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Iodine in PDB 5ijs: Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog

Enzymatic activity of Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog

All present enzymatic activity of Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog, PDB code: 5ijs 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) 40.00 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 53.750, 63.450, 70.550, 99.33, 105.91, 99.51
R / Rfree (%) 20.3 / 23.9

Other elements in 5ijs:

The structure of Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog also contains other interesting chemical elements:

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

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog (pdb code 5ijs). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog, PDB code: 5ijs:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 5ijs

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Iodine binding site 1 out of 6 in the Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog


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 with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I907

b:69.5
occ:0.50
NH2 A:ARG393 3.5 42.4 1.0
C A:MET232 3.7 27.8 1.0
N A:MET232 3.8 28.0 1.0
CA A:MET232 3.8 28.3 1.0
N A:TYR233 3.9 27.9 1.0
O A:MET232 4.1 27.3 1.0
C A:SER231 4.2 29.7 1.0
OG A:SER240 4.2 34.0 1.0
CG2 A:VAL385 4.2 33.0 1.0
CB A:SER231 4.3 35.2 1.0
CB A:TYR233 4.4 27.5 1.0
CE1 A:HIS242 4.4 39.1 1.0
O A:SER231 4.6 29.3 1.0
CA A:TYR233 4.6 27.8 1.0
CZ A:ARG393 4.6 42.3 1.0
O A:HOH1017 4.7 31.4 1.0
CA A:SER231 4.8 33.0 1.0
CB A:SER240 4.9 33.2 1.0
NH1 A:ARG393 4.9 42.9 1.0

Iodine binding site 2 out of 6 in 5ijs

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Iodine binding site 2 out of 6 in the Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog


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 with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I908

b:91.4
occ:0.55
NE2 A:HIS251 3.7 33.1 1.0
CD2 A:HIS251 3.7 32.3 1.0
N A:ARG252 3.9 27.9 1.0
CB A:ASN250 3.9 36.2 1.0
CB A:ARG252 3.9 28.3 1.0
CG A:ARG252 3.9 28.4 1.0
N A:HIS251 4.0 30.8 1.0
CE1 A:HIS251 4.1 32.3 1.0
CG A:HIS251 4.2 31.1 1.0
CD A:ARG252 4.3 29.5 1.0
CG A:ASN250 4.3 39.7 1.0
ND1 A:HIS251 4.4 31.3 1.0
CA A:ASN250 4.4 34.7 1.0
C A:ASN250 4.5 32.8 1.0
CA A:ARG252 4.5 27.7 1.0
OD1 A:ASN250 4.6 39.8 1.0
CA A:HIS251 4.8 29.6 1.0
C A:HIS251 4.8 28.1 1.0
NE A:ARG252 4.9 30.0 1.0

Iodine binding site 3 out of 6 in 5ijs

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Iodine binding site 3 out of 6 in the Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog


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 with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I909

b:42.4
occ:1.00
N A:ASN230 3.6 32.4 1.0
NH1 A:ARG391 3.7 35.8 1.0
CA A:GLY229 4.0 29.8 1.0
CD2 A:LEU389 4.0 38.5 1.0
N A:SER231 4.0 33.0 1.0
CG1 A:VAL385 4.1 30.5 1.0
O A:SER231 4.2 29.3 1.0
C A:GLY229 4.2 31.9 1.0
CE A:LYS208 4.3 31.2 1.0
CB A:ASN230 4.4 30.7 1.0
CG A:LYS208 4.4 28.2 1.0
CA A:ASN230 4.4 32.1 1.0
CD1 A:LEU389 4.7 36.9 1.0
CG A:LEU389 4.7 35.0 1.0
CZ A:ARG391 4.7 34.0 1.0
C A:ASN230 4.7 31.6 1.0
NH2 A:ARG391 4.8 35.8 1.0
CD A:LYS208 4.8 30.8 1.0
CA A:SER231 4.9 33.0 1.0
CB A:SER231 5.0 35.2 1.0
C A:SER231 5.0 29.7 1.0

