 17.6 1.0 CG A:HIS330 4.3 17.5 1.0 NE2 A:HIS326 4.4 19.7 1.0 H01 A:D0E605 4.4 20.9 0.8 CB A:ASP484 4.4 15.4 1.0 C15 A:D0E605 4.7 17.4 0.8 CG2 A:VAL334 4.7 17.3 1.0 O A:HOH781 4.8 17.8 1.0 CA A:ASP484 5.0 16.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18A


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- 18A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:20.6 occ:1.00 OD2 B:ASP367 2.1 15.7 1.0 O B:HOH853 2.1 18.7 1.0 OD1 B:ASP484 2.2 16.9 1.0 NE2 B:HIS366 2.2 16.1 1.0 NE2 B:HIS330 2.2 16.9 1.0 O B:HOH749 2.2 19.0 1.0 CD2 B:HIS366 3.1 14.0 1.0 CG B:ASP484 3.1 18.7 1.0 CG B:ASP367 3.1 17.8 1.0 CD2 B:HIS330 3.1 18.5 1.0 CE1 B:HIS330 3.2 18.1 1.0 CE1 B:HIS366 3.2 17.2 1.0 OD2 B:ASP484 3.3 24.1 1.0 OD1 B:ASP367 3.6 17.7 1.0 O B:HOH701 3.7 28.3 1.0 MG B:MG602 3.8 15.4 1.0 H19 B:D0E604 4.0 25.7 0.8 O B:HOH890 4.0 15.8 1.0 O B:HOH787 4.1 22.5 1.0 CD2 B:HIS326 4.1 16.6 1.0 CG B:HIS366 4.2 12.9 1.0 ND1 B:HIS366 4.3 15.8 1.0 CB B:ASP367 4.3 15.9 1.0 ND1 B:HIS330 4.3 16.1 1.0 CG B:HIS330 4.3 18.0 1.0 H01 B:D0E604 4.4 25.7 0.8 NE2 B:HIS326 4.4 18.9 1.0 CB B:ASP484 4.4 16.1 1.0 CG2 B:VAL334 4.7 17.3 1.0 C15 B:D0E604 4.7 21.4 0.8 O B:HOH799 4.7 16.2 1.0 CA B:ASP484 4.9 16.7 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