Sodium in PDB 9ent: Ssx Structure of Autotaxin in Cryogenic Conditions

All present enzymatic activity of Ssx Structure of Autotaxin in Cryogenic Conditions:
3.1.4.39;

The structure of Ssx Structure of Autotaxin in Cryogenic Conditions, PDB code: 9ent was solved by M.C.Eymery, A.A.Mccarthy, N.Foos, S.Basu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.51 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.51, 61.19, 65.01, 102.57, 99.13, 93.67
R / Rfree (%)	19.4 / 23.6

The structure of Ssx Structure of Autotaxin in Cryogenic Conditions also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Calcium	(Ca)	1 atom
Iodine	(I)	15 atoms

The binding sites of Sodium atom in the Ssx Structure of Autotaxin in Cryogenic Conditions (pdb code 9ent). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ssx Structure of Autotaxin in Cryogenic Conditions, PDB code: 9ent:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Ssx Structure of Autotaxin in Cryogenic Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ssx Structure of Autotaxin in Cryogenic Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na921 b:58.7 occ:1.00 O A:MET675 2.5 50.2 1.0 O A:HOH1379 2.5 59.2 1.0 O A:HOH1312 2.5 53.5 1.0 O A:ASP672 2.6 56.0 1.0 O A:TYR669 2.8 53.5 1.0 O A:HOH1348 2.9 58.5 1.0 C A:MET675 3.5 48.1 1.0 C A:ASP672 3.8 55.0 1.0 C A:TYR669 4.0 58.0 1.0 CA A:LYS673 4.1 46.4 1.0 C A:LYS673 4.2 55.1 1.0 O A:LYS673 4.2 44.4 1.0 N A:SER676 4.3 41.9 1.0 N A:MET675 4.3 50.1 1.0 CA A:SER676 4.3 36.3 1.0 N A:LYS673 4.4 59.8 1.0 CA A:MET675 4.5 46.9 1.0 N A:GLN674 4.7 54.8 1.0 CB A:SER676 4.8 38.0 1.0 O A:LYS670 4.8 55.3 1.0 CA A:TYR669 4.8 49.0 1.0 N A:LYS670 4.9 52.6 1.0 CA A:LYS670 4.9 54.3 1.0 CA A:ASP672 5.0 44.9 1.0 C A:GLN674 5.0 47.3 1.0

Sodium binding site 2 out of 3 in the Ssx Structure of Autotaxin in Cryogenic Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ssx Structure of Autotaxin in Cryogenic Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na922 b:40.1 occ:1.00 O A:SER804 2.4 42.4 1.0 O A:HOH1321 2.5 37.1 1.0 OG A:SER807 2.5 38.9 1.0 O A:HOH1378 2.5 61.3 1.0 O A:HOH1146 2.5 36.5 1.0 O A:ASN801 2.5 31.3 1.0 C A:ASN801 3.5 32.6 1.0 CB A:SER807 3.5 42.3 1.0 C A:SER804 3.6 42.1 1.0 CA A:ASP802 3.9 42.7 1.0 N A:ASP802 4.1 31.2 1.0 O A:HOH1046 4.2 46.0 1.0 C A:ASP802 4.3 40.6 1.0 N A:SER807 4.3 42.5 1.0 O A:HOH1292 4.3 50.0 1.0 O A:ASP802 4.3 33.0 1.0 CA A:CYS805 4.4 53.2 1.0 CB A:ASN801 4.4 36.0 1.0 CA A:SER807 4.4 41.8 1.0 N A:CYS805 4.5 40.6 1.0 CA A:ASN801 4.5 30.7 1.0 N A:SER804 4.5 39.8 1.0 O A:HOH1240 4.5 53.1 1.0 CA A:SER804 4.6 33.7 1.0 C A:CYS805 4.6 46.4 1.0 O A:CYS805 4.6 44.3 1.0 O A:HOH1328 4.7 44.7 1.0 OD1 A:ASP802 4.8 45.7 1.0 CB A:SER804 4.9 40.1 1.0 C A:SER807 5.0 50.8 1.0

Sodium binding site 3 out of 3 in the Ssx Structure of Autotaxin in Cryogenic Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ssx Structure of Autotaxin in Cryogenic Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na923 b:59.9 occ:1.00 O A:HOH1366 2.5 73.3 1.0 CB A:LYS588 3.6 66.8 1.0 N A:GLY589 4.5 87.9 1.0 N A:LYS588 4.5 75.1 1.0 CD A:LYS588 4.5 78.9 1.0 CA A:LYS588 4.6 65.4 1.0 CG A:LYS588 4.7 80.1 1.0 N A:SER590 4.8 79.0 1.0 C A:LYS588 5.0 80.7 1.0

N.Foos, J.B.Florial, M.Eymery, J.Sinoir, F.Felisaz, M.Oscarsson, A.Beteva, M.W.Bowler, D.Nurizzo, G.Papp, M.Soler-Lopez, M.Nanao, S.Basu, A.A.Mccarthy. In Situ Serial Crystallography Facilitates 96-Well Plate Structural Analysis at Low Symmetry. Iucrj 2024.
ISSN: ESSN 2052-2525
PubMed: 39008358
DOI: 10.1107/S2052252524005785