Iodine binding site 4 out of 6 in 5ijs

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Iodine binding site 4 out of 6 in the Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog


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 with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I910

b:49.1
occ:0.45
OD1 A:ASP782 3.4 48.2 1.0
CG A:ASP782 3.6 47.8 1.0
CA A:SER636 3.9 37.1 1.0
N A:ASP782 3.9 40.9 1.0
N A:ALA781 3.9 36.5 1.0
OD2 A:ASP782 4.0 50.5 1.0
CG2 A:THR634 4.1 33.5 1.0
CB A:SER636 4.1 39.6 1.0
CA A:GLY729 4.1 26.9 1.0
CB A:ALA781 4.1 36.8 1.0
CB A:ASP782 4.2 45.8 1.0
CB A:PRO780 4.3 38.2 1.0
O A:ILE635 4.3 36.1 1.0
CA A:ALA781 4.4 37.5 1.0
N A:SER636 4.4 36.4 1.0
C A:ALA781 4.6 38.4 1.0
O A:ASN728 4.6 28.7 1.0
C A:ILE635 4.7 35.2 1.0
CA A:ASP782 4.7 43.0 1.0
C A:PRO780 4.7 36.2 1.0
C A:GLY729 4.8 26.3 1.0
CA A:PRO780 4.9 36.9 1.0
N A:GLY729 5.0 27.7 1.0
C A:SER636 5.0 36.6 1.0
N A:LYS637 5.0 36.9 1.0

Iodine binding site 5 out of 6 in 5ijs

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Iodine binding site 5 out of 6 in the Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog


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 with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I911

b:49.2
occ:0.30
OE2 A:GLU847 2.8 51.2 1.0
N A:LEU788 3.6 31.4 1.0
CD A:GLU847 3.7 54.5 1.0
CG A:GLU847 3.7 50.1 1.0
CB A:PRO787 3.9 33.8 1.0
CA A:PRO787 4.0 33.6 1.0
O A:GLU847 4.1 33.3 1.0
CD2 A:LEU851 4.1 31.4 1.0
O A:LEU788 4.2 30.3 1.0
CB A:LEU851 4.2 29.6 1.0
CG A:ARG843 4.2 38.6 1.0
CD1 A:LEU851 4.3 30.9 1.0
C A:PRO787 4.3 32.6 1.0
CG A:LEU851 4.4 31.1 1.0
CB A:LEU788 4.4 30.5 1.0
CA A:LEU788 4.5 31.6 1.0
CD1 A:ILE848 4.6 37.3 1.0
C A:GLU847 4.6 37.4 1.0
CG A:LEU788 4.6 31.3 1.0
CB A:GLU847 4.6 44.4 1.0
CB A:ARG843 4.7 37.1 1.0
NE A:ARG843 4.8 42.2 1.0
C A:LEU788 4.8 31.8 1.0
OE1 A:GLU847 4.8 59.6 1.0
CD A:ARG843 4.9 41.0 1.0

Iodine binding site 6 out of 6 in 5ijs

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Iodine binding site 6 out of 6 in the Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog


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 with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I912

b:80.1
occ:0.40
NH1 A:ARG746 3.8 39.3 1.0
N A:GLU749 3.9 56.0 1.0
CA A:THR748 4.1 49.1 1.0
CB A:THR748 4.4 51.2 1.0
C A:THR748 4.4 54.2 1.0
CZ A:PHE625 4.5 82.0 1.0
CG2 A:THR748 4.6 50.8 1.0
CB A:GLU749 4.7 62.7 1.0
CA A:GLU749 4.8 58.6 1.0
O A:ARG606 4.9 48.2 1.0
CE2 A:TYR605 4.9 35.4 1.0
CD2 A:TYR605 4.9 35.9 1.0
CZ A:ARG746 5.0 38.3 1.0

Reference:

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
Page generated: Sun Dec 13 19:39:29 2020

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