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Iodine in PDB 5dlt: Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5dlt:

The structure of Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol also contains other interesting chemical elements:

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

Iodine Binding Sites:

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

Iodine binding site 1 out of 10 in 5dlt

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Iodine binding site 1 out of 10 in the Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol


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 7-Alpha-Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I908

b:22.4
occ:0.95
 N A:ASN230 3.6 16.4 1.0
NH1 A:ARG391 3.7 21.5 1.0
CA A:GLY229 3.9 15.5 1.0
N A:SER231 4.0 17.7 1.0
CD2 A:LEU389 4.1 19.0 0.5
CE A:LYS208 4.1 25.5 1.0
CG1 A:VAL385 4.2 24.0 1.0
C A:GLY229 4.2 17.1 1.0
O A:SER231 4.3 20.4 1.0
CD1 A:LEU389 4.3 19.5 0.5
CG A:LYS208 4.4 20.6 1.0
CD2 A:LEU389 4.4 16.5 0.5
CB A:ASN230 4.4 18.0 1.0
CA A:ASN230 4.5 18.2 1.0
CD1 A:LEU389 4.6 16.6 0.5
CD A:LYS208 4.6 22.6 1.0
CG A:LEU389 4.6 18.9 0.5
NZ A:LYS208 4.7 30.4 1.0
CZ A:ARG391 4.8 21.3 1.0
C A:ASN230 4.8 18.8 1.0
CG A:LEU389 4.8 16.8 0.5
O A:HOH1334 4.9 35.9 1.0
CA A:SER231 4.9 20.2 1.0
CB A:SER231 4.9 21.9 1.0
NH2 A:ARG391 5.0 21.9 1.0

Iodine binding site 2 out of 10 in 5dlt

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Iodine binding site 2 out of 10 in the Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol


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 7-Alpha-Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I909

b:37.6
occ:0.45
 C A:MET232 3.6 20.9 1.0
NH1 A:ARG393 3.6 26.3 1.0
N A:MET232 3.8 18.5 1.0
O A:MET232 3.8 20.9 1.0
N A:TYR233 3.9 20.0 1.0
NH2 A:ARG393 3.9 30.9 1.0
CA A:MET232 3.9 19.9 1.0
CG2 A:VAL385 4.0 25.4 1.0
O A:HOH1508 4.2 45.8 1.0
C A:SER231 4.2 19.5 1.0
CZ A:ARG393 4.2 28.5 1.0
CB A:SER231 4.2 21.9 1.0
CB A:TYR233 4.3 21.3 1.0
CE1 A:HIS242 4.4 31.6 1.0
CA A:TYR233 4.5 20.7 1.0
OG A:SER240 4.6 28.5 1.0
O A:SER231 4.6 20.4 1.0
O A:HOH1197 4.7 20.6 1.0
CA A:SER231 4.8 20.2 1.0
CB A:SER240 4.9 26.3 1.0

Iodine binding site 3 out of 10 in 5dlt

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Iodine binding site 3 out of 10 in the Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol


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 7-Alpha-Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I910

b:37.0
occ:0.35
 C A:ARG162 3.7 21.7 1.0
CA A:ARG162 3.7 23.2 1.0
N A:ARG162 3.7 24.4 1.0
SG A:CYS156 3.8 32.5 1.0
N A:PRO163 3.9 20.6 1.0
CD A:PRO163 3.9 21.6 1.0
CB A:CYS156 4.0 30.0 1.0
C A:VAL161 4.0 29.5 1.0
O A:PHE160 4.0 31.5 1.0
O A:ARG162 4.2 20.3 1.0
O A:VAL161 4.3 28.3 1.0
CB A:PRO154 4.3 25.8 1.0
C A:PHE160 4.5 28.8 1.0
CA A:PRO163 4.7 20.4 1.0
CA A:VAL161 4.7 29.5 1.0
N A:VAL161 4.8 29.9 1.0
CB A:PHE160 4.8 24.4 1.0
CG A:PRO154 4.8 26.7 1.0
CG A:PRO163 5.0 22.8 1.0

Iodine binding site 4 out of 10 in 5dlt

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Iodine binding site 4 out of 10 in the Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol


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 7-Alpha-Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I911

b:36.6
occ:0.35
 N A:ARG252 3.7 18.6 1.0
NE2 A:HIS251 3.8 25.0 1.0
CB A:ARG252 3.8 19.7 1.0
CG A:ARG252 3.8 19.6 1.0
CB A:ASN250 3.9 23.9 1.0
CE1 A:HIS251 3.9 24.6 1.0
CD2 A:HIS251 3.9 24.6 1.0
N A:HIS251 4.0 21.1 1.0
CD A:ARG252 4.0 21.1 1.0
ND1 A:HIS251 4.2 23.5 1.0
CG A:HIS251 4.2 22.8 1.0
CA A:ARG252 4.3 19.4 1.0
CA A:ASN250 4.3 22.8 1.0
C A:ASN250 4.4 21.4 1.0
CG A:ASN250 4.4 28.3 1.0
OD1 A:ASN250 4.6 29.6 1.0
O A:HOH1161 4.6 41.2 1.0
C A:HIS251 4.7 19.5 1.0
CA A:HIS251 4.7 20.8 1.0
NE A:ARG252 4.8 21.3 1.0
O A:HOH1333 4.9 33.5 1.0

Iodine binding site 5 out of 10 in 5dlt

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Iodine binding site 5 out of 10 in the Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol


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 7-Alpha-Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I912

b:38.9
occ:0.35
 CD A:PRO416 3.8 32.4 1.0
CB A:LYS415 4.6 30.6 1.0
CG A:PRO416 4.6 33.4 1.0
CG A:LYS415 4.6 33.7 1.0
CD A:LYS415 4.7 37.6 1.0
CA A:LYS415 4.9 28.3 1.0
N A:PRO416 5.0 29.7 1.0

Iodine binding site 6 out of 10 in 5dlt

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Iodine binding site 6 out of 10 in the Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol


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 7-Alpha-Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I913

b:54.6
occ:0.55
 CG A:PRO654 3.6 41.4 1.0
N A:LEU564 3.6 54.9 1.0
CB A:LEU564 3.8 51.3 1.0
CG A:LEU564 4.0 52.2 1.0
O A:PHE562 4.0 54.1 1.0
CB A:PHE562 4.1 51.4 1.0
N A:CYS566 4.1 51.4 1.0
O A:CYS566 4.1 58.2 1.0
CA A:LEU564 4.1 52.8 1.0
CB A:CYS566 4.2 55.0 1.0
C A:PHE562 4.3 55.7 1.0
CD1 A:LEU564 4.4 49.1 1.0
N A:GLY565 4.4 50.8 1.0
CD A:PRO654 4.4 39.6 1.0
C A:LEU564 4.5 51.1 1.0
CA A:CYS566 4.6 54.2 1.0
N A:ASP563 4.6 57.3 1.0
C A:ASP563 4.7 56.6 1.0
C A:CYS566 4.7 55.8 1.0
CB A:PRO654 4.7 39.6 1.0
CA A:ASP563 4.8 58.5 1.0
SG A:CYS566 4.8 55.9 1.0
CA A:PHE562 4.9 54.4 1.0

Iodine binding site 7 out of 10 in 5dlt

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Iodine binding site 7 out of 10 in the Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol


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 7-Alpha-Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I914

b:46.4
occ:0.40
 ND2 A:ASN576 3.5 63.6 1.0
ND2 A:ASN582 3.6 40.4 1.0
N A:GLU579 4.0 49.3 1.0
CG A:GLU579 4.1 52.2 1.0
CA A:GLU579 4.1 49.5 1.0
CD2 A:LEU578 4.1 60.1 1.0
CG A:LEU578 4.1 60.0 1.0
CB A:ASN582 4.1 39.2 1.0
C A:LEU578 4.1 53.0 1.0
CB A:LEU578 4.2 58.0 1.0
O A:LEU578 4.3 49.9 1.0
CG A:ASN582 4.3 39.4 1.0
CG A:ASN576 4.4 62.8 1.0
OD1 A:ASN576 4.7 62.7 1.0
CB A:GLU579 4.7 49.2 1.0
CD1 A:LEU585 4.8 41.1 1.0
CA A:LEU578 4.8 55.9 1.0
CB A:GLU690 4.9 41.0 1.0

Iodine binding site 8 out of 10 in 5dlt

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Iodine binding site 8 out of 10 in the Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol


