Iodine 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
Calcium	(Ca)	2 atoms
Sodium	(Na)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Iodine 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 Iodine atom.
In total 27 binding sites of Iodine where determined in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca), PDB code: 5dlv:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 27 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I 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:I913 b:26.1 occ:1.00 N A:ASN230 3.7 22.0 1.0 NH1 A:ARG391 3.7 21.5 1.0 CA A:GLY229 3.9 21.0 1.0 CE A:LYS208 4.0 22.9 1.0 N A:SER231 4.1 25.0 1.0 C A:GLY229 4.3 21.4 1.0 O A:SER231 4.3 21.8 1.0 CG1 A:VAL385 4.3 24.3 1.0 CD2 A:LEU389 4.3 26.2 1.0 CG A:LYS208 4.4 21.7 1.0 CB A:ASN230 4.5 23.6 1.0 CA A:ASN230 4.5 23.8 1.0 CD A:LYS208 4.6 22.1 1.0 CD1 A:LEU389 4.7 26.7 1.0 NZ A:LYS208 4.8 23.9 1.0 C A:ASN230 4.8 24.3 1.0 CG A:LEU389 4.8 24.6 1.0 CZ A:ARG391 4.9 20.9 1.0 CA A:SER231 4.9 25.0 1.0 CB A:SER231 5.0 27.1 1.0

Iodine binding site 2 out of 27 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I 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 A:I914 b:50.7 occ:0.75 CD A:PRO457 3.9 38.9 1.0 N A:LEU458 4.1 41.7 1.0 CD A:LYS456 4.1 48.5 1.0 CG A:LEU458 4.1 41.2 1.0 N A:PRO457 4.3 37.9 1.0 CB A:LEU458 4.4 42.0 1.0 CB A:LYS456 4.4 39.8 1.0 CB A:PRO457 4.4 41.0 1.0 CG A:PRO457 4.4 40.5 1.0 CD1 A:LEU458 4.5 42.6 1.0 CG A:LYS456 4.6 43.0 1.0 CA A:PRO457 4.8 39.2 1.0 CA A:LEU458 4.9 43.0 1.0 C A:PRO457 4.9 40.4 1.0 C A:LYS456 4.9 36.0 1.0

Iodine binding site 3 out of 27 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) within 5.0Å range: probe atom residue distance (Å) B Occ A:I915 b:68.1 occ:0.65 O A:CYS566 3.7 56.9 1.0 N A:LEU564 3.8 56.3 1.0 CB A:LEU564 3.9 53.7 1.0 N A:CYS566 4.0 53.1 1.0 CB A:PHE562 4.0 59.5 1.0 O A:PHE562 4.1 64.8 1.0 CG A:LEU564 4.1 54.5 1.0 CB A:CYS566 4.1 54.1 1.0 CA A:LEU564 4.3 54.6 1.0 C A:PHE562 4.3 61.5 1.0 N A:GLY565 4.4 50.2 1.0 CD1 A:LEU564 4.4 54.9 1.0 CA A:CYS566 4.4 54.5 1.0 CG A:PRO654 4.4 49.5 1.0 C A:CYS566 4.5 54.6 1.0 CD A:PRO654 4.5 48.8 1.0 C A:LEU564 4.6 52.8 1.0 N A:ASP563 4.8 62.3 1.0 CB A:PRO654 4.8 48.5 1.0 CA A:PHE562 4.9 61.2 1.0 C A:ASP563 4.9 60.7 1.0 SG A:CYS566 4.9 54.7 1.0 CA A:ASP563 5.0 63.0 1.0

Iodine binding site 4 out of 27 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) within 5.0Å range: probe atom residue distance (Å) B Occ A:I916 b:37.6 occ:0.50 OG1 A:THR334 3.3 18.6 1.0 OG A:SER307 3.3 28.9 1.0 ND1 A:HIS281 3.4 42.9 1.0 CE1 A:HIS281 3.5 36.8 1.0 CB A:THR334 3.8 19.2 1.0 CB A:SER307 3.9 27.3 1.0 CG A:HIS281 4.0 36.8 1.0 CA A:ILE331 4.1 21.6 1.0 CG2 A:THR334 4.1 19.0 1.0 NE2 A:HIS281 4.1 36.2 1.0 CE2 A:PHE305 4.2 25.5 1.0 CZ A:PHE305 4.3 27.0 1.0 CG1 A:ILE331 4.4 22.8 1.0 CD2 A:HIS281 4.4 36.7 1.0 O A:GLU330 4.4 22.6 1.0 N A:ILE331 4.6 22.7 1.0 CB A:HIS281 4.6 30.9 1.0 CB A:ILE331 4.7 22.6 1.0 C A:GLU330 4.7 24.6 1.0 O A:HOH1245 4.8 45.0 1.0 CA A:SER307 4.8 24.7 1.0 CG2 A:ILE331 4.9 22.3 1.0 O A:ILE331 4.9 19.3 1.0

