Zinc in PDB 4md6: Crystal Structure of PDE5 in Complex with Inhibitor 5R

All present enzymatic activity of Crystal Structure of PDE5 in Complex with Inhibitor 5R:
3.1.4.35;

The structure of Crystal Structure of PDE5 in Complex with Inhibitor 5R, PDB code: 4md6 was solved by W.Cui, M.Huang, Y.Shao, H.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.106, 74.106, 132.344, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 24.7

The structure of Crystal Structure of PDE5 in Complex with Inhibitor 5R also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of PDE5 in Complex with Inhibitor 5R (pdb code 4md6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of PDE5 in Complex with Inhibitor 5R, PDB code: 4md6:

Zinc binding site 1 out of 1 in the Crystal Structure of PDE5 in Complex with Inhibitor 5R


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 PDE5 in Complex with Inhibitor 5R within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:38.3 occ:1.00 O3 A:SO4901 2.2 34.6 1.0 NE2 A:HIS653 2.2 29.9 1.0 NE2 A:HIS617 2.3 27.7 1.0 OD1 A:ASP764 2.3 33.6 1.0 OD2 A:ASP654 2.3 31.6 1.0 O A:HOH1001 2.4 33.7 1.0 CD2 A:HIS653 3.0 30.8 1.0 CG A:ASP764 3.1 35.5 1.0 CD2 A:HIS617 3.2 28.7 1.0 CG A:ASP654 3.2 35.1 1.0 CE1 A:HIS617 3.3 31.9 1.0 OD2 A:ASP764 3.4 37.1 1.0 CE1 A:HIS653 3.4 33.0 1.0 S A:SO4901 3.5 24.7 1.0 MG A:MG904 3.6 41.8 1.0 OD1 A:ASP654 3.6 34.0 1.0 O A:HOH1002 3.8 34.8 1.0 O4 A:SO4901 3.9 40.3 1.0 O2 A:SO4901 4.0 38.9 1.0 CG A:HIS653 4.2 33.4 1.0 CG A:HIS617 4.4 29.9 1.0 ND1 A:HIS653 4.4 32.4 1.0 CD2 A:HIS613 4.4 32.4 1.0 ND1 A:HIS617 4.4 27.9 1.0 CB A:ASP654 4.5 33.3 1.0 CB A:ASP764 4.5 33.6 1.0 O1 A:SO4901 4.7 36.5 1.0 O A:ASP764 4.8 32.0 1.0 O A:HOH1003 4.8 31.7 1.0 NE2 A:HIS613 4.9 35.6 1.0 CA A:ASP764 5.0 33.5 1.0 OG1 A:THR621 5.0 28.2 1.0

N.N.Shang, Y.X.Shao, Y.H.Cai, M.Guan, M.Huang, W.Cui, L.He, Y.J.Yu, L.Huang, Z.Li, X.Z.Bu, H.Ke, H.B.Luo. Discovery of 3-(4-Hydroxybenzyl)-1-(Thiophen-2-Yl)Chromeno[2,3-C]Pyrrol- 9(2H)-One As A Phosphodiesterase-5 Inhibitor and Its Complex Crystal Structure. Biochem Pharmacol V. 89 86 2014.
PubMed: 24565909
DOI: 10.1016/J.BCP.2014.02.013