Zinc in PDB 8k4c: Crystal Structure of PDE4D Complexed with Ethaverine Hydrochloride

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

The structure of Crystal Structure of PDE4D Complexed with Ethaverine Hydrochloride, PDB code: 8k4c 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)	39.93 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.691, 79.863, 162.862, 90, 90, 90
R / Rfree (%)	23.5 / 26.9

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

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D Complexed with Ethaverine Hydrochloride (pdb code 8k4c). 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 Ethaverine Hydrochloride, PDB code: 8k4c:
Jump to Zinc binding site number: 1; 2;

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


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 Ethaverine Hydrochloride within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:20.4 occ:1.00 OD2 A:ASP201 2.1 18.6 1.0 O A:HOH863 2.1 23.4 1.0 OD1 A:ASP318 2.2 16.6 1.0 O A:HOH806 2.2 17.6 1.0 NE2 A:HIS200 2.3 18.1 1.0 NE2 A:HIS164 2.3 14.1 1.0 CG A:ASP318 3.0 18.1 1.0 CD2 A:HIS200 3.0 18.3 1.0 CG A:ASP201 3.1 18.2 1.0 CD2 A:HIS164 3.2 15.2 1.0 OD2 A:ASP318 3.2 19.2 1.0 CE1 A:HIS164 3.3 15.4 1.0 CE1 A:HIS200 3.4 19.4 1.0 O A:HOH868 3.5 21.0 1.0 MG A:MG702 3.6 19.1 1.0 OD1 A:ASP201 3.7 17.4 1.0 O A:HOH852 3.9 43.2 1.0 CG A:HIS200 4.3 18.7 1.0 CB A:ASP201 4.3 18.9 1.0 CD2 A:HIS160 4.3 14.1 1.0 CG A:HIS164 4.3 15.8 1.0 ND1 A:HIS164 4.4 15.5 1.0 ND1 A:HIS200 4.4 19.1 1.0 CB A:ASP318 4.4 17.3 1.0 O A:HOH810 4.7 16.2 1.0 NE2 A:HIS160 4.8 14.4 1.0 CG2 A:VAL168 4.8 17.0 1.0 CA A:ASP318 4.9 17.7 1.0 O A:HOH826 5.0 14.9 1.0

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


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 Ethaverine Hydrochloride within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:31.6 occ:1.00 OD2 B:ASP201 2.0 27.2 1.0 O B:HOH609 2.2 24.8 1.0 NE2 B:HIS164 2.2 28.3 1.0 O B:HOH634 2.3 27.9 1.0 OD1 B:ASP318 2.3 29.1 1.0 NE2 B:HIS200 2.3 26.9 1.0 CD2 B:HIS200 3.0 26.8 1.0 CG B:ASP318 3.1 28.3 1.0 CD2 B:HIS164 3.1 28.6 1.0 CG B:ASP201 3.1 26.1 1.0 CE1 B:HIS164 3.3 29.2 1.0 OD2 B:ASP318 3.3 29.3 1.0 CE1 B:HIS200 3.5 28.5 1.0 O B:HOH627 3.5 28.9 1.0 MG B:MG502 3.6 23.3 1.0 OD1 B:ASP201 3.7 25.5 1.0 CG B:HIS200 4.2 27.5 1.0 CD2 B:HIS160 4.2 21.6 1.0 CG B:HIS164 4.3 29.4 1.0 CB B:ASP201 4.3 25.4 1.0 ND1 B:HIS164 4.4 30.1 1.0 ND1 B:HIS200 4.4 28.2 1.0 CB B:ASP318 4.5 26.3 1.0 NE2 B:HIS160 4.7 21.3 1.0 O B:HOH604 4.8 21.1 1.0 CG2 B:VAL168 4.9 33.0 1.0 O B:HOH611 5.0 20.9 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