Zinc in PDB 7xbb: Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 23A

All present enzymatic activity of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 23A:
3.1.4.53;

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 23A, PDB code: 7xbb 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)	24.34 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.057, 80.416, 162.918, 90, 90, 90
R / Rfree (%)	21.1 / 24.4

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 23A 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 Compound 23A (pdb code 7xbb). 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 23A, PDB code: 7xbb:
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 23A


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 23A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:18.6 occ:1.00 OD2 A:ASP201 2.1 9.1 1.0 O A:HOH756 2.2 13.5 1.0 O27 A:B6V603 2.2 8.2 1.0 OD1 A:ASP318 2.2 10.6 1.0 NE2 A:HIS164 2.2 12.0 1.0 NE2 A:HIS200 2.2 10.9 1.0 N22 A:B6V603 2.8 13.5 1.0 CG A:ASP318 3.0 14.5 1.0 CD2 A:HIS200 3.1 11.4 1.0 CD2 A:HIS164 3.1 11.2 1.0 CG A:ASP201 3.2 11.7 1.0 CE1 A:HIS164 3.2 15.1 1.0 OD2 A:ASP318 3.2 13.7 1.0 CE1 A:HIS200 3.3 9.9 1.0 OD1 A:ASP201 3.6 9.2 1.0 MG A:MG602 3.8 10.3 1.0 O A:HOH799 3.8 8.1 1.0 C21 A:B6V603 4.0 19.6 1.0 CD2 A:HIS160 4.2 9.0 1.0 CG A:HIS200 4.3 11.6 1.0 ND1 A:HIS164 4.3 12.5 1.0 CG A:HIS164 4.3 12.6 1.0 CB A:ASP201 4.4 11.6 1.0 ND1 A:HIS200 4.4 10.0 1.0 NE2 A:HIS160 4.4 9.4 1.0 CB A:ASP318 4.4 10.2 1.0 CG2 A:VAL168 4.9 7.8 1.0 O A:HOH772 4.9 13.0 1.0 CA A:ASP318 4.9 9.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 23A


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 23A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:18.3 occ:1.00 O B:HOH759 2.0 11.3 1.0 OD2 B:ASP201 2.0 9.9 1.0 OD1 B:ASP318 2.2 15.0 1.0 O27 B:B6V603 2.2 15.2 1.0 NE2 B:HIS164 2.3 16.3 1.0 NE2 B:HIS200 2.3 9.4 1.0 N22 B:B6V603 2.9 13.3 1.0 CG B:ASP318 3.0 16.0 1.0 CG B:ASP201 3.1 12.2 1.0 CD2 B:HIS200 3.1 8.7 1.0 CD2 B:HIS164 3.2 14.4 1.0 OD2 B:ASP318 3.3 20.9 1.0 CE1 B:HIS164 3.3 16.3 1.0 CE1 B:HIS200 3.3 17.5 1.0 OD1 B:ASP201 3.5 12.3 1.0 MG B:MG602 3.7 13.0 1.0 O B:HOH766 3.8 11.0 1.0 CD2 B:HIS160 4.1 10.4 1.0 C21 B:B6V603 4.1 18.6 1.0 CG B:HIS200 4.3 12.9 1.0 CB B:ASP201 4.3 9.1 1.0 NE2 B:HIS160 4.3 15.8 1.0 CG B:HIS164 4.3 13.4 1.0 ND1 B:HIS164 4.4 15.5 1.0 ND1 B:HIS200 4.4 13.9 1.0 CB B:ASP318 4.4 15.4 1.0 O B:HOH714 4.8 7.0 1.0 CG2 B:VAL168 4.9 16.0 1.0 CA B:ASP318 5.0 15.2 1.0

F.Zhou, Y.Huang, L.Liu, Z.Song, K.Q.Hou, Y.Yang, H.B.Luo, Y.Y.Huang, X.F.Xiong. Structure-Based Optimization of Toddacoumalone As Highly Potent and Selective PDE4 Inhibitors with Anti-Inflammatory Effects. Biochem Pharmacol V. 202 15123 2022.
ISSN: ISSN 1873-2968
PubMed: 35688178
DOI: 10.1016/J.BCP.2022.115123