Magnesium 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:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Tetrahydrobenzothiophene Inhibitor, PDB code: 3hmv:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg529 b:28.1 occ:1.00 O A:HOH14 2.0 23.9 1.0 O A:HOH13 2.0 28.5 1.0 OD1 A:ASP275 2.0 29.9 1.0 O A:HOH9 2.1 28.2 1.0 O A:HOH15 2.1 26.7 1.0 O A:HOH10 2.2 26.7 1.0 CG A:ASP275 3.1 31.3 1.0 OD2 A:ASP275 3.5 30.0 1.0 ZN A:ZN1 4.0 32.1 1.0 OE2 A:GLU304 4.0 31.1 1.0 OG1 A:THR345 4.1 24.6 1.0 NE2 A:HIS307 4.1 29.1 1.0 O A:HIS274 4.1 31.4 1.0 CD2 A:HIS274 4.2 24.5 1.0 O A:HOH532 4.2 33.3 1.0 O A:HOH12 4.2 28.3 1.0 CD2 A:HIS307 4.4 29.2 1.0 CB A:ASP275 4.4 29.2 1.0 OD2 A:ASP392 4.4 30.9 1.0 O A:HOH81 4.4 50.9 1.0 C12 A:HBT530 4.4 31.7 1.0 O A:THR345 4.5 25.1 1.0 CD2 A:HIS278 4.5 30.1 1.0 C11 A:HBT530 4.6 34.1 1.0 CA A:ASP275 4.7 29.9 1.0 NE2 A:HIS234 4.7 27.1 1.0 NE2 A:HIS274 4.7 27.4 1.0 CB A:THR345 4.7 25.8 1.0 CG A:GLU304 4.7 25.9 1.0 CD A:GLU304 4.8 27.5 1.0 NE2 A:HIS278 4.8 31.4 1.0 CD2 A:HIS234 4.9 27.1 1.0 C A:HIS274 4.9 30.3 1.0 O A:HOH45 5.0 29.2 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg529 b:29.5 occ:1.00 OD1 B:ASP275 2.0 29.2 1.0 O B:HOH130 2.1 23.5 1.0 O B:HOH126 2.1 28.8 1.0 O B:HOH131 2.1 29.3 1.0 O B:HOH129 2.1 28.3 1.0 O B:HOH86 2.2 24.8 1.0 CG B:ASP275 3.2 30.8 1.0 OD2 B:ASP275 3.6 28.2 1.0 OE2 B:GLU304 3.9 28.6 1.0 NE2 B:HIS307 4.1 28.2 1.0 O B:HOH117 4.1 26.4 1.0 ZN B:ZN2 4.1 30.5 1.0 OG1 B:THR345 4.1 26.2 1.0 O B:HIS274 4.2 31.4 1.0 O B:HOH128 4.3 26.9 1.0 CD2 B:HIS307 4.4 26.5 1.0 CD2 B:HIS274 4.4 24.3 1.0 C12 B:HBT530 4.4 29.0 1.0 CB B:ASP275 4.5 29.4 1.0 OD2 B:ASP392 4.5 29.1 1.0 O B:THR345 4.5 25.9 1.0 CD2 B:HIS278 4.6 27.3 1.0 C11 B:HBT530 4.6 31.9 1.0 CD B:GLU304 4.7 30.4 1.0 CA B:ASP275 4.7 30.1 1.0 NE2 B:HIS234 4.8 25.9 1.0 CB B:THR345 4.8 25.8 1.0 CG B:GLU304 4.8 25.6 1.0 O B:HOH85 4.8 26.8 1.0 CD2 B:HIS234 4.9 26.8 1.0 NE2 B:HIS274 4.9 25.8 1.0 NE2 B:HIS278 4.9 29.0 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