Iodine binding site 5 out of 27 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) within 5.0Å range: probe atom residue distance (Å) B Occ A:I917 b:43.0 occ:0.50 N A:LEU788 3.6 37.5 1.0 OE1 A:GLU847 4.0 57.9 1.0 CA A:PRO787 4.1 43.0 1.0 O A:GLU847 4.2 25.6 1.0 CB A:LEU851 4.2 24.1 1.0 CG A:ARG843 4.3 40.4 1.0 CB A:GLU847 4.3 36.6 1.0 CD2 A:LEU851 4.3 26.3 1.0 CB A:PRO787 4.3 41.6 1.0 CB A:LEU788 4.3 33.4 1.0 C A:PRO787 4.4 40.8 1.0 O A:LEU788 4.4 30.3 1.0 NE A:ARG843 4.4 42.2 1.0 CD1 A:LEU851 4.4 23.5 1.0 CA A:LEU788 4.4 35.0 1.0 C A:GLU847 4.5 28.7 1.0 CG A:LEU851 4.6 23.7 1.0 CD1 A:ILE848 4.6 25.1 1.0 CG A:LEU788 4.6 32.5 1.0 CB A:ARG843 4.7 38.7 1.0 CD A:ARG843 4.8 42.5 1.0 C A:LEU788 4.9 34.4 1.0 CD A:GLU847 4.9 52.9 1.0 N A:ILE848 5.0 27.1 1.0

Iodine binding site 6 out of 27 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) within 5.0Å range: probe atom residue distance (Å) B Occ A:I918 b:39.9 occ:0.60 C A:MET232 3.6 26.3 1.0 O A:MET232 3.8 27.4 1.0 NH1 A:ARG393 3.9 29.9 1.0 N A:TYR233 3.9 25.2 1.0 N A:MET232 3.9 24.8 1.0 NH2 A:ARG393 4.0 33.0 1.0 CA A:MET232 4.1 25.7 1.0 CB A:SER231 4.2 27.1 1.0 CG2 A:VAL385 4.2 25.3 1.0 CB A:TYR233 4.2 26.3 1.0 C A:SER231 4.4 24.9 1.0 CE1 A:HIS242 4.4 31.0 1.0 CZ A:ARG393 4.5 30.4 1.0 OG A:SER240 4.5 35.1 1.0 CA A:TYR233 4.5 25.6 1.0 CB A:SER240 4.8 30.5 1.0 CA A:SER231 4.8 25.0 1.0 O A:SER231 4.8 21.8 1.0 NE2 A:HIS242 4.9 31.5 1.0 O A:HOH1044 4.9 19.5 1.0

Iodine binding site 7 out of 27 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) within 5.0Å range: probe atom residue distance (Å) B Occ A:I919 b:58.1 occ:0.65 OD1 A:ASP782 3.5 53.1 1.0 N A:ASP782 3.6 47.2 1.0 CG A:ASP782 3.7 53.1 1.0 N A:ALA781 3.8 46.5 1.0 CA A:SER636 3.9 44.5 1.0 CB A:SER636 3.9 46.7 1.0 CB A:ALA781 4.0 45.2 1.0 CB A:ASP782 4.0 49.1 1.0 CA A:GLY729 4.0 38.8 1.0 CB A:PRO780 4.1 50.3 1.0 CG2 A:THR634 4.2 33.8 1.0 CA A:ALA781 4.2 45.2 1.0 OD2 A:ASP782 4.3 54.8 1.0 O A:ASN728 4.3 38.4 1.0 C A:ALA781 4.4 45.4 1.0 CA A:ASP782 4.4 48.0 1.0 N A:SER636 4.5 42.3 1.0 C A:PRO780 4.5 48.3 1.0 O A:ILE635 4.8 35.4 1.0 CA A:PRO780 4.8 49.4 1.0 C A:GLY729 4.8 37.9 1.0 N A:GLY729 4.9 40.8 1.0 C A:ILE635 4.9 37.8 1.0 C A:ASN728 5.0 41.2 1.0

