Zinc in PDB 1udu: Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis)

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis):
3.1.4.17;

The structure of Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis), PDB code: 1udu was solved by B.-J.Sung, J.I.Lee, Y.-S.Heo, J.H.Kim, J.Moon, J.M.Yoon, Y.-L.Hyun, E.Kim, S.J.Eum, T.G.Lee, J.M.Cho, S.-Y.Park, J.-O.Lee, Y.H.Jeon, K.Y.Hwang, S.Ro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.59 / 2.83
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	131.352, 48.561, 123.863, 90.00, 117.28, 90.00
R / Rfree (%)	26.3 / 37.4

The structure of Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis) (pdb code 1udu). 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 Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis), PDB code: 1udu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis)


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 Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:0.0 occ:1.00 OD2 A:ASP654 1.8 31.7 1.0 NE2 A:HIS653 1.9 6.0 1.0 NE2 A:HIS617 2.3 36.4 1.0 CD2 A:HIS653 2.5 29.1 1.0 CD2 A:HIS617 2.7 16.4 1.0 OD2 A:ASP764 3.0 29.1 1.0 CG A:ASP654 3.1 38.3 1.0 CE1 A:HIS653 3.2 47.1 1.0 OD1 A:ASP764 3.2 21.9 1.0 CG A:ASP764 3.4 69.4 1.0 CE1 A:HIS617 3.6 36.0 1.0 CG A:HIS653 3.8 20.1 1.0 OD1 A:ASP654 3.9 19.8 1.0 CB A:ASP654 4.0 20.7 1.0 ND1 A:HIS653 4.0 18.1 1.0 CG A:HIS617 4.1 47.8 1.0 CD2 A:HIS613 4.2 40.8 1.0 MG A:MG1002 4.4 36.6 1.0 ND1 A:HIS617 4.4 85.0 1.0 NE2 A:HIS613 4.5 6.0 1.0 CB A:ASP764 4.7 53.5 1.0 CA A:ASP764 5.0 19.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis)


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 Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:0.0 occ:1.00 OD2 B:ASP764 2.3 33.9 1.0 OD1 B:ASP764 2.3 71.0 1.0 OD2 B:ASP654 2.4 22.2 1.0 NE2 B:HIS653 2.5 28.0 1.0 CG B:ASP764 2.5 95.8 1.0 CD2 B:HIS653 2.7 26.4 1.0 NE2 B:HIS617 2.7 30.8 1.0 CD2 B:HIS617 3.3 74.7 1.0 CG B:ASP654 3.5 54.7 1.0 CE1 B:HIS653 3.8 29.2 1.0 CE1 B:HIS617 3.8 20.4 1.0 CB B:ASP764 3.9 0.0 1.0 MG B:MG2002 4.0 16.0 1.0 CG B:HIS653 4.0 34.7 1.0 OD1 B:ASP654 4.1 6.0 1.0 CA B:ASP764 4.4 13.2 1.0 ND1 B:HIS653 4.5 15.6 1.0 CG B:HIS617 4.5 50.5 1.0 NE2 B:HIS613 4.6 13.9 1.0 CD2 B:HIS613 4.6 17.0 1.0 CB B:ASP654 4.7 11.9 1.0 ND1 B:HIS617 4.8 31.1 1.0 O B:ASP764 4.8 70.3 1.0 C B:ASP764 4.9 58.2 1.0

B.-J.Sung, K.Y.Hwang, Y.H.Jeon, J.I.Lee, Y.-S.Heo, J.H.Kim, J.Moon, J.M.Yoon, Y.-L.Hyun, E.Kim, S.J.Eum, S.-Y.Park, J.-O.Lee, T.G.Lee, S.Ro, J.M.Cho. Structure of the Catalytic Domain of Human Phosphodiesterase 5 with Bound Drug Molecules Nature V. 425 98 2003.
ISSN: ISSN 0028-0836
PubMed: 12955149
DOI: 10.1038/NATURE01914