Zinc in PDB 5wh6: Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91)

All present enzymatic activity of Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91):
3.1.4.53;

The structure of Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91), PDB code: 5wh6 was solved by H.Ke, H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.948, 80.197, 163.670, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 22.4

The structure of Crystal Structure of PDE4D2 in Complex with Inhibitor (S_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 PDE4D2 in Complex with Inhibitor (S_ZL-N-91) (pdb code 5wh6). 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 PDE4D2 in Complex with Inhibitor (S_ZL-N-91), PDB code: 5wh6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE4D2 in Complex with Inhibitor (S_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 PDE4D2 in Complex with Inhibitor (S_ZL-N-91) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:17.9 occ:1.00 OD2 A:ASP201 2.0 15.7 1.0 OD1 A:ASP318 2.0 15.7 1.0 O A:HOH806 2.1 15.1 1.0 NE2 A:HIS164 2.1 16.4 1.0 NE2 A:HIS200 2.2 15.2 1.0 O A:HOH702 2.4 16.2 1.0 CG A:ASP318 3.0 17.0 1.0 CD2 A:HIS200 3.0 15.2 1.0 CG A:ASP201 3.1 15.7 1.0 CD2 A:HIS164 3.1 16.2 1.0 CE1 A:HIS164 3.1 16.4 1.0 CE1 A:HIS200 3.2 15.3 1.0 OD2 A:ASP318 3.3 17.9 1.0 OD1 A:ASP201 3.6 15.4 1.0 MG A:MG603 3.9 16.4 1.0 O A:HOH752 4.1 17.2 1.0 O A:HOH850 4.1 15.1 1.0 CD2 A:HIS160 4.2 18.5 1.0 CG A:HIS200 4.2 15.1 1.0 ND1 A:HIS164 4.2 15.9 1.0 CB A:ASP201 4.2 15.3 1.0 CG A:HIS164 4.3 16.0 1.0 ND1 A:HIS200 4.3 15.2 1.0 NE2 A:HIS160 4.4 18.7 1.0 CB A:ASP318 4.4 16.9 1.0 CG2 A:VAL168 4.6 16.3 1.0 O A:HOH726 4.8 14.2 1.0 CA A:ASP318 4.9 17.3 1.0 C16 A:AKJ601 4.9 26.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE4D2 in Complex with Inhibitor (S_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 PDE4D2 in Complex with Inhibitor (S_ZL-N-91) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:20.1 occ:1.00 OD2 B:ASP201 2.0 17.6 1.0 OD1 B:ASP318 2.1 19.9 1.0 NE2 B:HIS164 2.1 17.7 1.0 NE2 B:HIS200 2.1 17.9 1.0 O B:HOH740 2.3 17.7 1.0 O B:HOH702 2.3 19.4 1.0 CG B:ASP318 3.0 20.2 1.0 CD2 B:HIS200 3.1 17.5 1.0 CE1 B:HIS164 3.1 17.7 1.0 CE1 B:HIS200 3.1 17.4 1.0 CG B:ASP201 3.1 16.0 1.0 CD2 B:HIS164 3.1 17.6 1.0 OD2 B:ASP318 3.3 20.4 1.0 OD1 B:ASP201 3.7 15.8 1.0 MG B:MG603 4.0 15.8 1.0 O B:HOH733 4.1 21.1 1.0 O B:HOH820 4.1 15.5 1.0 CD2 B:HIS160 4.1 17.5 1.0 ND1 B:HIS200 4.2 17.8 1.0 ND1 B:HIS164 4.2 17.4 1.0 CG B:HIS200 4.2 17.3 1.0 CG B:HIS164 4.3 17.7 1.0 CB B:ASP201 4.3 16.2 1.0 NE2 B:HIS160 4.3 17.4 1.0 CB B:ASP318 4.4 20.3 1.0 CG2 B:VAL168 4.6 21.1 1.0 O B:HOH716 4.8 17.1 1.0 CA B:ASP318 4.9 20.1 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