Zinc in PDB 1rkp: Crystal Structure of PDE5A1-Ibmx

All present enzymatic activity of Crystal Structure of PDE5A1-Ibmx:
3.1.4.17;

The structure of Crystal Structure of PDE5A1-Ibmx, PDB code: 1rkp was solved by Q.Huai, Y.Liu, S.H.Francis, J.D.Corbin, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 2.05
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.456, 74.456, 130.132, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 24.3

The structure of Crystal Structure of PDE5A1-Ibmx also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of PDE5A1-Ibmx (pdb code 1rkp). 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 PDE5A1-Ibmx, PDB code: 1rkp:

Zinc binding site 1 out of 1 in the Crystal Structure of PDE5A1-Ibmx


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 PDE5A1-Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:34.4 occ:1.00 OD2 A:ASP654 2.1 20.2 1.0 OD1 A:ASP764 2.1 21.6 1.0 NE2 A:HIS653 2.1 17.3 1.0 NE2 A:HIS617 2.1 19.3 1.0 O A:HOH1 2.2 22.1 1.0 O A:HOH2 2.5 20.2 1.0 CD2 A:HIS653 2.9 17.6 1.0 CG A:ASP764 3.0 23.4 1.0 CD2 A:HIS617 3.0 19.4 1.0 CE1 A:HIS617 3.1 19.9 1.0 CE1 A:HIS653 3.2 17.5 1.0 CG A:ASP654 3.2 20.7 1.0 OD2 A:ASP764 3.2 22.8 1.0 OD1 A:ASP654 3.7 21.4 1.0 O A:HOH10 4.0 23.3 1.0 MG A:MG502 4.0 29.8 1.0 CG A:HIS653 4.1 19.0 1.0 CD2 A:HIS613 4.2 22.4 1.0 ND1 A:HIS617 4.2 18.0 1.0 CG A:HIS617 4.2 19.1 1.0 ND1 A:HIS653 4.2 19.2 1.0 O A:HOH6 4.3 19.5 1.0 CB A:ASP654 4.4 19.9 1.0 CB A:ASP764 4.4 21.8 1.0 NE2 A:HIS613 4.4 23.9 1.0 O A:ASP764 4.6 22.3 1.0 OG1 A:THR621 4.7 21.3 1.0 CA A:ASP764 4.8 21.9 1.0 O A:HOH97 4.9 31.8 1.0 O A:HOH5 5.0 20.0 1.0

Q.Huai, Y.Liu, S.H.Francis, J.D.Corbin, H.Ke. Crystal Structures of Phosphodiesterases 4 and 5 in Complex with Inhibitor Ibmx Suggest A Conformation Determinant of Inhibitor Selectivity J.Biol.Chem. V. 279 13095 2004.
ISSN: ISSN 0021-9258
PubMed: 14668322
DOI: 10.1074/JBC.M311556200