Zinc in PDB 2h40: Crystal Structure of the Catalytic Domain of Unliganded PDE5

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Unliganded PDE5:
3.1.4.35;

The structure of Crystal Structure of the Catalytic Domain of Unliganded PDE5, PDB code: 2h40 was solved by H.Wang, Y.Liu, Q.Huai, J.Cai, R.Zoraghi, S.H.Francis, J.D.Corbin, H.Robinson, Z.Xin, G.Lin, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.735, 74.735, 130.690, 90.00, 90.00, 120.00
R / Rfree (%)	22.1 / 23.6

The structure of Crystal Structure of the Catalytic Domain of Unliganded PDE5 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Unliganded PDE5 (pdb code 2h40). 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 the Catalytic Domain of Unliganded PDE5, PDB code: 2h40:

Zinc binding site 1 out of 1 in the Crystal Structure of the Catalytic Domain of Unliganded PDE5


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 the Catalytic Domain of Unliganded PDE5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:46.2 occ:1.00 OD2 A:ASP654 2.1 21.9 1.0 OD1 A:ASP764 2.1 23.0 1.0 NE2 A:HIS653 2.2 19.4 1.0 NE2 A:HIS617 2.2 21.8 1.0 O A:HOH3 2.2 24.8 1.0 O A:HOH2 2.3 25.1 1.0 CG A:ASP764 3.0 24.6 1.0 CD2 A:HIS653 3.0 18.5 1.0 CD2 A:HIS617 3.1 22.9 1.0 CG A:ASP654 3.1 24.5 1.0 OD2 A:ASP764 3.2 26.8 1.0 CE1 A:HIS617 3.2 23.0 1.0 CE1 A:HIS653 3.3 19.7 1.0 OD1 A:ASP654 3.6 23.6 1.0 MG A:MG502 3.7 33.5 1.0 O A:HOH1 3.9 21.3 1.0 O A:HOH64 4.1 41.0 1.0 CD2 A:HIS613 4.1 26.8 1.0 CG A:HIS653 4.2 20.1 1.0 CG A:HIS617 4.3 21.7 1.0 ND1 A:HIS617 4.3 21.3 1.0 ND1 A:HIS653 4.3 20.0 1.0 CB A:ASP654 4.3 21.7 1.0 CB A:ASP764 4.4 22.6 1.0 NE2 A:HIS613 4.4 28.7 1.0 O A:ASP764 4.8 19.9 1.0 O A:HOH5 4.8 25.2 1.0 CA A:ASP764 4.8 21.3 1.0 OG1 A:THR621 4.9 20.6 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