Zinc in PDB 7w4y: Crystal Structure of PDE4D Catalytic Domain Complexed with 33A

All present enzymatic activity of Crystal Structure of PDE4D Catalytic Domain Complexed with 33A:
3.1.4.53;

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with 33A, PDB code: 7w4y was solved by Y.-Y.Huang, H.-B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.19 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.294, 80.834, 163.423, 90, 90, 90
R / Rfree (%)	19.7 / 24.4

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with 33A also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D Catalytic Domain Complexed with 33A (pdb code 7w4y). 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 PDE4D Catalytic Domain Complexed with 33A, PDB code: 7w4y:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE4D Catalytic Domain Complexed with 33A


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 PDE4D Catalytic Domain Complexed with 33A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:16.4 occ:1.00 O A:HOH700 2.0 9.1 1.0 OD2 A:ASP201 2.1 8.0 1.0 OD1 A:ASP318 2.2 5.9 1.0 O A:HOH717 2.2 8.0 1.0 NE2 A:HIS164 2.2 8.8 1.0 NE2 A:HIS200 2.2 7.6 1.0 CG A:ASP318 3.0 10.2 1.0 CD2 A:HIS200 3.1 9.3 1.0 CE1 A:HIS164 3.1 11.7 1.0 CG A:ASP201 3.1 9.9 1.0 CD2 A:HIS164 3.3 7.1 1.0 OD2 A:ASP318 3.3 10.0 1.0 CE1 A:HIS200 3.3 7.9 1.0 OD1 A:ASP201 3.6 7.6 1.0 MG A:MG502 3.7 6.6 1.0 O A:HOH690 4.0 10.2 1.0 O A:HOH768 4.0 9.7 1.0 CD2 A:HIS160 4.2 8.4 1.0 ND1 A:HIS164 4.2 9.5 1.0 CG A:HIS200 4.3 9.1 1.0 ND1 A:HIS200 4.3 8.0 1.0 CB A:ASP201 4.3 9.0 1.0 CG A:HIS164 4.3 9.0 1.0 NE2 A:HIS160 4.4 9.0 1.0 CB A:ASP318 4.4 9.8 1.0 O A:HOH627 4.7 10.4 1.0 C22 A:8GO503 4.9 13.9 1.0 CG2 A:VAL168 4.9 7.6 1.0 CA A:ASP318 5.0 9.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE4D Catalytic Domain Complexed with 33A


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 PDE4D Catalytic Domain Complexed with 33A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:19.2 occ:1.00 O B:HOH677 2.0 10.2 1.0 OD2 B:ASP201 2.0 10.2 1.0 OD1 B:ASP318 2.1 12.4 1.0 NE2 B:HIS200 2.2 10.4 1.0 NE2 B:HIS164 2.3 12.6 1.0 O B:HOH625 2.4 10.4 1.0 CG B:ASP318 3.0 18.1 1.0 CD2 B:HIS200 3.0 10.6 1.0 CG B:ASP201 3.1 12.4 1.0 CD2 B:HIS164 3.2 12.1 1.0 CE1 B:HIS200 3.3 14.0 1.0 CE1 B:HIS164 3.3 12.9 1.0 OD2 B:ASP318 3.3 17.4 1.0 OD1 B:ASP201 3.6 9.1 1.0 MG B:MG502 3.7 8.6 1.0 O B:HOH743 3.9 11.3 1.0 O B:HOH627 4.0 14.9 1.0 CD2 B:HIS160 4.1 11.1 1.0 CG B:HIS200 4.2 13.5 1.0 NE2 B:HIS160 4.3 11.1 1.0 ND1 B:HIS200 4.3 10.9 1.0 CG B:HIS164 4.3 11.4 1.0 CB B:ASP201 4.3 6.0 1.0 CB B:ASP318 4.4 14.5 1.0 ND1 B:HIS164 4.4 14.8 1.0 CG2 B:VAL168 4.8 10.9 1.0 O B:HOH626 4.8 9.0 1.0 CA B:ASP318 4.9 13.2 1.0

Z.Song, Y.Y.Huang, K.Q.Hou, L.Liu, F.Zhou, Y.Huang, G.Wan, H.B.Luo, X.F.Xiong. Discovery and Structural Optimization of Toddacoumalone Derivatives As Novel PDE4 Inhibitors For the Topical Treatment of Psoriasis. J.Med.Chem. V. 65 4238 2022.
ISSN: ISSN 0022-2623
PubMed: 35188767
DOI: 10.1021/ACS.JMEDCHEM.1C02058