Zinc in PDB 5wh5: Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91

All present enzymatic activity of Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91:
3.1.4.53;

The structure of Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91, PDB code: 5wh5 was solved by H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.467, 79.883, 163.444, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 21.4

The structure of Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91 also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Magnesium	(Mg)	3 atoms

The binding sites of Zinc atom in the Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91 (pdb code 5wh5). 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 PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91, PDB code: 5wh5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91


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 PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:19.0 occ:1.00 OD2 A:ASP201 2.0 17.2 1.0 OD1 A:ASP318 2.1 16.7 1.0 NE2 A:HIS164 2.1 16.2 1.0 NE2 A:HIS200 2.2 16.4 1.0 O A:HOH717 2.2 16.9 1.0 O A:HOH601 2.3 15.0 1.0 CG A:ASP318 3.0 16.4 1.0 CD2 A:HIS200 3.1 16.1 1.0 CG A:ASP201 3.1 16.7 1.0 CE1 A:HIS164 3.1 16.0 1.0 CD2 A:HIS164 3.1 16.0 1.0 CE1 A:HIS200 3.2 16.2 1.0 OD2 A:ASP318 3.2 17.0 1.0 OD1 A:ASP201 3.7 16.7 1.0 MG A:MG503 3.9 17.1 1.0 O A:HOH655 4.0 18.1 1.0 O A:HOH729 4.1 13.5 1.0 CD2 A:HIS160 4.2 18.9 1.0 ND1 A:HIS164 4.2 15.9 1.0 CG A:HIS200 4.2 16.0 1.0 CB A:ASP201 4.3 16.4 1.0 ND1 A:HIS200 4.3 16.0 1.0 CG A:HIS164 4.3 16.0 1.0 NE2 A:HIS160 4.4 18.9 1.0 CB A:ASP318 4.4 16.3 1.0 CG2 A:VAL168 4.6 16.2 1.0 O A:HOH628 4.8 16.3 1.0 CA A:ASP318 4.9 16.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91


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 PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:20.4 occ:1.00 OD2 B:ASP201 2.0 17.5 1.0 OD1 B:ASP318 2.1 18.5 1.0 NE2 B:HIS164 2.1 19.3 1.0 NE2 B:HIS200 2.2 18.4 1.0 O B:HOH663 2.3 18.2 1.0 O B:HOH605 2.3 19.6 1.0 CG B:ASP318 3.0 19.0 1.0 CD2 B:HIS200 3.1 18.1 1.0 CE1 B:HIS164 3.1 19.1 1.0 CG B:ASP201 3.1 17.0 1.0 CD2 B:HIS164 3.1 19.1 1.0 CE1 B:HIS200 3.2 18.0 1.0 OD2 B:ASP318 3.3 19.5 1.0 OD1 B:ASP201 3.7 16.7 1.0 MG B:MG503 4.0 17.6 1.0 O B:HOH649 4.0 18.8 1.0 O B:HOH723 4.1 14.5 1.0 CD2 B:HIS160 4.1 18.6 1.0 CG B:HIS200 4.2 17.7 1.0 ND1 B:HIS164 4.2 19.1 1.0 ND1 B:HIS200 4.2 18.1 1.0 CG B:HIS164 4.3 19.0 1.0 CB B:ASP201 4.3 17.1 1.0 NE2 B:HIS160 4.3 18.6 1.0 CB B:ASP318 4.4 19.0 1.0 CG2 B:VAL168 4.6 19.2 1.0 O B:HOH620 4.8 16.5 1.0 CA B:ASP318 4.9 19.2 1.0

X.Feng, H.Wang, M.Ye, X.T.Xu, Y.Xu, W.Yang, H.T.Zhang, G.Song, H.Ke. Identification of A PDE4-Specific Pocket For the Design of Selective Inhibitors. Biochemistry V. 57 4518 2018.
ISSN: ISSN 0006-2960
PubMed: 29975048
DOI: 10.1021/ACS.BIOCHEM.8B00336