Sodium in PDB 4nw7: PDE4 Catalytic Domain

All present enzymatic activity of PDE4 Catalytic Domain:
3.1.4.17;

The structure of PDE4 Catalytic Domain, PDB code: 4nw7 was solved by D.Fox Iii, T.E.Edwards, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.29 / 2.15
Space group	P 42
Cell size a, b, c (Å), α, β, γ (°)	98.580, 98.580, 47.570, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 20.7

The structure of PDE4 Catalytic Domain also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the PDE4 Catalytic Domain (pdb code 4nw7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the PDE4 Catalytic Domain, PDB code: 4nw7:

Sodium binding site 1 out of 1 in the PDE4 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of PDE4 Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:38.6 occ:1.00 O A:HOH957 2.2 45.9 1.0 O A:HOH956 2.2 48.4 1.0 O A:ASP397 2.3 19.9 1.0 O A:TYR399 2.4 23.3 1.0 O A:HOH910 2.4 39.1 1.0 O A:HOH908 2.4 45.0 1.0 C A:ASP397 3.3 19.8 1.0 C A:TYR399 3.5 19.4 1.0 O A:HOH909 3.8 49.1 1.0 O A:HOH907 3.9 31.6 1.0 CA A:ASP397 3.9 20.7 1.0 CA A:HIS400 4.0 25.0 1.0 N A:HIS400 4.2 19.9 1.0 N A:SER401 4.3 26.4 1.0 N A:TYR399 4.3 19.5 1.0 N A:HIS398 4.3 19.3 1.0 O A:GLU396 4.4 18.7 1.0 C A:HIS398 4.6 19.1 1.0 CA A:TYR399 4.6 19.4 1.0 CA A:HIS398 4.6 19.1 1.0 CD2 A:HIS400 4.7 39.1 1.0 C A:HIS400 4.7 24.8 1.0 CB A:ASP397 4.7 23.0 1.0 OG A:SER401 4.7 45.0 1.0 O A:HOH958 4.7 50.4 1.0

T.J.Hagen, X.Mo, A.B.Burgin, D.Fox, Z.Zhang, M.E.Gurney. Discovery of Triazines As Selective PDE4B Versus PDE4D Inhibitors. Bioorg.Med.Chem.Lett. V. 24 4031 2014.
ISSN: ISSN 0960-894X
PubMed: 24998378
DOI: 10.1016/J.BMCL.2014.06.002