Zinc 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:

Iodine	(I)	10 atoms
Calcium	(Ca)	1 atom
Sodium	(Na)	2 atoms

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

Zinc 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 Zinc with other atoms in the Zn 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:Zn904 b:18.4 occ:1.00 NE2 A:HIS474 2.0 15.4 1.0 OD2 A:ASP311 2.1 19.2 1.0 NE2 A:HIS315 2.1 18.3 1.0 O A:HOH1236 2.1 32.8 1.0 O1P A:TPO209 2.5 27.2 1.0 OD1 A:ASP311 2.7 18.9 1.0 CG A:ASP311 2.7 17.7 1.0 CE1 A:HIS315 3.0 19.2 1.0 CE1 A:HIS474 3.0 15.7 1.0 CD2 A:HIS474 3.0 15.1 1.0 CD2 A:HIS315 3.1 18.4 1.0 P A:TPO209 3.7 43.0 1.0 O A:HOH1135 3.9 32.7 1.0 O2P A:TPO209 4.0 21.3 1.0 ND1 A:HIS474 4.1 15.3 1.0 ND1 A:HIS315 4.1 19.4 1.0 CB A:ASP311 4.2 17.9 1.0 CG A:HIS474 4.2 15.2 1.0 CG A:HIS315 4.2 19.1 1.0 CE1 A:HIS359 4.2 15.3 1.0 O3P A:TPO209 4.4 29.6 1.0 NE2 A:HIS359 4.5 15.4 1.0 ZN A:ZN905 4.5 21.0 1.0 O A:HOH1003 4.6 31.3 1.0 CE A:MET361 4.6 16.6 1.0 OD1 A:ASP171 4.6 17.6 1.0 O A:HOH1428 4.7 27.1 1.0 OG1 A:TPO209 4.8 21.8 1.0 O A:ASP311 5.0 18.5 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn905 b:21.0 occ:1.00 OD1 A:ASP171 1.9 17.6 1.0 OG1 A:TPO209 2.0 21.8 1.0 NE2 A:HIS359 2.0 15.4 1.0 OD2 A:ASP358 2.2 20.8 1.0 O1P A:TPO209 2.5 27.2 1.0 CG A:ASP171 2.7 20.4 1.0 OD2 A:ASP171 2.9 24.0 1.0 P A:TPO209 2.9 43.0 1.0 CD2 A:HIS359 2.9 15.6 1.0 CE1 A:HIS359 3.0 15.3 1.0 CG A:ASP358 3.0 17.2 1.0 CB A:TPO209 3.1 19.6 1.0 OD1 A:ASP358 3.2 15.1 1.0 CA A:TPO209 3.5 16.5 1.0 CG2 A:TPO209 3.6 19.4 1.0 O2P A:TPO209 3.8 21.3 1.0 N A:TPO209 3.8 15.6 1.0 CB A:ASP171 4.0 18.7 1.0 O3P A:TPO209 4.0 29.6 1.0 ND1 A:HIS359 4.0 14.8 1.0 CG A:HIS359 4.0 14.6 1.0 N A:GLY172 4.1 16.1 1.0 OD1 A:ASP311 4.2 18.9 1.0 CG A:ASP311 4.2 17.7 1.0 CE1 A:HIS474 4.2 15.7 1.0 OD2 A:ASP311 4.4 19.2 1.0 CA A:ASP171 4.4 17.2 1.0 CB A:ASP358 4.4 17.1 1.0 ZN A:ZN904 4.5 18.4 1.0 NE2 A:HIS474 4.5 15.4 1.0 C A:ASP171 4.6 18.8 1.0 C A:LYS208 4.7 16.1 1.0 CB A:ASP311 4.8 17.9 1.0 CA A:GLY172 4.9 16.5 1.0 C A:TPO209 4.9 15.5 1.0 ND1 A:HIS474 5.0 15.3 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