Iodine binding site 8 out of 27 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) within 5.0Å range: probe atom residue distance (Å) B Occ A:I920 b:48.9 occ:0.40 O A:HOH1290 3.0 39.6 1.0 O A:VAL453 3.7 24.6 1.0 CA A:GLY387 3.8 22.4 1.0 N A:GLY387 3.9 22.8 1.0 ND1 A:HIS452 3.9 29.1 1.0 CG A:HIS452 4.0 26.5 1.0 CB A:HIS452 4.1 26.3 1.0 CB A:ALA454 4.2 28.9 1.0 CB A:PRO386 4.2 24.3 1.0 C A:VAL453 4.4 26.5 1.0 CE1 A:HIS452 4.6 27.3 1.0 C A:PRO386 4.6 23.0 1.0 CG A:PRO386 4.7 24.2 1.0 CD2 A:HIS452 4.7 25.9 1.0 CA A:ALA454 4.7 27.7 1.0 N A:ALA454 4.9 27.1 1.0 NE2 A:HIS452 5.0 25.4 1.0 C A:GLY387 5.0 21.8 1.0 N A:VAL453 5.0 24.9 1.0

Iodine binding site 9 out of 27 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) within 5.0Å range: probe atom residue distance (Å) B Occ A:I921 b:59.4 occ:0.40 NE2 A:HIS197 3.0 42.9 1.0 CD2 A:HIS197 3.2 42.0 1.0 O B:PRO70 3.3 0.4 1.0 C B:PRO70 3.6 0.9 1.0 N A:PRO199 3.7 22.9 1.0 CA A:PRO199 3.7 23.5 1.0 CD A:LYS499 3.7 40.1 1.0 CE A:LYS499 3.7 43.0 1.0 CG A:LYS499 3.9 34.8 1.0 N B:PRO71 3.9 0.5 1.0 CB B:PRO70 3.9 0.5 1.0 CG A:PRO199 3.9 24.8 1.0 O A:HOH1271 4.1 54.8 1.0 CA B:PRO71 4.1 0.8 1.0 C A:ALA198 4.1 22.8 1.0 CD A:PRO199 4.1 24.2 1.0 CB A:PRO199 4.1 24.1 1.0 CE1 A:HIS197 4.3 40.0 1.0 O A:ALA198 4.3 21.4 1.0 CA B:PRO70 4.4 0.4 1.0 NZ A:LYS499 4.4 50.6 1.0 CG A:HIS197 4.5 33.9 1.0 CG B:PRO70 4.5 0.6 1.0 NH1 A:ARG192 4.5 46.7 1.0 CD B:PRO71 4.5 0.5 1.0 CG B:PRO71 4.7 0.3 1.0 CB B:PRO71 4.9 0.0 1.0 CB A:LYS499 4.9 30.4 1.0 CA A:ALA198 4.9 22.8 1.0 ND1 A:HIS197 5.0 40.2 1.0

Iodine binding site 10 out of 27 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) within 5.0Å range: probe atom residue distance (Å) B Occ A:I922 b:48.6 occ:0.40 NH2 A:ARG746 3.4 29.1 0.5 NH1 A:ARG746 3.6 26.9 0.5 OE2 A:GLU749 3.8 41.6 1.0 N A:GLU749 4.0 37.5 1.0 CG A:GLU749 4.0 41.7 1.0 CZ A:ARG746 4.0 27.8 0.5 CA A:THR748 4.2 30.8 1.0 NH2 A:ARG746 4.3 27.3 0.5 CD A:GLU749 4.4 42.9 1.0 CB A:THR748 4.4 30.5 1.0 CE1 A:PHE625 4.5 51.9 1.0 C A:THR748 4.6 32.8 1.0 CE2 A:TYR605 4.7 29.1 1.0 CZ A:PHE625 4.7 51.5 1.0 CB A:GLU749 4.8 39.5 1.0 CG2 A:THR748 4.8 30.8 1.0 CD2 A:TYR605 4.8 29.3 1.0 O A:ARG606 4.9 37.2 1.0 CA A:GLU749 4.9 38.1 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