Zinc in PDB 7f2m: Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 18D

All present enzymatic activity of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 18D:
3.1.4.53;

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 18D, PDB code: 7f2m was solved by Y.-Y.Huang, X.He, H.-B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.21 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.487, 80.157, 162.787, 90, 90, 90
R / Rfree (%)	19.8 / 24.7

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 18D also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Fluorine	(F)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 18D (pdb code 7f2m). 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 Compound 18D, PDB code: 7f2m:
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 Compound 18D


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 Compound 18D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:16.5 occ:1.00 OD1 A:ASP318 2.2 10.6 1.0 NE2 A:HIS200 2.2 9.6 1.0 OD2 A:ASP201 2.2 10.0 1.0 NE2 A:HIS164 2.3 11.2 1.0 O41 A:1GF603 2.3 11.9 1.0 O A:HOH753 2.3 5.0 1.0 CG A:ASP318 3.0 12.5 1.0 OD2 A:ASP318 3.1 13.0 1.0 CD2 A:HIS200 3.1 8.7 1.0 CG A:ASP201 3.2 11.3 1.0 CD2 A:HIS164 3.2 10.5 1.0 CE1 A:HIS200 3.2 10.1 1.0 CE1 A:HIS164 3.2 10.2 1.0 C43 A:1GF603 3.4 14.4 1.0 MG A:MG602 3.6 4.7 1.0 OD1 A:ASP201 3.7 9.6 1.0 O A:HOH822 3.8 10.1 1.0 C44 A:1GF603 3.9 12.1 1.0 CD2 A:HIS160 4.3 9.9 1.0 CG A:HIS200 4.3 9.5 1.0 CB A:ASP201 4.3 12.3 1.0 ND1 A:HIS200 4.3 10.0 1.0 O42 A:1GF603 4.4 17.6 1.0 ND1 A:HIS164 4.4 11.1 1.0 CG A:HIS164 4.4 11.6 1.0 CB A:ASP318 4.4 11.6 1.0 NE2 A:HIS160 4.8 13.1 1.0 CG2 A:VAL168 4.8 9.7 1.0 CA A:ASP318 5.0 12.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 18D


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 Compound 18D within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:22.9 occ:1.00 O B:HOH730 2.1 15.3 1.0 O41 B:1GF603 2.1 15.7 1.0 OD2 B:ASP201 2.2 12.3 1.0 OD1 B:ASP318 2.2 16.0 1.0 NE2 B:HIS164 2.2 12.5 1.0 NE2 B:HIS200 2.3 14.8 1.0 CD2 B:HIS200 3.1 12.3 1.0 CG B:ASP318 3.1 19.0 1.0 CG B:ASP201 3.1 15.5 1.0 CD2 B:HIS164 3.2 14.3 1.0 CE1 B:HIS164 3.2 13.8 1.0 CE1 B:HIS200 3.3 12.2 1.0 C43 B:1GF603 3.3 18.4 1.0 OD2 B:ASP318 3.3 20.4 1.0 MG B:MG602 3.5 7.6 1.0 OD1 B:ASP201 3.6 14.3 1.0 O B:HOH792 3.9 10.1 1.0 C44 B:1GF603 4.0 19.7 1.0 CD2 B:HIS160 4.1 14.4 1.0 O42 B:1GF603 4.2 18.8 1.0 CG B:HIS200 4.3 13.0 1.0 CB B:ASP201 4.3 13.9 1.0 ND1 B:HIS164 4.3 13.6 1.0 ND1 B:HIS200 4.3 11.9 1.0 CG B:HIS164 4.3 12.5 1.0 CB B:ASP318 4.5 16.3 1.0 O B:HOH734 4.6 12.2 1.0 NE2 B:HIS160 4.7 13.5 1.0 CG2 B:VAL168 4.9 12.9 1.0

Y.Y.Huang, J.Deng, Y.J.Tian, J.Liang, X.Xie, Y.Huang, J.Zhu, Z.Zhu, Q.Zhou, X.He, H.B.Luo. Mangostanin Derivatives As Novel and Orally Active Phosphodiesterase 4 Inhibitors For the Treatment of Idiopathic Pulmonary Fibrosis with Improved Safety. J.Med.Chem. V. 64 13736 2021.
ISSN: ISSN 0022-2623
PubMed: 34520193
DOI: 10.1021/ACS.JMEDCHEM.1C01085