Zinc in PDB 2h42: Crystal Structure of PDE5 in Complex with Sildenafil

All present enzymatic activity of Crystal Structure of PDE5 in Complex with Sildenafil:
3.1.4.35;

The structure of Crystal Structure of PDE5 in Complex with Sildenafil, PDB code: 2h42 was solved by H.Wang, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	164.575, 164.575, 193.127, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 24.6

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

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE5 in Complex with Sildenafil (pdb code 2h42). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of PDE5 in Complex with Sildenafil, PDB code: 2h42:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of PDE5 in Complex with Sildenafil


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 Sildenafil within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:42.0 occ:1.00 OD2 A:ASP654 2.1 32.2 1.0 OD1 A:ASP764 2.1 26.8 1.0 NE2 A:HIS653 2.1 28.8 1.0 NE2 A:HIS617 2.1 30.6 1.0 CD2 A:HIS653 2.9 25.0 1.0 CD2 A:HIS617 3.0 27.2 1.0 CG A:ASP764 3.0 22.1 1.0 CG A:ASP654 3.2 28.2 1.0 CE1 A:HIS653 3.2 26.4 1.0 CE1 A:HIS617 3.2 28.7 1.0 O A:HOH45 3.2 29.3 1.0 OD2 A:ASP764 3.3 22.4 1.0 OD1 A:ASP654 3.7 31.1 1.0 CD2 A:HIS613 3.9 26.9 1.0 CG A:HIS653 4.1 25.0 1.0 NE2 A:HIS613 4.2 27.6 1.0 CG A:HIS617 4.2 26.0 1.0 ND1 A:HIS653 4.2 25.9 1.0 O A:HOH111 4.2 37.2 1.0 ND1 A:HIS617 4.3 26.7 1.0 CB A:ASP764 4.3 20.5 1.0 CB A:ASP654 4.4 26.0 1.0 MG A:MG502 4.4 39.0 1.0 O A:HOH86 4.6 24.5 1.0 OG1 A:THR621 4.7 17.7 1.0 O A:ASP764 4.8 17.7 1.0 CA A:ASP764 4.9 19.0 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of PDE5 in Complex with Sildenafil


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 PDE5 in Complex with Sildenafil within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:45.4 occ:1.00 OD1 B:ASP764 2.1 27.9 1.0 OD2 B:ASP654 2.1 29.7 1.0 NE2 B:HIS653 2.1 29.8 1.0 NE2 B:HIS617 2.1 27.9 1.0 CD2 B:HIS617 2.9 22.8 1.0 CG B:ASP764 3.0 22.9 1.0 CD2 B:HIS653 3.1 25.5 1.0 CE1 B:HIS653 3.1 27.2 1.0 CG B:ASP654 3.2 25.2 1.0 O B:HOH228 3.2 38.5 1.0 CE1 B:HIS617 3.3 23.3 1.0 OD2 B:ASP764 3.3 24.3 1.0 OD1 B:ASP654 3.7 27.2 1.0 MG B:MG504 3.9 38.3 1.0 CG B:HIS617 4.1 21.6 1.0 CD2 B:HIS613 4.2 20.9 1.0 ND1 B:HIS653 4.2 25.9 1.0 CG B:HIS653 4.2 24.4 1.0 ND1 B:HIS617 4.3 22.5 1.0 CB B:ASP764 4.3 20.0 1.0 O B:HOH254 4.4 22.7 1.0 CB B:ASP654 4.5 22.1 1.0 NE2 B:HIS613 4.6 21.5 1.0 O B:ASP764 4.6 15.4 1.0 O B:HOH32 4.7 21.8 1.0 O B:HOH282 4.7 27.9 1.0 OG1 B:THR621 4.7 16.5 1.0 CA B:ASP764 4.8 17.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of PDE5 in Complex with Sildenafil


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of PDE5 in Complex with Sildenafil within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn505 b:46.2 occ:1.00 OD1 C:ASP764 2.1 28.8 1.0 OD2 C:ASP654 2.1 32.0 1.0 NE2 C:HIS653 2.1 28.6 1.0 NE2 C:HIS617 2.1 28.9 1.0 CD2 C:HIS617 2.8 24.1 1.0 O C:HOH255 2.9 21.1 1.0 CG C:ASP764 2.9 23.6 1.0 CD2 C:HIS653 3.0 23.6 1.0 CE1 C:HIS653 3.1 26.2 1.0 OD2 C:ASP764 3.2 25.1 1.0 CG C:ASP654 3.2 26.2 1.0 O C:HOH152 3.3 26.5 1.0 CE1 C:HIS617 3.3 24.4 1.0 OD1 C:ASP654 3.8 28.1 1.0 CG C:HIS617 4.1 23.0 1.0 CD2 C:HIS613 4.1 18.4 1.0 CG C:HIS653 4.2 24.3 1.0 ND1 C:HIS653 4.2 24.9 1.0 ND1 C:HIS617 4.3 24.1 1.0 CB C:ASP764 4.3 21.2 1.0 MG C:MG506 4.3 35.3 1.0 CB C:ASP654 4.5 23.9 1.0 OG1 C:THR621 4.5 16.0 1.0 O C:HOH257 4.5 20.1 1.0 NE2 C:HIS613 4.6 18.2 1.0 O C:ASP764 4.6 18.5 1.0 O C:HOH71 4.7 22.3 1.0 CA C:ASP764 4.8 18.2 1.0

H.Wang, Y.Liu, Q.Huai, J.Cai, R.Zoraghi, S.H.Francis, J.D.Corbin, H.Robinson, Z.Xin, G.Lin, H.Ke. Multiple Conformations of Phosphodiesterase-5: Implications For Enzyme Function and Drug Development J.Biol.Chem. V. 281 21469 2006.
ISSN: ISSN 0021-9258
PubMed: 16735511
DOI: 10.1074/JBC.M512527200