Sodium in PDB 5ijq: Crystal Structure of Autotaxin (ENPP2) Re-Refined

All present enzymatic activity of Crystal Structure of Autotaxin (ENPP2) Re-Refined:
3.1.4.39;

The structure of Crystal Structure of Autotaxin (ENPP2) Re-Refined, PDB code: 5ijq 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)	20.00 / 2.05
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.808, 63.289, 70.471, 98.78, 106.22, 99.77
R / Rfree (%)	15.4 / 19.7

The structure of Crystal Structure of Autotaxin (ENPP2) Re-Refined also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Iodine	(I)	25 atoms
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Autotaxin (ENPP2) Re-Refined (pdb code 5ijq). 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) Re-Refined, PDB code: 5ijq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Autotaxin (ENPP2) Re-Refined


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) Re-Refined within 5.0Å range: probe atom residue distance (Å) B Occ A:Na933 b:58.8 occ:1.00 O A:MET675 2.6 44.8 1.0 O A:ASP672 2.6 53.4 1.0 O2 A:GOL939 2.7 53.3 1.0 O A:TYR669 2.7 55.9 1.0 C A:MET675 3.7 42.7 1.0 C2 A:GOL939 3.8 43.0 1.0 C A:ASP672 3.8 54.4 1.0 C1 A:GOL939 3.8 44.4 1.0 C A:TYR669 3.9 53.7 1.0 O A:LYS673 4.1 65.3 1.0 CA A:LYS673 4.3 63.0 1.0 C A:LYS673 4.3 60.9 1.0 N A:MET675 4.4 44.0 1.0 N A:LYS673 4.5 55.4 1.0 C3 A:GOL939 4.5 52.0 1.0 N A:SER676 4.6 40.5 1.0 CA A:MET675 4.6 43.8 1.0 CA A:SER676 4.7 38.7 1.0 O A:LYS670 4.7 58.7 1.0 CA A:TYR669 4.8 48.0 1.0 N A:LYS670 4.8 56.5 1.0 CA A:LYS670 4.8 60.1 1.0 CA A:ASP672 4.9 51.3 1.0 C A:LYS670 4.9 59.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Autotaxin (ENPP2) Re-Refined


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) Re-Refined within 5.0Å range: probe atom residue distance (Å) B Occ A:Na934 b:59.6 occ:1.00 O A:HOH1204 2.3 35.9 1.0 O A:HOH1148 2.4 46.6 1.0 OG A:SER807 2.4 34.6 1.0 O A:SER804 2.9 28.2 1.0 O A:ASN801 3.0 26.6 1.0 CB A:SER807 3.7 30.7 1.0 C A:ASN801 3.8 27.2 1.0 C A:SER804 4.0 29.9 1.0 CA A:ASP802 4.0 29.0 1.0 N A:SER807 4.2 30.2 1.0 N A:ASP802 4.2 27.1 1.0 O A:HOH1168 4.3 47.9 1.0 O A:CYS805 4.4 34.7 1.0 CA A:SER807 4.5 31.8 1.0 CA A:CYS805 4.5 36.0 1.0 O A:ASP802 4.5 26.7 1.0 C A:ASP802 4.5 28.1 1.0 C A:CYS805 4.6 35.9 1.0 OD1 A:ASP802 4.6 33.7 1.0 N A:CYS805 4.7 29.8 1.0 O A:HOH1021 4.7 47.5 1.0 CB A:ASN801 4.8 31.2 1.0 CA A:ASN801 4.8 29.1 1.0 N A:SER808 4.9 39.9 1.0 N A:SER804 4.9 29.2 1.0 CA A:SER804 5.0 28.7 1.0 C A:SER807 5.0 38.1 1.0

J.Hausmann, W.J.Keune, A.L.Hipgrave Ederveen, L.Van Zeijl, R.P.Joosten, A.Perrakis. Structural Snapshots of the Catalytic Cycle of the Phosphodiesterase Autotaxin. J.Struct.Biol. V. 195 199 2016.
ISSN: ESSN 1095-8657
PubMed: 27268273
DOI: 10.1016/J.JSB.2016.06.002