Calcium in PDB 5dlv: Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)

All present enzymatic activity of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca):
3.1.4.39;

The structure of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca), PDB code: 5dlv was solved by W.J.Keune, T.Heidebrecht, E.Von Castelmur, R.P.Joosten, A.Perrakis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.61 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	62.880, 77.832, 92.437, 83.84, 79.29, 77.08
R / Rfree (%)	19.3 / 22.7

The structure of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Iodine	(I)	27 atoms
Sodium	(Na)	4 atoms

The binding sites of Calcium atom in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) (pdb code 5dlv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca), PDB code: 5dlv:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca912 b:23.5 occ:1.00 OD1 A:ASP747 2.2 21.5 1.0 OD1 A:ASP739 2.3 19.3 1.0 O A:HOH1159 2.3 24.1 1.0 O A:LEU745 2.3 20.2 1.0 OD1 A:ASN741 2.4 24.2 1.0 OD1 A:ASP743 2.4 20.2 1.0 CG A:ASP743 3.3 21.3 1.0 CG A:ASP739 3.4 19.9 1.0 CG A:ASN741 3.4 24.6 1.0 C A:LEU745 3.5 20.2 1.0 CG A:ASP747 3.5 23.4 1.0 OD2 A:ASP743 3.7 21.8 1.0 ND2 A:ASN741 3.9 26.4 1.0 CA A:ASP739 3.9 20.8 1.0 N A:ASP747 3.9 23.1 1.0 N A:LEU745 4.0 18.4 1.0 C A:ARG746 4.1 23.0 1.0 CB A:ASP739 4.1 20.1 1.0 CA A:ASP747 4.1 24.2 1.0 CA A:LEU745 4.2 19.4 1.0 O A:ARG746 4.3 22.8 1.0 OD2 A:ASP739 4.3 18.8 1.0 N A:ASP743 4.3 19.8 1.0 O A:PHE738 4.3 21.0 1.0 OD2 A:ASP747 4.3 21.9 1.0 CB A:ASP747 4.4 24.2 1.0 OE1 A:GLU751 4.5 32.4 1.0 CB A:LEU745 4.5 19.4 1.0 C A:ASP739 4.5 21.0 1.0 N A:ARG746 4.5 21.3 1.0 CB A:ASP743 4.6 19.7 1.0 N A:ASN741 4.6 23.5 1.0 N A:TYR742 4.7 21.6 1.0 CB A:ASN741 4.8 23.8 1.0 CA A:ARG746 4.8 22.9 0.5 CA A:ARG746 4.8 23.0 0.5 N A:TYR740 4.8 22.4 1.0 N A:GLY744 4.8 18.9 1.0 CA A:ASP743 4.9 19.7 1.0 C A:ASN741 4.9 22.5 1.0 CA A:ASN741 5.0 23.1 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca910 b:21.0 occ:1.00 O B:HOH1181 2.2 21.2 1.0 OD1 B:ASP747 2.3 24.5 1.0 OD1 B:ASP739 2.3 16.9 1.0 OD1 B:ASN741 2.3 21.3 1.0 O B:LEU745 2.3 20.2 1.0 OD1 B:ASP743 2.4 20.9 1.0 CG B:ASP743 3.3 21.6 1.0 CG B:ASP739 3.4 17.1 1.0 CG B:ASN741 3.4 21.8 1.0 C B:LEU745 3.5 20.6 1.0 CG B:ASP747 3.5 26.4 1.0 OD2 B:ASP743 3.7 23.7 1.0 ND2 B:ASN741 3.8 23.2 1.0 CA B:ASP739 3.9 19.2 1.0 N B:ASP747 3.9 24.2 1.0 N B:LEU745 4.1 18.7 1.0 C B:ARG746 4.1 23.8 1.0 CA B:ASP747 4.1 25.3 1.0 CB B:ASP739 4.1 18.2 1.0 CA B:LEU745 4.2 19.4 1.0 O B:ARG746 4.2 24.4 1.0 N B:ASP743 4.3 19.9 1.0 OD2 B:ASP739 4.3 16.3 1.0 OD2 B:ASP747 4.3 25.5 1.0 O B:PHE738 4.4 18.6 1.0 CB B:ASP747 4.4 26.8 1.0 C B:ASP739 4.5 20.5 1.0 OE1 B:GLU751 4.5 31.8 1.0 CB B:LEU745 4.5 19.6 1.0 N B:ARG746 4.5 21.9 1.0 CB B:ASP743 4.6 20.0 1.0 N B:ASN741 4.6 21.8 1.0 N B:TYR742 4.7 20.4 1.0 CB B:ASN741 4.8 21.8 1.0 CA B:ARG746 4.8 23.6 0.5 CA B:ARG746 4.8 23.7 0.5 N B:TYR740 4.8 22.1 1.0 CA B:ASP743 4.9 19.2 1.0 N B:GLY744 4.9 18.8 1.0 C B:ASN741 4.9 21.1 1.0 CA B:ASN741 5.0 21.5 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