Zinc in PDB 2qyn: Crystal Structure of PDE4D2 in Complex with Inhibitor Npv

All present enzymatic activity of Crystal Structure of PDE4D2 in Complex with Inhibitor Npv:
3.1.4.17;

The structure of Crystal Structure of PDE4D2 in Complex with Inhibitor Npv, PDB code: 2qyn was solved by H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.100, 80.626, 163.315, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 24.8

The structure of Crystal Structure of PDE4D2 in Complex with Inhibitor Npv also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D2 in Complex with Inhibitor Npv (pdb code 2qyn). 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 Npv, PDB code: 2qyn:
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 Npv


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 Npv within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:14.8 occ:1.00 OD2 A:ASP201 2.1 9.3 1.0 OD1 A:ASP318 2.2 11.2 1.0 O A:HOH504 2.2 11.9 1.0 NE2 A:HIS200 2.2 9.7 1.0 NE2 A:HIS164 2.2 12.5 1.0 O A:HOH503 2.3 14.3 1.0 CD2 A:HIS200 3.1 12.4 1.0 CG A:ASP318 3.1 14.3 1.0 CG A:ASP201 3.1 10.4 1.0 CD2 A:HIS164 3.2 13.0 1.0 CE1 A:HIS164 3.2 11.4 1.0 CE1 A:HIS200 3.2 10.9 1.0 OD2 A:ASP318 3.3 16.9 1.0 OD1 A:ASP201 3.7 10.8 1.0 MG A:MG502 3.8 12.6 1.0 O A:HOH505 4.1 11.7 1.0 CD2 A:HIS160 4.1 12.5 1.0 O A:HOH513 4.2 13.9 1.0 CG A:HIS200 4.2 11.4 1.0 CB A:ASP201 4.3 10.7 1.0 ND1 A:HIS200 4.3 11.0 1.0 ND1 A:HIS164 4.3 9.9 1.0 CG A:HIS164 4.3 10.7 1.0 NE2 A:HIS160 4.4 14.0 1.0 CB A:ASP318 4.4 13.5 1.0 CG2 A:VAL168 4.7 11.1 1.0 O A:HOH508 4.7 11.3 1.0 CA A:ASP318 4.9 13.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE4D2 in Complex with Inhibitor Npv


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 Npv within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:18.1 occ:1.00 OD2 B:ASP201 2.1 13.5 1.0 O B:HOH503 2.2 15.6 1.0 NE2 B:HIS164 2.2 13.8 1.0 NE2 B:HIS200 2.2 11.5 1.0 OD1 B:ASP318 2.2 16.1 1.0 O B:HOH504 2.3 13.5 1.0 CD2 B:HIS200 3.1 13.9 1.0 CE1 B:HIS164 3.1 14.9 1.0 CG B:ASP318 3.1 17.7 1.0 CD2 B:HIS164 3.1 13.9 1.0 CG B:ASP201 3.2 11.9 1.0 CE1 B:HIS200 3.3 13.9 1.0 OD2 B:ASP318 3.4 21.2 1.0 OD1 B:ASP201 3.6 13.2 1.0 MG B:MG502 3.8 15.0 1.0 CD2 B:HIS160 4.0 13.4 1.0 O B:HOH505 4.1 13.9 1.0 ND1 B:HIS164 4.3 16.2 1.0 NE2 B:HIS160 4.3 16.1 1.0 CG B:HIS200 4.3 14.8 1.0 CG B:HIS164 4.3 15.4 1.0 O B:HOH521 4.3 17.3 1.0 ND1 B:HIS200 4.3 13.6 1.0 CB B:ASP201 4.4 13.0 1.0 CB B:ASP318 4.5 17.6 1.0 CG2 B:VAL168 4.7 18.1 1.0 O B:HOH508 4.8 12.7 1.0 CA B:ASP318 5.0 17.4 1.0

H.Wang, M.S.Peng, Y.Chen, J.Geng, H.Robinson, M.D.Houslay, J.Cai, H.Ke. Structures of the Four Subfamilies of Phosphodiesterase-4 Provide Insight Into the Selectivity of Their Inhibitors. Biochem.J. V. 408 193 2007.
ISSN: ISSN 0264-6021
PubMed: 17727341
DOI: 10.1042/BJ20070970