Sodium in PDB 5olb: Crystal Structure of Autotaxin in Complex with Pf-8380

All present enzymatic activity of Crystal Structure of Autotaxin in Complex with Pf-8380:
3.1.4.39;

The structure of Crystal Structure of Autotaxin in Complex with Pf-8380, PDB code: 5olb was solved by S.Hoerer, A.Lammens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.65 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	124.734, 100.045, 78.778, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.1

The structure of Crystal Structure of Autotaxin in Complex with Pf-8380 also contains other interesting chemical elements:

Potassium	(K)	1 atom
Zinc	(Zn)	2 atoms
Calcium	(Ca)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of Autotaxin in Complex with Pf-8380 (pdb code 5olb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Autotaxin in Complex with Pf-8380, PDB code: 5olb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Autotaxin in Complex with Pf-8380


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 Pf-8380 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na918 b:24.2 occ:1.00 O A:ASN797 2.3 16.4 1.0 OG A:SER803 2.3 21.9 1.0 O A:HOH1686 2.4 30.9 1.0 O A:SER800 2.4 18.7 1.0 O A:HOH1547 2.4 23.7 1.0 O A:HOH1385 2.5 23.4 1.0 C A:ASN797 3.2 17.5 1.0 CB A:SER803 3.3 19.2 1.0 C A:SER800 3.4 19.4 1.0 CA A:ASP798 3.8 14.7 1.0 N A:ASP798 3.8 15.0 1.0 N A:SER803 4.1 18.2 1.0 C A:ASP798 4.1 17.2 1.0 O A:HOH1772 4.1 41.0 1.0 CB A:ASN797 4.2 15.4 1.0 CA A:ASN797 4.2 14.9 1.0 N A:CYS801 4.2 16.8 1.0 O A:ASP798 4.3 15.7 1.0 CA A:SER803 4.3 17.6 1.0 CA A:CYS801 4.3 17.9 1.0 N A:SER800 4.3 15.2 1.0 CA A:SER800 4.4 15.2 1.0 O A:HOH1103 4.4 22.6 1.0 C A:CYS801 4.5 21.8 1.0 O A:CYS801 4.6 21.4 1.0 OD1 A:ASP798 4.6 22.4 1.0 CB A:SER800 4.7 17.4 1.0 O A:HOH1021 4.8 24.5 1.0 N A:GLU799 4.9 13.9 1.0 O A:HOH1591 4.9 19.1 1.0 C A:SER803 5.0 21.1 1.0 N A:ASN797 5.0 15.5 1.0 N A:ASN802 5.0 18.4 0.6 N A:ASN802 5.0 19.0 0.4

Sodium binding site 2 out of 2 in the Crystal Structure of Autotaxin in Complex with Pf-8380


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Autotaxin in Complex with Pf-8380 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na922 b:37.8 occ:0.54 O A:ASN77 2.2 43.9 1.0 OG A:SER276 2.2 43.3 0.5 CA A:LEU78 2.6 38.4 1.0 C A:LEU78 2.7 40.0 1.0 O A:LEU78 2.8 40.5 1.0 C A:ASN77 3.0 43.1 1.0 N A:LEU78 3.2 38.9 1.0 N A:LYS80 3.4 36.2 1.0 N A:SER81 3.5 41.5 1.0 N A:CYS79 3.5 34.0 1.0 O A:HOH1020 3.5 52.4 1.0 CB A:SER276 3.6 32.0 0.5 CB A:SER276 3.6 33.3 0.5 CB A:LYS80 3.7 40.1 1.0 OG A:SER81 3.7 58.0 1.0 CA A:LYS80 3.9 37.4 1.0 CB A:LEU78 3.9 38.6 1.0 C A:LYS80 4.1 44.0 1.0 CB A:SER81 4.1 46.4 1.0 C A:CYS79 4.2 37.5 1.0 CG A:LEU78 4.4 43.1 0.0 CA A:CYS79 4.4 32.2 1.0 CA A:SER81 4.4 42.0 1.0 OG A:SER276 4.4 39.0 0.5 CA A:SER276 4.5 29.0 0.5 CA A:ASN77 4.5 38.4 1.0 CA A:SER276 4.5 29.4 0.5 N A:SER276 4.5 28.8 0.5 N A:SER276 4.5 29.1 0.5 CG A:LYS80 4.8 52.8 1.0 CD1 A:PHE274 5.0 42.5 1.0

C.A.Kuttruff, M.Ferrara, T.Bretschneider, S.Hoerer, S.Handschuh, B.Nosse, H.Romig, P.Nicklin, G.J.Roth. Discovery of Bi-2545: A Novel Autotaxin Inhibitor That Significantly Reduces Lpa Levels in Vivo. Acs Med Chem Lett V. 8 1252 2017.
ISSN: ISSN 1948-5875
PubMed: 29259743
DOI: 10.1021/ACSMEDCHEMLETT.7B00312