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

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Autotaxin (ENPP2) Re-Refined (pdb code 5ijq). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 25 binding sites of Iodine where determined in the Crystal Structure of Autotaxin (ENPP2) Re-Refined, PDB code: 5ijq:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 25 in the Crystal Structure of Autotaxin (ENPP2) Re-Refined


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) Re-Refined within 5.0Å range: probe atom residue distance (Å) B Occ A:I910 b:34.2 occ:1.00 N A:ASN230 3.7 29.3 1.0 NH1 A:ARG391 3.8 35.3 1.0 CA A:GLY229 4.0 26.9 1.0 N A:SER231 4.0 30.3 1.0 CD2 A:LEU389 4.2 45.0 1.0 O A:SER231 4.3 27.4 1.0 C A:GLY229 4.3 30.8 1.0 CG1 A:VAL385 4.4 39.0 1.0 CG A:LYS208 4.4 34.9 1.0 CB A:ASN230 4.5 27.8 1.0 CA A:ASN230 4.5 31.0 1.0 CE A:LYS208 4.6 35.4 1.0 CD1 A:LEU389 4.6 41.8 1.0 CG A:LEU389 4.7 38.0 1.0 C A:ASN230 4.8 33.3 1.0 CB A:SER231 4.8 34.1 1.0 CZ A:ARG391 4.9 34.9 1.0 CA A:SER231 4.9 30.8 1.0

Iodine binding site 2 out of 25 in the Crystal Structure of Autotaxin (ENPP2) Re-Refined


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) Re-Refined within 5.0Å range: probe atom residue distance (Å) B Occ A:I911 b:42.5 occ:0.75 O A:HOH1134 3.3 39.1 1.0 N A:LEU788 3.6 31.0 1.0 CA A:PRO787 4.0 35.7 1.0 CG A:ARG843 4.1 39.9 1.0 O A:GLU847 4.2 32.3 1.0 NE A:ARG843 4.3 47.6 1.0 CB A:LEU851 4.3 29.7 1.0 C A:PRO787 4.3 32.5 1.0 CB A:PRO787 4.4 38.6 1.0 CB A:LEU788 4.4 30.1 1.0 CB A:GLU847 4.5 44.1 1.0 C A:GLU847 4.5 35.0 1.0 CD1 A:LEU851 4.5 30.3 1.0 CD2 A:LEU851 4.5 31.7 1.0 O A:LEU788 4.5 26.2 1.0 CA A:LEU788 4.5 31.4 1.0 CD1 A:ILE848 4.6 36.9 1.0 CB A:ARG843 4.6 35.8 1.0 CG A:LEU788 4.7 32.5 1.0 CD A:ARG843 4.7 40.5 1.0 CG A:LEU851 4.7 29.3 1.0 N A:ILE848 4.9 30.9 1.0 C A:LEU788 5.0 30.0 1.0

Iodine binding site 3 out of 25 in the Crystal Structure of Autotaxin (ENPP2) Re-Refined


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) Re-Refined within 5.0Å range: probe atom residue distance (Å) B Occ A:I912 b:49.1 occ:0.70 I A:IOD912 0.0 49.1 0.7 I A:IOD912 3.0 61.7 0.3 N A:PHE679 3.8 32.7 1.0 O A:PHE679 3.9 27.4 1.0 CD1 A:TRP712 4.0 28.8 1.0 NE2 A:GLN716 4.1 43.4 1.0 CG A:GLN716 4.2 40.8 1.0 CB A:PHE679 4.3 35.6 1.0 CE2 A:TYR684 4.3 47.3 1.0 NE1 A:TRP712 4.3 30.8 1.0 CA A:PHE679 4.4 32.9 1.0 CD A:PRO683 4.5 43.7 1.0 N A:SCN905 4.6 57.7 1.0 CD2 A:PHE679 4.6 40.0 1.0 C A:PHE679 4.6 32.6 1.0 CA A:GLY678 4.7 32.3 1.0 CB A:GLN716 4.7 37.4 1.0 CD A:GLN716 4.7 42.9 1.0 C A:GLY678 4.7 33.9 1.0 CA A:ALA713 4.9 31.1 1.0 CG A:PHE679 4.9 37.2 1.0 OH A:TYR684 5.0 47.9 1.0

