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Iodine in PDB 5dlw: Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa)

Enzymatic activity of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa)

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

Protein crystallography data

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

Resolution Low / High (Å) 79.03 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.197, 93.051, 149.680, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 21.6

Other elements in 5dlw:

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

Zinc (Zn) 2 atoms
Calcium (Ca) 1 atom
Sodium (Na) 2 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa) (pdb code 5dlw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 13 binding sites of Iodine where determined in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa), PDB code: 5dlw:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 13 in 5dlw

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Iodine binding site 1 out of 13 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa)


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) and Lysophosphatidic Acid (Lpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I915

b:33.9
occ:1.00
 N A:ASN230 3.6 24.0 1.0
NH1 A:ARG391 3.7 29.9 1.0
CA A:GLY229 3.9 23.0 1.0
N A:SER231 4.0 28.4 1.0
CE A:LYS208 4.1 29.0 1.0
CG1 A:VAL385 4.2 28.2 1.0
O A:SER231 4.2 27.5 1.0
C A:GLY229 4.2 23.3 1.0
CD2 A:LEU389 4.4 33.2 1.0
CG A:LYS208 4.4 25.9 1.0
CB A:ASN230 4.4 24.7 1.0
CA A:ASN230 4.5 26.1 1.0
CD1 A:LEU389 4.6 31.1 1.0
CD A:LYS208 4.7 27.9 1.0
CG A:LEU389 4.8 29.8 1.0
C A:ASN230 4.8 26.8 1.0
CZ A:ARG391 4.8 29.9 1.0
CA A:SER231 4.9 29.7 1.0
CB A:SER231 4.9 32.5 1.0
NZ A:LYS208 5.0 31.4 1.0

Iodine binding site 2 out of 13 in 5dlw

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Iodine binding site 2 out of 13 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa)


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) and Lysophosphatidic Acid (Lpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I916

b:44.1
occ:0.65
 N A:LEU564 3.8 42.3 1.0
O A:CYS566 3.9 42.4 1.0
N A:CYS566 3.9 39.7 1.0
CB A:CYS566 4.0 42.7 1.0
CB A:LEU564 4.1 41.4 1.0
CB A:PHE562 4.1 38.1 1.0
O A:PHE562 4.1 43.7 1.0
CD A:PRO654 4.2 30.4 1.0
CG A:PRO654 4.2 31.7 1.0
CA A:CYS566 4.3 42.2 1.0
C A:PHE562 4.3 45.1 1.0
CG A:LEU564 4.4 43.7 1.0
CA A:LEU564 4.4 40.1 1.0
C A:CYS566 4.4 42.4 1.0
O A:HOH1223 4.4 42.1 1.0
CB A:PRO654 4.6 29.5 1.0
N A:GLY565 4.6 38.4 1.0
CA A:ASP563 4.6 52.4 1.0
CD1 A:LEU564 4.7 43.1 1.0
N A:ASP563 4.7 49.1 1.0
C A:LEU564 4.7 39.2 1.0
C A:ASP563 4.7 47.1 1.0
SG A:CYS566 4.9 48.3 1.0
CA A:PHE562 4.9 41.4 1.0
O A:HOH1266 4.9 44.2 1.0

Iodine binding site 3 out of 13 in 5dlw

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Iodine binding site 3 out of 13 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa)


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) and Lysophosphatidic Acid (Lpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I917

b:38.7
occ:0.60
 O A:HOH1204 3.3 28.2 1.0
OD1 A:ASP782 3.4 38.1 1.0
O2 A:GOL931 3.4 53.3 1.0
CG A:ASP782 3.7 40.1 1.0
N A:ASP782 3.7 31.0 1.0
N A:ALA781 3.9 27.3 1.0
CA A:SER636 3.9 28.3 1.0
CB A:ASP782 4.0 34.9 1.0
CG2 A:THR634 4.0 24.8 1.0
CA A:GLY729 4.1 23.5 1.0
CB A:ALA781 4.1 25.4 1.0
CB A:SER636 4.1 31.1 1.0
CB A:PRO780 4.2 30.5 1.0
CA A:ALA781 4.4 26.6 1.0
O A:ASN728 4.4 27.8 1.0
OD2 A:ASP782 4.4 43.9 1.0
C2 A:GOL931 4.5 54.0 1.0
N A:SER636 4.5 28.2 1.0
C A:ALA781 4.5 28.6 1.0
CA A:ASP782 4.5 33.3 1.0
C3 A:GOL931 4.5 52.8 1.0
C A:PRO780 4.6 28.5 1.0
O A:ILE635 4.6 25.6 1.0
CA A:PRO780 4.7 28.9 1.0
C A:ILE635 4.8 27.2 1.0
C A:GLY729 4.9 21.9 1.0
N A:GLY729 5.0 24.1 1.0
N A:LYS637 5.0 29.6 1.0

