Zinc in PDB 8k4h: Crystal Structure of PDE4D Complexed with Benzbromarone

All present enzymatic activity of Crystal Structure of PDE4D Complexed with Benzbromarone:
3.1.4.53;

The structure of Crystal Structure of PDE4D Complexed with Benzbromarone, PDB code: 8k4h was solved by J.Y.Liu, M.J.Li, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.45 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.507, 79.808, 162.27, 90, 90, 90
R / Rfree (%)	24.7 / 27.9

The structure of Crystal Structure of PDE4D Complexed with Benzbromarone also contains other interesting chemical elements:

Bromine	(Br)	4 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D Complexed with Benzbromarone (pdb code 8k4h). 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 Complexed with Benzbromarone, PDB code: 8k4h:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE4D Complexed with Benzbromarone


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 Complexed with Benzbromarone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:19.5 occ:1.00 OD1 A:ASP318 2.2 17.5 1.0 OD2 A:ASP201 2.3 20.7 1.0 NE2 A:HIS164 2.3 30.4 1.0 NE2 A:HIS200 2.3 35.6 1.0 O A:HOH612 2.5 17.5 1.0 O A:HOH626 2.5 17.7 1.0 CD2 A:HIS200 3.0 25.3 1.0 CG A:ASP318 3.1 30.0 1.0 CG A:ASP201 3.1 28.2 1.0 OD2 A:ASP318 3.2 17.4 1.0 CD2 A:HIS164 3.2 30.4 1.0 CE1 A:HIS164 3.3 29.6 1.0 CE1 A:HIS200 3.4 40.9 1.0 OD1 A:ASP201 3.6 20.4 1.0 MG A:MG502 3.7 21.7 1.0 O A:HOH618 4.0 21.4 1.0 CG A:HIS200 4.3 40.6 1.0 CD2 A:HIS160 4.3 31.6 1.0 CB A:ASP201 4.3 32.1 1.0 ND1 A:HIS164 4.4 28.0 1.0 CG A:HIS164 4.4 28.0 1.0 O A:HOH621 4.4 29.1 1.0 ND1 A:HIS200 4.4 38.8 1.0 CB A:ASP318 4.5 23.6 1.0 BR2 A:R75503 4.6 7.7 1.0 O A:HOH614 4.7 18.0 1.0 CG2 A:VAL168 4.7 28.9 1.0 NE2 A:HIS160 4.8 30.6 1.0 OAG A:R75503 4.9 29.9 1.0 O A:HOH628 5.0 14.1 1.0 CA A:ASP318 5.0 34.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE4D Complexed with Benzbromarone


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 Complexed with Benzbromarone within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:11.4 occ:1.00 OD2 B:ASP201 2.1 25.9 1.0 NE2 B:HIS164 2.3 49.6 1.0 OD1 B:ASP318 2.3 41.6 1.0 NE2 B:HIS200 2.4 41.4 1.0 O B:HOH606 2.4 26.3 1.0 O B:HOH603 2.6 23.3 1.0 CD2 B:HIS200 3.0 38.5 1.0 CD2 B:HIS164 3.0 39.7 1.0 CG B:ASP201 3.1 38.3 1.0 CG B:ASP318 3.2 42.0 1.0 OD2 B:ASP318 3.4 41.8 1.0 CE1 B:HIS164 3.4 44.5 1.0 CE1 B:HIS200 3.5 41.1 1.0 OD1 B:ASP201 3.5 29.0 1.0 MG B:MG502 3.7 15.3 1.0 O B:HOH621 3.8 19.9 1.0 CG B:HIS200 4.3 45.4 1.0 CG B:HIS164 4.3 49.6 1.0 CD2 B:HIS160 4.3 38.0 1.0 CB B:ASP201 4.3 45.0 1.0 ND1 B:HIS164 4.4 54.5 1.0 ND1 B:HIS200 4.4 45.9 1.0 O B:HOH620 4.5 40.7 1.0 CB B:ASP318 4.6 42.7 1.0 CG2 B:VAL168 4.6 36.9 1.0 BR2 B:R75503 4.7 21.2 1.0 O B:HOH602 4.8 22.4 1.0 NE2 B:HIS160 4.8 40.1 1.0 OAG B:R75503 4.8 33.6 1.0

J.Liu, X.Zhang, G.Chen, Q.Shao, Y.Zou, Z.Li, H.Su, M.Li, Y.Xu. Drug Repurposing and Structure-Based Discovery of New PDE4 and PDE5 Inhibitors. Eur.J.Med.Chem. V. 262 15893 2023.
ISSN: ISSN 0223-5234
PubMed: 37918035
DOI: 10.1016/J.EJMECH.2023.115893