Sodium in PDB 3wav: Crystal Structure of Autotaxin in Complex with Compound 10

All present enzymatic activity of Crystal Structure of Autotaxin in Complex with Compound 10:
3.1.4.39;

The structure of Crystal Structure of Autotaxin in Complex with Compound 10, PDB code: 3wav was solved by H.Nishimasu, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.24 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.505, 94.015, 75.446, 90.00, 94.52, 90.00
R / Rfree (%)	18.8 / 22.3

The structure of Crystal Structure of Autotaxin in Complex with Compound 10 also contains other interesting chemical elements:

Potassium	(K)	1 atom
Zinc	(Zn)	2 atoms
Calcium	(Ca)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Autotaxin in Complex with Compound 10 (pdb code 3wav). 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 Crystal Structure of Autotaxin in Complex with Compound 10, PDB code: 3wav:

Sodium binding site 1 out of 1 in the Crystal Structure of Autotaxin in Complex with Compound 10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Autotaxin in Complex with Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na914 b:30.2 occ:1.00 OG A:SER803 2.3 34.1 1.0 O A:HOH1419 2.5 50.0 1.0 O A:HOH1418 2.6 43.5 1.0 O A:ASN797 2.7 22.0 1.0 O A:HOH1417 2.8 37.1 1.0 O A:SER800 2.8 27.9 1.0 C A:ASN797 3.4 24.0 1.0 CB A:SER803 3.6 26.1 1.0 CA A:ASP798 3.9 25.2 1.0 C A:SER800 3.9 24.8 1.0 N A:ASP798 4.0 23.0 1.0 N A:SER803 4.3 25.5 1.0 C A:ASP798 4.3 21.2 1.0 O A:HOH1408 4.3 44.9 1.0 CB A:ASN797 4.4 27.2 1.0 O A:ASP798 4.4 22.2 1.0 CA A:SER803 4.5 29.5 1.0 CA A:ASN797 4.5 29.1 1.0 OD1 A:ASP798 4.5 32.5 1.0 CA A:CYS801 4.5 24.3 1.0 C A:CYS801 4.6 30.0 1.0 O A:CYS801 4.6 29.6 1.0 N A:CYS801 4.6 24.1 1.0 N A:SER800 4.8 23.7 1.0 O A:HOH1059 4.8 36.3 1.0 CA A:SER800 4.8 23.2 1.0 O A:HOH1395 5.0 39.2 1.0

M.Kawaguchi, T.Okabe, S.Okudaira, H.Nishimasu, R.Ishitani, H.Kojima, O.Nureki, J.Aoki, T.Nagano. Screening and X-Ray Crystal Structure-Based Optimization of Autotaxin (ENPP2) Inhibitors, Using A Newly Developed Fluorescence Probe Acs Chem.Biol. V. 8 1713 2013.
ISSN: ISSN 1554-8929
PubMed: 23688339
DOI: 10.1021/CB400150C