Iodine binding site 4 out of 13 in 5dlw

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Iodine binding site 4 out of 13 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa)


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) and Lysophosphatidic Acid (Lpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I918

b:52.7
occ:0.61
 CD A:PRO163 4.3 29.2 1.0
CG A:PRO154 4.4 33.2 1.0
O A:VAL161 4.7 33.7 1.0

Iodine binding site 5 out of 13 in 5dlw

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Iodine binding site 5 out of 13 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa)


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) and Lysophosphatidic Acid (Lpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I919

b:43.8
occ:0.45
 OG A:SER307 3.3 30.9 1.0
OG1 A:THR334 3.3 23.2 1.0
ND1 A:HIS281 3.5 52.3 1.0
CE1 A:HIS281 3.7 53.2 1.0
CB A:THR334 3.8 21.8 1.0
CB A:SER307 3.8 29.0 1.0
CG2 A:THR334 4.0 21.8 1.0
CG A:HIS281 4.1 44.3 1.0
CA A:ILE331 4.1 23.7 1.0
CG1 A:ILE331 4.1 26.9 1.0
CE2 A:PHE305 4.2 26.8 1.0
CZ A:PHE305 4.2 27.0 1.0
NE2 A:HIS281 4.3 55.9 1.0
O A:GLU330 4.5 23.4 1.0
CD2 A:HIS281 4.5 49.6 1.0
CB A:ILE331 4.6 25.5 1.0
N A:ILE331 4.7 23.5 1.0
CB A:HIS281 4.7 33.7 1.0
CA A:SER307 4.8 26.6 1.0
C A:GLU330 4.9 26.2 1.0
CG2 A:ILE331 4.9 24.1 1.0
O A:ILE331 4.9 22.1 1.0
CZ A:PHE168 4.9 23.3 1.0

Iodine binding site 6 out of 13 in 5dlw

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Iodine binding site 6 out of 13 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa)


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) and Lysophosphatidic Acid (Lpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I920

b:52.2
occ:0.41
 SG A:CYS85 3.7 44.8 1.0
CB A:CYS85 3.8 42.3 1.0
N A:CYS85 3.8 42.3 1.0
CA A:SER83 3.9 45.0 1.0
C A:SER83 4.0 46.9 1.0
N A:SER84 4.0 45.2 1.0
CD A:LYS80 4.1 47.8 1.0
CA A:LYS80 4.3 40.5 1.0
CA A:CYS85 4.3 43.3 1.0
O A:CYS79 4.6 37.8 1.0
NZ A:LYS80 4.6 58.1 1.0
O A:LYS80 4.6 39.6 1.0
O A:SER83 4.7 50.7 1.0
O A:CYS85 4.7 44.7 1.0
N A:SER83 4.8 43.3 1.0
CB A:SER83 4.8 45.9 1.0
C A:SER84 4.8 41.6 1.0
CE A:LYS80 4.9 50.9 1.0
N A:LYS80 4.9 37.5 1.0
CG A:LYS80 4.9 44.9 1.0
C A:CYS85 5.0 44.5 1.0
CA A:SER84 5.0 43.6 1.0
C A:LYS80 5.0 39.9 1.0

Iodine binding site 7 out of 13 in 5dlw

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Iodine binding site 7 out of 13 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa)


