Sodium in PDB 5dlt: Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol

All present enzymatic activity of Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol:
3.1.4.39;

The structure of Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol, PDB code: 5dlt was solved by J.Hausmann, R.P.Joosten, A.Perrakis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.02 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.671, 63.482, 70.715, 98.72, 105.80, 99.97
R / Rfree (%)	17.1 / 19.6

The structure of Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Iodine	(I)	10 atoms
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol (pdb code 5dlt). 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 (ENPP2) with 7-Alpha-Hydroxycholesterol, PDB code: 5dlt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol


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 (ENPP2) with 7-Alpha-Hydroxycholesterol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na928 b:31.1 occ:1.00 O A:MET675 2.2 26.6 1.0 O A:ASP672 2.3 34.9 1.0 O2 A:GOL931 2.4 52.2 1.0 O A:TYR669 2.4 34.0 1.0 O A:HOH1357 2.4 35.8 1.0 O A:HOH1414 2.8 39.6 1.0 C A:MET675 3.4 25.9 1.0 C A:TYR669 3.5 34.0 1.0 C A:ASP672 3.5 35.1 1.0 C2 A:GOL931 3.7 50.1 1.0 N A:MET675 4.0 27.5 1.0 C1 A:GOL931 4.1 54.3 1.0 CA A:MET675 4.3 26.1 1.0 CA A:TYR669 4.3 32.0 1.0 N A:SER676 4.3 24.0 1.0 N A:LYS673 4.4 36.2 1.0 CA A:LYS673 4.4 36.5 1.0 O3 A:GOL931 4.4 58.2 1.0 CA A:SER676 4.5 24.1 1.0 N A:LYS670 4.5 38.4 1.0 CA A:ASP672 4.5 35.8 1.0 C A:LYS673 4.5 34.9 1.0 O A:LYS670 4.5 41.0 1.0 CB A:ASP672 4.6 34.4 1.0 CA A:LYS670 4.6 39.8 1.0 C A:LYS670 4.6 39.4 1.0 C3 A:GOL931 4.7 55.0 1.0 CB A:TYR669 4.7 31.1 1.0 N A:ASP672 4.7 37.4 1.0 O A:LYS673 4.8 34.4 1.0 N A:GLN674 4.9 33.3 1.0 CB A:MET675 4.9 26.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol


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 (ENPP2) with 7-Alpha-Hydroxycholesterol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na929 b:18.5 occ:1.00 O A:HOH1361 2.3 20.0 1.0 O A:HOH1400 2.3 24.6 1.0 O A:SER804 2.4 17.8 1.0 O A:HOH1438 2.4 24.4 1.0 OG A:SER807 2.4 18.4 1.0 O A:ASN801 2.4 16.3 1.0 C A:ASN801 3.3 16.5 1.0 CB A:SER807 3.4 18.5 1.0 C A:SER804 3.4 18.5 1.0 CA A:ASP802 3.8 17.9 1.0 N A:ASP802 3.9 17.7 1.0 N A:SER807 4.1 19.5 1.0 C A:ASP802 4.2 17.3 1.0 O A:ASP802 4.2 17.2 1.0 CA A:CYS805 4.2 20.1 1.0 N A:CYS805 4.3 17.7 1.0 O A:HOH1009 4.3 24.7 1.0 N A:SER804 4.3 17.6 1.0 CB A:ASN801 4.3 17.3 1.0 CA A:SER807 4.3 19.7 1.0 CA A:SER804 4.3 17.5 1.0 CA A:ASN801 4.4 17.1 1.0 C A:CYS805 4.4 19.4 1.0 O A:CYS805 4.5 19.4 1.0 CB A:SER804 4.6 17.1 1.0 OD1 A:ASP802 4.8 20.3 1.0 O A:HOH1095 5.0 27.4 1.0 N A:ALA806 5.0 19.4 1.0 N A:GLU803 5.0 17.5 1.0

W.J.Keune, J.Hausmann, R.Bolier, D.Tolenaars, A.Kremer, T.Heidebrecht, R.P.Joosten, M.Sunkara, A.J.Morris, E.Matas-Rico, W.H.Moolenaar, R.P.Oude Elferink, A.Perrakis. Steroid Binding to Autotaxin Links Bile Salts and Lysophosphatidic Acid Signalling. Nat Commun V. 7 11248 2016.
ISSN: ESSN 2041-1723
PubMed: 27075612
DOI: 10.1038/NCOMMS11248