Iodine binding site 4 out of 25 in the Crystal Structure of Autotaxin (ENPP2) Re-Refined


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) Re-Refined within 5.0Å range: probe atom residue distance (Å) B Occ A:I912 b:61.7 occ:0.30 I A:IOD912 0.0 61.7 0.3 I A:IOD912 3.0 49.1 0.7 NZ A:LYS709 3.3 50.8 1.0 CB A:ALA713 3.9 32.0 1.0 CD1 A:TRP712 3.9 28.8 1.0 N A:ALA713 4.0 29.2 1.0 CA A:ALA713 4.1 31.1 1.0 CG A:LYS709 4.1 38.0 1.0 O A:LYS709 4.2 30.6 1.0 CA A:GLY678 4.2 32.3 1.0 CB A:LYS709 4.2 35.0 1.0 CA A:LYS709 4.5 32.5 1.0 N A:SCN905 4.5 57.7 1.0 CE A:LYS709 4.5 48.2 1.0 CB A:TRP712 4.5 28.7 1.0 CG A:TRP712 4.6 28.7 1.0 C A:TRP712 4.7 30.5 1.0 SD A:MET704 4.7 34.2 1.0 C A:LYS709 4.8 28.7 1.0 CD A:LYS709 4.9 42.9 1.0 C A:SCN905 4.9 60.4 1.0 O A:TYR677 4.9 32.8 1.0 N A:PHE679 4.9 32.7 1.0

Iodine binding site 5 out of 25 in the Crystal Structure of Autotaxin (ENPP2) Re-Refined


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) Re-Refined within 5.0Å range: probe atom residue distance (Å) B Occ A:I913 b:54.3 occ:0.60 O A:HOH1290 3.1 48.6 1.0 CA A:GLY387 3.8 31.8 1.0 N A:GLY387 3.9 33.5 1.0 O A:VAL453 3.9 32.6 1.0 ND1 A:HIS452 4.0 39.6 1.0 CG A:HIS452 4.1 35.6 1.0 CB A:ALA454 4.2 34.6 1.0 CB A:PRO386 4.2 38.8 1.0 CB A:HIS452 4.3 34.9 1.0 CE1 A:HIS452 4.5 37.4 1.0 C A:VAL453 4.6 35.9 1.0 C A:PRO386 4.6 35.6 1.0 CA A:ALA454 4.7 35.5 1.0 CD2 A:HIS452 4.7 35.3 1.0 CG A:PRO386 4.7 37.9 1.0 NE2 A:HIS452 4.9 33.7 1.0 N A:ALA454 4.9 32.8 1.0

Iodine binding site 6 out of 25 in the Crystal Structure of Autotaxin (ENPP2) Re-Refined


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) Re-Refined within 5.0Å range: probe atom residue distance (Å) B Occ A:I914 b:52.3 occ:0.90 C A:MET232 3.8 32.5 1.0 NH2 A:ARG393 3.9 43.2 1.0 O A:MET232 4.0 32.7 1.0 N A:TYR233 4.1 30.8 1.0 N A:MET232 4.1 27.0 1.0 NH1 A:ARG393 4.1 43.3 1.0 CA A:MET232 4.1 29.9 1.0 CE1 A:HIS242 4.1 53.7 1.0 O A:HOH1276 4.1 40.7 1.0 OG A:SER240 4.1 40.8 1.0 CG2 A:VAL385 4.2 40.0 1.0 CB A:TYR233 4.3 33.6 1.0 CB A:SER231 4.4 34.1 1.0 CZ A:ARG393 4.4 42.9 1.0 CB A:SER240 4.5 37.1 1.0 C A:SER231 4.5 28.5 1.0 CA A:TYR233 4.6 32.7 1.0 NE2 A:HIS242 4.8 55.7 1.0

Iodine binding site 7 out of 25 in the Crystal Structure of Autotaxin (ENPP2) Re-Refined