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) and Lysophosphatidic Acid (Lpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I921

b:37.8
occ:0.60
 N A:LEU788 3.6 23.5 1.0
CA A:PRO787 4.1 27.3 1.0
CG A:ARG843 4.1 30.2 1.0
O A:GLU847 4.1 21.4 1.0
CB A:LEU788 4.2 22.6 1.0
CB A:LEU851 4.3 19.2 1.0
NE A:ARG843 4.3 35.9 1.0
C A:PRO787 4.3 25.2 1.0
CB A:GLU847 4.4 29.4 1.0
CA A:LEU788 4.4 22.1 1.0
CD1 A:LEU851 4.4 19.4 1.0
CD2 A:LEU851 4.4 21.7 1.0
CB A:PRO787 4.4 29.4 1.0
C A:GLU847 4.4 21.4 1.0
CD1 A:ILE848 4.5 21.1 1.0
O A:LEU788 4.5 20.2 1.0
CB A:ARG843 4.5 28.4 1.0
CG A:LEU788 4.6 23.4 1.0
CG A:LEU851 4.6 19.5 1.0
CD A:ARG843 4.6 33.1 1.0
C A:LEU788 4.9 21.1 1.0
N A:ILE848 4.9 19.3 1.0
CD1 A:LEU788 4.9 24.5 1.0

Iodine binding site 8 out of 13 in 5dlw

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Iodine binding site 8 out of 13 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa)


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) and Lysophosphatidic Acid (Lpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I922

b:50.8
occ:0.55
 C A:MET232 3.7 28.9 1.0
NH2 A:ARG393 3.8 38.0 1.0
CA A:MET232 3.9 27.1 1.0
N A:TYR233 3.9 27.5 1.0
N A:MET232 3.9 26.8 1.0
NH1 A:ARG393 3.9 34.7 1.0
O A:MET232 3.9 30.1 1.0
CB A:TYR233 4.2 30.5 1.0
CG2 A:VAL385 4.2 30.5 1.0
CB A:SER231 4.3 32.5 1.0
C A:SER231 4.3 27.8 1.0
CZ A:ARG393 4.3 37.0 1.0
CE1 A:HIS242 4.4 46.2 1.0
CA A:TYR233 4.5 30.0 1.0
OG A:SER240 4.6 39.7 1.0
CB A:SER240 4.7 36.5 1.0
O A:SER231 4.8 27.5 1.0
O A:HOH1073 4.8 27.1 1.0
CA A:SER231 4.9 29.7 1.0

Iodine binding site 9 out of 13 in 5dlw

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Iodine binding site 9 out of 13 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa)


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) and Lysophosphatidic Acid (Lpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I923

b:47.6
occ:0.33
 OG A:SER846 3.5 29.0 1.0
N A:SER846 3.6 21.9 1.0
O A:HOH1160 3.8 35.6 1.0
O A:HOH1252 3.9 42.3 1.0
CB A:SER846 3.9 25.9 1.0
N A:TYR845 4.1 23.2 1.0
CD A:PRO541 4.4 29.7 1.0
CA A:SER846 4.4 23.5 1.0
CB A:TYR845 4.4 23.9 1.0
CB A:SER844 4.4 26.8 1.0
C A:TYR845 4.5 23.0 1.0
CA A:TYR845 4.5 22.6 1.0
CG A:PRO541 4.6 28.9 1.0
OG A:SER844 4.6 25.2 1.0
C A:SER844 4.8 24.1 1.0

Iodine binding site 10 out of 13 in 5dlw

Go back to Iodine Binding Sites List in 5dlw
Iodine binding site 10 out of 13 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa)


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) and Lysophosphatidic Acid (Lpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I924

b:67.7
occ:0.33
 O A:HOH1092 3.1 35.4 1.0
O A:HOH1016 3.1 35.7 1.0
N A:GLU749 3.9 33.0 1.0
NH1 A:ARG746 4.0 29.3 1.0
CG A:GLU749 4.0 42.2 1.0
CA A:THR748 4.0 28.9 1.0
CE1 A:PHE625 4.2 43.6 1.0
CZ A:PHE625 4.3 45.9 1.0
OE2 A:GLU749 4.4 48.5 1.0
CB A:THR748 4.4 32.3 1.0
C A:THR748 4.4 31.4 1.0
CE2 A:TYR605 4.6 28.0 1.0
CD A:GLU749 4.7 47.1 1.0
CG2 A:THR748 4.7 33.4 1.0
CB A:GLU749 4.8 39.0 1.0
CD2 A:TYR605 4.8 28.5 1.0
CA A:GLU749 4.9 36.8 1.0
O A:ASP747 4.9 22.9 1.0

Reference:

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
Page generated: Sun Aug 11 20:46:13 2024

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