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 7-Alpha-Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I915

b:28.6
occ:0.60
 O A:HOH1244 3.6 28.7 1.0
N A:LEU788 3.6 18.9 1.0
O A:HOH1396 3.9 43.3 1.0
CG A:ARG843 4.0 27.0 1.0
CA A:PRO787 4.1 21.0 1.0
O A:GLU847 4.1 18.3 1.0
CB A:LEU851 4.2 15.9 1.0
CD2 A:LEU851 4.3 17.5 1.0
CB A:LEU788 4.3 20.0 1.0
O A:HOH1492 4.3 40.9 1.0
CB A:PRO787 4.4 22.8 1.0
NE A:ARG843 4.4 32.6 1.0
C A:PRO787 4.4 20.5 1.0
CD1 A:LEU851 4.4 16.7 1.0
CB A:GLU847 4.4 25.3 1.0
C A:GLU847 4.5 19.2 1.0
CA A:LEU788 4.5 19.2 1.0
CD1 A:ILE848 4.5 18.9 1.0
CG A:LEU851 4.5 16.2 1.0
CB A:ARG843 4.5 25.3 1.0
O A:LEU788 4.5 19.5 1.0
CG A:LEU788 4.6 20.3 1.0
CD A:ARG843 4.6 30.1 1.0
N A:ILE848 4.9 18.1 1.0
C A:LEU788 5.0 19.0 1.0
CD1 A:LEU788 5.0 20.9 1.0

Iodine binding site 9 out of 10 in 5dlt

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Iodine binding site 9 out of 10 in the Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol


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 7-Alpha-Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I916

b:31.1
occ:0.45
 O A:HOH1394 3.3 28.8 1.0
OD1 A:ASP782 3.6 36.9 1.0
N A:ASP782 3.7 26.4 1.0
CG A:ASP782 3.8 36.0 1.0
N A:ALA781 3.8 23.2 1.0
CA A:SER636 3.8 25.1 1.0
CB A:ASP782 4.0 33.6 1.0
CG2 A:THR634 4.0 24.2 1.0
CA A:GLY729 4.1 19.6 1.0
CB A:SER636 4.1 26.8 1.0
CB A:PRO780 4.1 24.8 1.0
CB A:ALA781 4.2 22.5 1.0
O A:ASN728 4.3 21.6 1.0
CA A:ALA781 4.3 22.2 1.0
OD2 A:ASP782 4.3 43.9 1.0
O A:ILE635 4.4 22.1 1.0
C A:ALA781 4.5 24.7 1.0
CA A:ASP782 4.5 29.6 1.0
N A:SER636 4.5 24.4 1.0
C A:PRO780 4.5 23.2 1.0
C A:ILE635 4.7 23.4 1.0
CA A:PRO780 4.7 23.8 1.0
C A:GLY729 4.8 20.1 1.0
C A:SER636 4.9 24.4 1.0
N A:LYS637 4.9 25.9 1.0
N A:GLY729 4.9 19.8 1.0
C A:ASN728 5.0 20.5 1.0

Iodine binding site 10 out of 10 in 5dlt

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Iodine binding site 10 out of 10 in the Crystal Structure of Autotaxin (ENPP2) with 7-Alpha-Hydroxycholesterol


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 7-Alpha-Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I917

b:42.2
occ:0.35
 OG A:SER846 3.4 22.6 0.5
N A:SER846 3.5 21.2 1.0
NH2 A:ARG540 3.6 52.6 1.0
OG A:SER846 3.7 22.3 0.5
O A:HOH1249 3.8 27.4 1.0
CB A:SER846 3.8 22.4 0.5
CB A:SER846 3.8 22.1 0.5
N A:TYR845 3.9 20.3 1.0
NE A:ARG540 4.0 54.9 1.0
CZ A:ARG540 4.1 57.7 1.0
CA A:SER846 4.2 21.2 0.5
CA A:SER846 4.2 21.1 0.5
CB A:TYR845 4.3 21.2 1.0
C A:TYR845 4.3 20.6 1.0
CB A:SER844 4.3 26.0 1.0
CA A:TYR845 4.3 20.5 1.0
OG A:SER844 4.4 26.9 1.0
CD A:PRO541 4.7 28.7 1.0
O1 A:GOL930 4.7 48.2 1.0
C A:SER844 4.7 22.1 1.0
CG A:PRO541 4.7 27.4 1.0
O A:HOH1100 4.8 36.0 1.0
CA A:SER844 5.0 23.5 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 Dec 13 19:38:53 2020

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