Zinc in PDB 3hmv: Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Tetrahydrobenzothiophene Inhibitor

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Tetrahydrobenzothiophene Inhibitor:
3.1.4.17;

The structure of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Tetrahydrobenzothiophene Inhibitor, PDB code: 3hmv was solved by D.O.Somers, M.Neu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.23
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	57.309, 57.309, 251.718, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 22.6

The structure of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Tetrahydrobenzothiophene Inhibitor also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Tetrahydrobenzothiophene Inhibitor (pdb code 3hmv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Tetrahydrobenzothiophene Inhibitor, PDB code: 3hmv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Tetrahydrobenzothiophene Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Tetrahydrobenzothiophene Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:32.1 occ:1.00 OD2 A:ASP275 1.9 30.0 1.0 OD1 A:ASP392 2.0 25.7 1.0 NE2 A:HIS238 2.1 28.2 1.0 NE2 A:HIS274 2.1 27.4 1.0 O A:HOH12 2.4 28.3 1.0 O A:HOH14 2.6 23.9 1.0 CG A:ASP392 3.0 28.1 1.0 CD2 A:HIS274 3.0 24.5 1.0 CD2 A:HIS238 3.0 23.1 1.0 CG A:ASP275 3.1 31.3 1.0 CE1 A:HIS238 3.2 29.6 1.0 CE1 A:HIS274 3.2 26.6 1.0 OD2 A:ASP392 3.2 30.9 1.0 OD1 A:ASP275 3.6 29.9 1.0 O A:HOH11 3.9 32.1 1.0 MG A:MG529 4.0 28.1 1.0 CG A:HIS274 4.2 31.2 1.0 CD2 A:HIS234 4.2 27.1 1.0 CG A:HIS238 4.2 31.7 1.0 ND1 A:HIS274 4.2 31.5 1.0 NE2 A:HIS234 4.2 27.1 1.0 ND1 A:HIS238 4.2 28.8 1.0 CB A:ASP275 4.2 29.2 1.0 O A:HOH15 4.3 26.7 1.0 CB A:ASP392 4.4 26.8 1.0 CG2 A:VAL242 4.6 28.8 1.0 C11 A:HBT530 4.8 34.1 1.0 O A:HOH13 4.9 28.5 1.0 CA A:ASP392 4.9 27.9 1.0

Zinc binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Tetrahydrobenzothiophene Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Tetrahydrobenzothiophene Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:30.5 occ:1.00 OD2 B:ASP275 1.9 28.2 1.0 OD1 B:ASP392 2.0 27.5 1.0 NE2 B:HIS238 2.1 25.9 1.0 NE2 B:HIS274 2.2 25.8 1.0 O B:HOH128 2.5 26.9 1.0 O B:HOH130 2.6 23.5 1.0 CG B:ASP392 3.0 29.0 1.0 CG B:ASP275 3.0 30.8 1.0 CD2 B:HIS274 3.0 24.3 1.0 CE1 B:HIS238 3.1 26.1 1.0 CD2 B:HIS238 3.1 24.9 1.0 OD2 B:ASP392 3.2 29.1 1.0 CE1 B:HIS274 3.3 28.6 1.0 OD1 B:ASP275 3.5 29.2 1.0 O B:HOH127 4.0 26.7 1.0 MG B:MG529 4.1 29.5 1.0 CD2 B:HIS234 4.1 26.8 1.0 ND1 B:HIS238 4.2 29.0 1.0 O B:HOH131 4.2 29.3 1.0 CB B:ASP275 4.2 29.4 1.0 CG B:HIS238 4.2 30.3 1.0 CG B:HIS274 4.2 29.8 1.0 ND1 B:HIS274 4.3 29.1 1.0 NE2 B:HIS234 4.3 25.9 1.0 CB B:ASP392 4.4 28.1 1.0 CG2 B:VAL242 4.7 30.0 1.0 C11 B:HBT530 4.8 31.9 1.0 O B:HOH129 4.8 28.3 1.0 CA B:ASP392 4.9 27.9 1.0

M.Kranz, M.Wall, B.Evans, A.Miah, S.Ballantine, C.Delves, B.Dombroski, J.Gross, J.Schneck, J.P.Villa, M.Neu, D.O.Somers. Identification of PDE4B Over 4D Subtype-Selective Inhibitors Revealing An Unprecedented Binding Mode Bioorg.Med.Chem. V. 17 5336 2009.
ISSN: ISSN 0968-0896
PubMed: 19525117
DOI: 10.1016/J.BMC.2009.03.061