Atomistry » Sodium » PDB 4njh-4nw8 » 4nw7
Atomistry »
  Sodium »
    PDB 4njh-4nw8 »
      4nw7 »

Sodium in PDB 4nw7: PDE4 Catalytic Domain

Enzymatic activity of PDE4 Catalytic Domain

All present enzymatic activity of PDE4 Catalytic Domain:
3.1.4.17;

Protein crystallography data

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

Other elements in 4nw7:

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

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

Sodium Binding Sites:

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 4nw7

Go back to Sodium Binding Sites List in 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

Reference:

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
Page generated: Tue Dec 15 06:56:01 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy