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Iodine in PDB 2xr9: Crystal Structure of Autotaxin (ENPP2)

Enzymatic activity of Crystal Structure of Autotaxin (ENPP2)

All present enzymatic activity of Crystal Structure of Autotaxin (ENPP2):
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Autotaxin (ENPP2), PDB code: 2xr9 was solved by S.Kamtekar, J.Hausmann, J.E.Day, E.Christodoulou, A.Perrakis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 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 (%) 17.3 / 22.1

Other elements in 2xr9:

The structure of Crystal Structure of Autotaxin (ENPP2) also contains other interesting chemical elements:

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

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Autotaxin (ENPP2) (pdb code 2xr9). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 28 binding sites of Iodine where determined in the Crystal Structure of Autotaxin (ENPP2), PDB code: 2xr9:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 28 in 2xr9

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Iodine binding site 1 out of 28 in the Crystal Structure of Autotaxin (ENPP2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1871

b:30.3
occ:1.00
N A:ASN230 3.5 24.1 1.0
NH1 A:ARG391 3.8 27.2 1.0
CA A:GLY229 3.9 23.9 1.0
N A:SER231 4.0 27.2 1.0
C A:GLY229 4.2 25.1 1.0
O A:SER231 4.3 25.6 1.0
CG1 A:VAL385 4.3 28.1 1.0
CG A:LYS208 4.3 25.8 1.0
CA A:ASN230 4.4 25.1 1.0
CB A:ASN230 4.5 24.7 1.0
CD2 A:LEU389 4.5 29.8 1.0
CE A:LYS208 4.6 30.5 1.0
CD1 A:LEU389 4.6 27.6 1.0
C A:ASN230 4.7 26.8 1.0
CB A:SER231 4.8 30.9 1.0
CG A:LEU389 4.8 26.1 1.0
CA A:SER231 4.8 28.3 1.0
CZ A:ARG391 4.9 27.9 1.0

Iodine binding site 2 out of 28 in 2xr9

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Iodine binding site 2 out of 28 in the Crystal Structure of Autotaxin (ENPP2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1872

b:33.9
occ:0.68
NH1 A:ARG843 3.2 44.9 1.0
O A:HOH2273 3.5 23.4 1.0
N A:LEU788 3.6 24.2 1.0
CA A:PRO787 4.0 28.6 1.0
CG A:ARG843 4.1 31.2 1.0
O A:GLU847 4.2 24.4 1.0
CB A:LEU851 4.3 22.0 1.0
CB A:PRO787 4.4 29.7 1.0
C A:PRO787 4.4 26.7 1.0
CB A:LEU788 4.4 22.2 1.0
CD2 A:LEU851 4.4 22.6 1.0
CB A:GLU847 4.4 31.4 1.0
CZ A:ARG843 4.5 43.9 1.0
CD1 A:ILE848 4.5 25.4 1.0
C A:GLU847 4.5 27.4 1.0
O A:LEU788 4.5 21.8 1.0
CA A:LEU788 4.5 24.2 1.0
CG A:LEU788 4.6 26.6 1.0
CD1 A:LEU851 4.6 21.9 1.0
CB A:ARG843 4.6 29.3 1.0
CD A:ARG843 4.7 34.9 1.0
CG A:LEU851 4.7 19.3 1.0
N A:ILE848 4.9 26.3 1.0
C A:LEU788 4.9 22.9 1.0

Iodine binding site 3 out of 28 in 2xr9

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Iodine binding site 3 out of 28 in the Crystal Structure of Autotaxin (ENPP2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1873

b:43.6
occ:0.70
OE1 A:GLN716 2.7 36.7 1.0
I A:IOD1883 3.1 42.8 0.2
N A:PHE679 3.8 29.1 1.0
CD A:GLN716 3.9 33.5 1.0
O A:PHE679 3.9 24.5 1.0
CD1 A:TRP712 4.0 24.7 1.0
CB A:PHE679 4.2 30.2 1.0
NE1 A:TRP712 4.4 26.7 1.0
CE2 A:TYR684 4.4 41.0 1.0
CD A:PRO683 4.4 35.6 1.0
CA A:PHE679 4.4 28.9 1.0
N A:SCN1864 4.5 69.3 1.0
CD2 A:PHE679 4.6 34.8 1.0
C A:PHE679 4.6 27.3 1.0
CA A:GLY678 4.6 29.3 1.0
C A:GLY678 4.7 30.4 1.0
NE2 A:GLN716 4.7 33.9 1.0
CB A:GLN716 4.8 27.9 1.0
CG A:PHE679 4.9 33.1 1.0
CG A:GLN716 4.9 30.6 1.0
CA A:ALA713 5.0 26.9 1.0

Iodine binding site 4 out of 28 in 2xr9

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Iodine binding site 4 out of 28 in the Crystal Structure of Autotaxin (ENPP2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1874

b:43.9
occ:0.53
O A:HOH2042 3.5 24.1 1.0
N A:GLY387 3.8 27.6 1.0
CA A:GLY387 3.8 25.9 1.0
ND1 A:HIS452 3.9 32.6 1.0
O A:VAL453 4.0 28.9 1.0
CG A:HIS452 4.1 28.2 1.0
CB A:ALA454 4.2 34.0 1.0
CB A:PRO386 4.3 30.8 1.0
CE1 A:HIS452 4.3 31.0 1.0
CB A:HIS452 4.4 29.0 1.0
C A:PRO386 4.6 28.0 1.0
C A:VAL453 4.6 30.8 1.0
CD2 A:HIS452 4.6 29.1 1.0
CG A:PRO386 4.7 32.0 1.0
CA A:ALA454 4.7 33.9 1.0
NE2 A:HIS452 4.8 26.9 1.0
C A:GLY387 5.0 24.2 1.0

Iodine binding site 5 out of 28 in 2xr9

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Iodine binding site 5 out of 28 in the Crystal Structure of Autotaxin (ENPP2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1875

b:42.2
occ:0.77
NH2 A:ARG393 3.6 36.5 1.0
C A:MET232 3.8 27.4 1.0
O A:MET232 3.9 28.1 1.0
N A:TYR233 4.0 27.0 1.0
N A:MET232 4.0 26.4 1.0
CA A:MET232 4.1 26.5 1.0
CE1 A:HIS242 4.1 46.0 1.0
CG2 A:VAL385 4.2 29.2 1.0
CB A:TYR233 4.3 29.1 1.0
OG A:SER240 4.4 37.8 1.0
CB A:SER231 4.4 30.9 1.0
CZ A:ARG393 4.5 39.0 1.0
NH1 A:ARG393 4.5 38.8 1.0
CB A:SER240 4.5 35.0 1.0
C A:SER231 4.5 26.8 1.0
CA A:TYR233 4.6 27.2 1.0
NE2 A:HIS242 4.8 47.3 1.0
ND1 A:HIS242 5.0 45.7 1.0

Iodine binding site 6 out of 28 in 2xr9

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Iodine binding site 6 out of 28 in the Crystal Structure of Autotaxin (ENPP2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1876

b:40.9
occ:0.38
OG A:SER278 2.5 47.3 1.0
CG2 A:VAL277 3.6 42.5 1.0
CB A:SER278 3.9 44.8 1.0
CB A:LYS80 3.9 41.9 1.0
N A:SER278 3.9 41.5 1.0
CB A:SER276 4.3 43.1 1.0
C A:LYS80 4.4 44.8 1.0
N A:VAL277 4.4 39.8 1.0
O A:LYS80 4.4 47.0 1.0
CA A:SER278 4.5 42.6 1.0
N A:SER81 4.5 45.0 1.0
CA A:LYS80 4.8 43.2 1.0
C A:VAL277 4.8 40.9 1.0
CA A:SER81 4.8 46.8 1.0
CB A:VAL277 4.8 40.6 1.0
C A:SER276 4.8 40.1 1.0
CG A:LYS80 4.9 41.8 1.0
CA A:VAL277 4.9 39.8 1.0
OG A:SER276 4.9 45.5 1.0
CA A:SER276 4.9 40.6 1.0

Iodine binding site 7 out of 28 in 2xr9

Go back to Iodine Binding Sites List in 2xr9
Iodine binding site 7 out of 28 in the Crystal Structure of Autotaxin (ENPP2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1877

b:45.5
occ:0.46
OG A:SER846 3.5 38.4 1.0
N A:SER846 3.6 29.6 1.0
CB A:SER846 3.7 32.9 1.0
O A:HOH2179 3.9 19.9 1.0
O A:HOH2316 4.1 19.6 1.0
N A:TYR845 4.2 28.1 1.0
CA A:SER846 4.3 30.7 1.0
CB A:SER844 4.4 31.8 1.0
CB A:TYR845 4.5 28.5 1.0
C A:TYR845 4.5 27.6 1.0
CG A:PRO541 4.6 43.7 1.0
CA A:TYR845 4.6 27.3 1.0
CD A:PRO541 4.6 47.2 1.0
OG A:SER844 4.7 30.1 1.0
C A:SER844 4.9 28.6 1.0

Iodine binding site 8 out of 28 in 2xr9

Go back to Iodine Binding Sites List in 2xr9
Iodine binding site 8 out of 28 in the Crystal Structure of Autotaxin (ENPP2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1878

b:0.4
occ:0.52
CD2 A:LEU124 2.8 48.3 1.0
CD1 A:LEU124 2.9 48.5 1.0
CG A:LEU124 3.1 47.0 1.0
CG A:GLN134 3.4 50.4 1.0
CD A:GLN134 3.5 52.0 1.0
NE2 A:GLN134 3.5 50.7 1.0
CD2 A:TYR133 3.6 41.0 1.0
OE1 A:GLN344 3.7 43.7 1.0
CD A:GLN344 3.7 43.8 1.0
CB A:GLN344 3.8 39.4 1.0
CE2 A:TYR133 3.9 43.0 1.0
NE2 A:GLN344 3.9 46.1 1.0
OE1 A:GLN134 4.1 54.1 1.0
O A:GLN344 4.2 36.7 1.0
CG A:GLN344 4.3 42.0 1.0
SG A:CYS129 4.3 42.0 1.0
CA A:GLN344 4.6 38.3 1.0
CB A:LEU124 4.6 48.2 1.0
C A:GLN344 4.7 37.4 1.0
CB A:GLN134 4.8 49.6 1.0
CG A:TYR133 4.8 38.3 1.0

Iodine binding site 9 out of 28 in 2xr9

Go back to Iodine Binding Sites List in 2xr9
Iodine binding site 9 out of 28 in the Crystal Structure of Autotaxin (ENPP2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1879

b:42.6
occ:0.46
ND1 A:HIS281 3.0 40.7 1.0
O A:HOH2065 3.1 26.0 1.0
OG1 A:THR334 3.2 27.8 1.0
CD1 A:ILE331 3.2 37.8 1.0
OG A:SER307 3.4 27.2 1.0
CE1 A:HIS281 3.5 40.7 1.0
CG A:HIS281 3.7 35.3 1.0
CB A:THR334 3.8 28.2 1.0
CB A:SER307 3.9 26.0 1.0
CA A:ILE331 3.9 30.7 1.0
CB A:HIS281 4.1 33.3 1.0
CG2 A:THR334 4.2 27.0 1.0
CZ A:PHE305 4.3 28.3 1.0
CG1 A:ILE331 4.3 33.8 1.0
O A:GLU330 4.3 35.3 1.0
NE2 A:HIS281 4.4 37.4 1.0
N A:ILE331 4.4 33.2 1.0
CD2 A:HIS281 4.5 39.3 1.0
CB A:ILE331 4.6 29.8 1.0
CE2 A:PHE305 4.6 27.8 1.0
C A:GLU330 4.6 34.9 1.0
CG2 A:ILE331 4.8 29.0 1.0
O A:ILE331 4.9 29.6 1.0
C A:ILE331 4.9 30.3 1.0

Iodine binding site 10 out of 28 in 2xr9

Go back to Iodine Binding Sites List in 2xr9
Iodine binding site 10 out of 28 in the Crystal Structure of Autotaxin (ENPP2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1880

b:45.5
occ:0.47
CG A:ARG252 3.7 25.9 1.0
CE1 A:HIS251 3.7 33.9 1.0
CB A:ARG252 3.8 25.0 1.0
N A:ARG252 3.9 24.1 1.0
ND1 A:HIS251 3.9 35.1 1.0
CB A:ASN250 4.0 32.4 1.0
CD A:ARG252 4.0 28.4 1.0
NE2 A:HIS251 4.1 32.5 1.0
N A:HIS251 4.2 26.2 1.0
CG A:HIS251 4.4 28.2 1.0
CG A:ASN250 4.4 40.2 1.0
CA A:ARG252 4.5 23.6 1.0
CD2 A:HIS251 4.5 26.8 1.0
C A:ASN250 4.5 27.9 1.0
CA A:ASN250 4.6 31.5 1.0
OD1 A:ASN250 4.6 44.2 1.0
NE A:ARG252 4.7 27.3 1.0
O A:HOH2056 4.9 32.3 1.0
C A:HIS251 4.9 22.1 1.0
CA A:HIS251 5.0 24.4 1.0

Reference:

J.Hausmann, S.Kamtekar, E.Christodoulou, J.E.Day, T.Wu, Z.Fulkerson, H.M.Albers, L.A.Van Meeteren, A.J.Houben, L.Van Zeijl, S.Jansen, M.Andries, T.Hall, L.E.Pegg, T.E.Benson, M.Kasiem, K.Harlos, C.W.Kooi, S.S.Smyth, H.Ovaa, M.Bollen, A.J.Morris, W.H.Moolenaar, A.Perrakis. Structural Basis of Substrate Discrimination and Integrin Binding By Autotaxin. Nat. Struct. Mol. Biol. V. 18 198 2011.
ISSN: ESSN 1545-9985
PubMed: 21240271
DOI: 10.1038/NSMB.1980
Page generated: Sun Dec 13 19:25:43 2020

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