Zinc in PDB 3wd9: Crystal Structure of Phosphodiesterase 4B in Complex with Compound 10F

All present enzymatic activity of Crystal Structure of Phosphodiesterase 4B in Complex with Compound 10F:
3.1.4.17;

The structure of Crystal Structure of Phosphodiesterase 4B in Complex with Compound 10F, PDB code: 3wd9 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)	19.81 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.305, 157.376, 58.050, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 26.7

The structure of Crystal Structure of Phosphodiesterase 4B in Complex with Compound 10F 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 10F (pdb code 3wd9). 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 10F, PDB code: 3wd9:
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 10F


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 10F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:51.8 occ:1.00 O A:HOH1004 1.7 42.4 1.0 OD2 A:ASP275 2.1 37.3 1.0 NE2 A:HIS238 2.2 36.7 1.0 OD1 A:ASP392 2.3 42.2 1.0 NE2 A:HIS274 2.4 38.5 1.0 O A:HOH1007 2.4 47.9 1.0 CD2 A:HIS274 3.0 37.6 1.0 CD2 A:HIS238 3.0 33.5 1.0 CG A:ASP275 3.2 35.4 1.0 CG A:ASP392 3.2 39.4 1.0 CE1 A:HIS238 3.3 32.5 1.0 OD2 A:ASP392 3.4 44.2 1.0 CE1 A:HIS274 3.5 37.7 1.0 OD1 A:ASP275 3.7 35.8 1.0 CA A:CA903 3.8 52.9 1.0 CD2 A:HIS234 4.2 35.7 1.0 CG A:HIS238 4.3 34.4 1.0 CG A:HIS274 4.3 36.6 1.0 O A:HOH1005 4.4 38.8 1.0 ND1 A:HIS238 4.4 34.0 1.0 CB A:ASP275 4.4 34.2 1.0 NE2 A:HIS234 4.4 38.7 1.0 ND1 A:HIS274 4.5 38.2 1.0 CB A:ASP392 4.6 37.8 1.0 O A:HOH1006 4.7 40.9 1.0 CG2 A:VAL242 4.8 39.2 1.0 O A:HOH1002 5.0 38.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Phosphodiesterase 4B in Complex with Compound 10F


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 10F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:47.4 occ:1.00 O B:HOH1006 2.0 39.7 1.0 NE2 B:HIS274 2.2 39.2 1.0 NE2 B:HIS238 2.2 38.5 1.0 OD2 B:ASP275 2.3 41.5 1.0 OD1 B:ASP392 2.3 38.5 1.0 O B:HOH1004 2.4 38.6 1.0 CD2 B:HIS274 3.0 36.9 1.0 CD2 B:HIS238 3.1 38.5 1.0 CG B:ASP392 3.2 39.8 1.0 CE1 B:HIS238 3.2 36.0 1.0 CG B:ASP275 3.3 39.5 1.0 CE1 B:HIS274 3.3 37.0 1.0 OD2 B:ASP392 3.4 42.7 1.0 OD1 B:ASP275 3.8 38.2 1.0 CA B:CA903 4.0 45.1 1.0 O B:HOH1005 4.1 39.6 1.0 CD2 B:HIS234 4.2 37.2 1.0 CG B:HIS274 4.2 37.5 1.0 O B:HOH1077 4.3 29.6 1.0 CG B:HIS238 4.3 39.4 1.0 ND1 B:HIS238 4.3 38.5 1.0 ND1 B:HIS274 4.3 36.4 1.0 NE2 B:HIS234 4.4 42.3 1.0 CB B:ASP275 4.4 38.1 1.0 CB B:ASP392 4.6 35.8 1.0 O B:HOH1002 4.7 34.3 1.0 CG2 B:VAL242 4.7 36.2 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. Synthesis and Biological Evaluation of 5-Carbamoyl-2-Phenylpyrimidine Derivatives As Novel and Potent PDE4 Inhibitors Bioorg.Med.Chem. V. 21 7025 2013.
ISSN: ISSN 0968-0896
PubMed: 24094436
DOI: 10.1016/J.BMC.2013.09.013