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) Re-Refined within 5.0Å range: probe atom residue distance (Å) B Occ A:I915 b:56.6 occ:0.50 OG A:SER278 3.4 52.9 1.0 CG2 A:VAL277 3.8 54.8 1.0 CB A:SER278 3.8 45.6 1.0 CB A:LYS80 4.0 50.8 1.0 N A:SER278 4.0 44.2 1.0 CB A:SER276 4.3 47.6 1.0 C A:LYS80 4.4 49.7 1.0 O A:LYS80 4.4 53.8 1.0 N A:VAL277 4.5 44.5 1.0 N A:SER81 4.5 49.3 1.0 CA A:SER278 4.6 45.2 1.0 OG A:SER276 4.8 52.3 1.0 CA A:SER81 4.8 54.5 1.0 OG A:SER81 4.8 52.3 1.0 CA A:LYS80 4.8 49.0 1.0 C A:SER276 4.9 44.2 1.0 CE A:LYS80 4.9 63.5 1.0 C A:VAL277 4.9 46.1 1.0 CA A:SER276 4.9 44.6 1.0 CG A:LYS80 5.0 56.1 1.0 CA A:VAL277 5.0 46.3 1.0

Iodine binding site 8 out of 25 in the Crystal Structure of Autotaxin (ENPP2) Re-Refined


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) Re-Refined within 5.0Å range: probe atom residue distance (Å) B Occ A:I916 b:59.4 occ:0.55 N A:SER846 3.6 33.6 1.0 CB A:SER846 3.8 37.5 1.0 OG A:SER846 3.8 44.5 1.0 O A:HOH1196 4.0 41.5 1.0 O A:HOH1250 4.1 42.8 1.0 N A:TYR845 4.2 29.9 1.0 CA A:SER846 4.3 36.0 1.0 CB A:TYR845 4.4 32.3 1.0 CG A:PRO541 4.5 45.9 1.0 CD A:PRO541 4.5 48.6 1.0 CB A:SER844 4.5 35.4 1.0 C A:TYR845 4.5 34.3 1.0 CA A:TYR845 4.6 30.8 1.0 OG A:SER844 4.7 35.7 1.0 O A:PRO541 4.9 44.0 1.0 C A:SER844 4.9 32.4 1.0

Iodine binding site 9 out of 25 in the Crystal Structure of Autotaxin (ENPP2) Re-Refined


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) Re-Refined within 5.0Å range: probe atom residue distance (Å) B Occ A:I917 b:67.9 occ:0.45 NH2 A:ARG535 3.6 55.6 1.0 N A:TYR496 3.7 40.0 1.0 CZ A:ARG535 3.8 55.1 1.0 CG A:LYS495 3.9 37.5 1.0 NH1 A:ARG535 3.9 56.2 1.0 CB A:LYS495 3.9 35.0 1.0 CA A:LYS495 4.0 35.6 1.0 OE2 A:GLU150 4.1 58.2 1.0 CB A:TYR496 4.2 39.2 1.0 C A:LYS495 4.4 36.2 1.0 CD A:LYS495 4.5 39.3 1.0 CA A:TYR496 4.5 36.2 1.0 O A:TYR496 4.6 34.3 1.0 NE A:ARG535 4.6 51.1 1.0 CB A:ARG535 4.9 43.1 1.0 CE A:LYS495 4.9 42.2 1.0 OG1 A:THR498 4.9 38.3 1.0

Iodine binding site 10 out of 25 in the Crystal Structure of Autotaxin (ENPP2) Re-Refined


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) Re-Refined within 5.0Å range: probe atom residue distance (Å) B Occ A:I918 b:58.9 occ:0.55 O A:HOH1255 3.1 42.5 1.0 ND1 A:HIS281 3.2 51.0 1.0 OG1 A:THR334 3.3 36.7 1.0 OG A:SER307 3.5 33.7 1.0 CE1 A:HIS281 3.7 48.7 1.0 CG A:HIS281 3.7 42.1 1.0 CG1 A:ILE331 3.8 39.1 1.0 CB A:THR334 3.8 35.2 1.0 CB A:SER307 3.9 31.9 1.0 CA A:ILE331 4.0 32.6 1.0 CB A:HIS281 4.2 38.1 1.0 CG2 A:THR334 4.2 35.8 1.0 CZ A:PHE305 4.3 34.6 1.0 O A:GLU330 4.4 36.6 1.0 NE2 A:HIS281 4.4 46.5 1.0 CB A:ILE331 4.4 34.2 1.0 N A:ILE331 4.4 34.6 1.0 CD2 A:HIS281 4.4 46.0 1.0 C A:GLU330 4.6 37.3 1.0 CE2 A:PHE305 4.7 32.2 1.0 CG2 A:ILE331 4.8 35.9 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