Zinc in PDB 3w5e: Crystal Structure of Phosphodiesterase 4B in Complex with Compound 31E

All present enzymatic activity of Crystal Structure of Phosphodiesterase 4B in Complex with Compound 31E:
3.1.4.17;

The structure of Crystal Structure of Phosphodiesterase 4B in Complex with Compound 31E, PDB code: 3w5e was solved by M.Takahashi, H.Hanzawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.77 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.064, 158.190, 58.157, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 26.9

The structure of Crystal Structure of Phosphodiesterase 4B in Complex with Compound 31E also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Phosphodiesterase 4B in Complex with Compound 31E (pdb code 3w5e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Phosphodiesterase 4B in Complex with Compound 31E, PDB code: 3w5e:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Phosphodiesterase 4B in Complex with Compound 31E


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 Phosphodiesterase 4B in Complex with Compound 31E within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:42.0 occ:1.00 O A:HOH1004 2.0 32.3 1.0 OD2 A:ASP275 2.1 32.8 1.0 NE2 A:HIS238 2.1 38.9 1.0 NE2 A:HIS274 2.2 31.5 1.0 OD1 A:ASP392 2.3 33.2 1.0 O A:HOH1007 2.5 31.7 1.0 CD2 A:HIS274 3.0 26.7 1.0 CD2 A:HIS238 3.1 35.6 1.0 CG A:ASP392 3.1 35.8 1.0 CE1 A:HIS238 3.2 37.0 1.0 CG A:ASP275 3.3 33.0 1.0 CE1 A:HIS274 3.3 29.2 1.0 OD2 A:ASP392 3.3 35.1 1.0 OD1 A:ASP275 3.9 33.5 1.0 CA A:CA903 4.0 40.9 1.0 O A:HOH1005 4.1 32.5 1.0 CG A:HIS274 4.2 27.0 1.0 CG A:HIS238 4.3 36.1 1.0 CD2 A:HIS234 4.3 35.0 1.0 ND1 A:HIS238 4.3 38.0 1.0 O A:HOH1006 4.3 32.9 1.0 CB A:ASP275 4.3 33.2 1.0 ND1 A:HIS274 4.3 28.0 1.0 NE2 A:HIS234 4.5 33.8 1.0 CB A:ASP392 4.5 34.4 1.0 CG2 A:VAL242 4.7 29.6 1.0 CA A:ASP392 4.9 34.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Phosphodiesterase 4B in Complex with Compound 31E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Phosphodiesterase 4B in Complex with Compound 31E within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:38.5 occ:1.00 O B:HOH1006 2.1 27.9 1.0 NE2 B:HIS238 2.2 30.8 1.0 OD2 B:ASP275 2.2 35.7 1.0 OD1 B:ASP392 2.2 32.9 1.0 NE2 B:HIS274 2.3 32.2 1.0 O B:HOH1004 2.4 28.3 1.0 CD2 B:HIS274 3.1 31.8 1.0 CD2 B:HIS238 3.1 30.2 1.0 CG B:ASP392 3.1 33.6 1.0 CE1 B:HIS238 3.2 28.7 1.0 CG B:ASP275 3.2 33.9 1.0 CE1 B:HIS274 3.4 33.1 1.0 OD2 B:ASP392 3.4 37.4 1.0 OD1 B:ASP275 3.7 31.2 1.0 CA B:CA903 3.9 38.9 1.0 O B:HOH1152 4.2 28.3 1.0 O B:HOH1005 4.2 29.1 1.0 CD2 B:HIS234 4.3 27.8 1.0 CG B:HIS238 4.3 32.9 1.0 ND1 B:HIS238 4.3 30.8 1.0 CG B:HIS274 4.3 35.3 1.0 CB B:ASP275 4.4 31.9 1.0 ND1 B:HIS274 4.4 32.3 1.0 NE2 B:HIS234 4.5 30.8 1.0 CB B:ASP392 4.5 30.8 1.0 O B:HOH1061 4.5 64.5 1.0 CG2 B:VAL242 4.7 29.1 1.0 O B:HOH1002 4.9 32.5 1.0 CA B:ASP392 5.0 31.3 1.0

T.Goto, A.Shiina, T.Yoshino, K.Mizukami, K.Hirahara, O.Suzuki, Y.Sogawa, T.Takahashi, T.Mikkaichi, N.Nakao, M.Takahashi, M.Hasegawa, S.Sasaki. Identification of the Fused Bicyclic 4-Amino-2-Phenylpyrimidine Derivatives As Novel and Potent PDE4 Inhibitors Bioorg.Med.Chem.Lett. V. 23 3325 2013.
ISSN: ISSN 0960-894X
PubMed: 23602400
DOI: 10.1016/J.BMCL.2013.03.104