Zinc in PDB 3o0j: PDE4B in Complex with Ligand AN2898

All present enzymatic activity of PDE4B in Complex with Ligand AN2898:
3.1.4.17;

The structure of PDE4B in Complex with Ligand AN2898, PDB code: 3o0j was solved by M.R.K.Alley, Y.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.26 / 1.95
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	53.611, 53.611, 229.014, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 23.6

The structure of PDE4B in Complex with Ligand AN2898 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the PDE4B in Complex with Ligand AN2898 (pdb code 3o0j). 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 PDE4B in Complex with Ligand AN2898, PDB code: 3o0j:

Zinc binding site 1 out of 1 in the PDE4B in Complex with Ligand AN2898


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PDE4B in Complex with Ligand AN2898 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:30.0 occ:1.00 O A:HOH78 2.1 26.5 1.0 NE2 A:HIS238 2.1 26.9 1.0 OD1 A:ASP392 2.2 22.7 1.0 O17 A:3OJ485 2.2 26.5 1.0 OD2 A:ASP275 2.2 21.3 1.0 NE2 A:HIS274 2.2 29.0 1.0 B16 A:3OJ485 2.7 44.8 1.0 CD2 A:HIS274 3.0 27.3 1.0 CG A:ASP392 3.1 24.4 1.0 CD2 A:HIS238 3.1 20.5 1.0 CE1 A:HIS238 3.1 23.5 1.0 CG A:ASP275 3.2 24.6 1.0 CE1 A:HIS274 3.3 21.4 1.0 OD2 A:ASP392 3.4 27.9 1.0 O15 A:3OJ485 3.6 32.1 1.0 OD1 A:ASP275 3.7 23.4 1.0 MG A:MG2 3.8 16.0 1.0 C8 A:3OJ485 4.0 48.0 1.0 CD2 A:HIS234 4.1 26.1 1.0 ND1 A:HIS238 4.2 22.5 1.0 CG A:HIS274 4.2 26.7 1.0 CG A:HIS238 4.3 22.5 1.0 NE2 A:HIS234 4.3 25.0 1.0 ND1 A:HIS274 4.3 27.3 1.0 CB A:ASP392 4.4 22.2 1.0 CB A:ASP275 4.4 23.8 1.0 C10 A:3OJ485 4.6 47.2 1.0 O A:HOH495 4.6 21.0 1.0 CG2 A:VAL242 4.8 21.5 1.0 C14 A:3OJ485 4.9 45.4 1.0 CA A:ASP392 5.0 23.3 1.0

Y.R.Freund, T.Akama, M.R.Alley, J.Antunes, C.Dong, K.Jarnagin, R.Kimura, J.A.Nieman, K.R.Maples, J.J.Plattner, F.Rock, R.Sharma, R.Singh, V.Sanders, Y.Zhou. Boron-Based Phosphodiesterase Inhibitors Show Novel Binding of Boron to PDE4 Bimetal Center. Febs Lett. V. 586 3410 2012.
ISSN: ISSN 0014-5793
PubMed: 22841723
DOI: 10.1016/J.FEBSLET.2012.07.058