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Iodine in PDB 1gw9: Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus

Enzymatic activity of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus

All present enzymatic activity of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus:
5.3.1.5;

Protein crystallography data

The structure of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus, PDB code: 1gw9 was solved by G.Evans, G.Bricogne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.05 / 1.55
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.354, 98.540, 102.507, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 18.8

Other elements in 1gw9:

The structure of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Iodine atom in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus (pdb code 1gw9). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 29 binding sites of Iodine where determined in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus, PDB code: 1gw9:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 29 in 1gw9

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Iodine binding site 1 out of 29 in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1391

b:26.2
occ:0.61
I A:IOD1392 2.1 28.0 0.3
CD2 A:HIS49 3.4 28.3 1.0
CG2 A:THR12 3.9 10.6 1.0
CG A:HIS49 4.0 25.1 1.0
CB A:HIS49 4.2 18.9 1.0
CG A:PRO87 4.3 16.6 1.0
CA A:ARG10 4.3 11.6 1.0
CB A:LYS85 4.3 13.1 1.0
CB A:ARG10 4.3 13.9 1.0
O A:HIS49 4.4 12.5 1.0
C A:HIS49 4.4 14.4 1.0
NE2 A:HIS49 4.4 28.4 1.0
CG A:ARG10 4.5 21.6 1.0
CG A:LYS85 4.6 22.2 1.0
N A:GLY50 4.6 10.2 1.0
C A:ARG10 4.7 13.7 1.0
O A:ARG10 4.7 13.6 1.0
CA A:GLY50 4.7 9.6 1.0
I A:IOD1393 4.8 32.0 0.3
CB A:PRO87 4.8 11.4 1.0
CD A:PRO87 4.9 11.2 1.0
CA A:HIS49 4.9 15.2 1.0

Iodine binding site 2 out of 29 in 1gw9

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Iodine binding site 2 out of 29 in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1392

b:28.0
occ:0.33
I A:IOD1391 2.1 26.2 0.6
I A:IOD1393 2.7 32.0 0.3
CG A:ARG10 3.9 21.6 1.0
CB A:ARG10 3.9 13.9 1.0
CG A:PRO283 4.0 16.3 1.0
CD A:ARG10 4.1 32.6 1.0
CB A:PRO87 4.3 11.4 1.0
CA A:PRO283 4.3 10.1 1.0
CB A:PRO283 4.3 12.1 1.0
CG A:PRO87 4.3 16.6 1.0
N A:PRO283 4.5 11.1 1.0
I A:IOD1394 4.5 31.4 0.2
CA A:ARG10 4.6 11.6 1.0
CD A:PRO283 4.7 11.8 1.0
CG2 A:THR12 4.7 10.6 1.0
O A:ARG10 4.8 13.6 1.0
CD2 A:HIS49 5.0 28.3 1.0

Iodine binding site 3 out of 29 in 1gw9

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Iodine binding site 3 out of 29 in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1393

b:32.0
occ:0.31
I A:IOD1394 2.6 31.4 0.2
I A:IOD1392 2.7 28.0 0.3
O A:SER281 3.7 18.2 1.0
CD A:PRO283 3.9 11.8 1.0
CD A:ARG10 3.9 32.6 1.0
N A:PRO283 4.0 11.1 1.0
CG A:PRO283 4.1 16.3 1.0
C A:GLY282 4.1 14.3 1.0
CA A:GLY282 4.1 11.5 1.0
CA A:PRO283 4.6 10.1 1.0
CG A:ARG10 4.7 21.6 1.0
C A:SER281 4.7 17.1 1.0
O A:GLY282 4.8 14.4 1.0
I A:IOD1391 4.8 26.2 0.6
O A:HOH2160 4.8 31.1 1.0
CB A:PRO283 5.0 12.1 1.0
N A:GLY282 5.0 11.9 1.0
OE1 A:GLU132 5.0 87.8 1.0

Iodine binding site 4 out of 29 in 1gw9

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Iodine binding site 4 out of 29 in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1394

b:31.4
occ:0.21
I A:IOD1393 2.6 32.0 0.3
CD A:GLU132 2.6 81.5 1.0
OE1 A:GLU132 2.7 87.8 1.0
OE2 A:GLU132 2.7 82.5 1.0
CG A:GLU132 3.6 39.0 1.0
O A:HOH2160 3.7 31.1 1.0
CD A:PRO283 3.9 11.8 1.0
CG A:PRO283 4.2 16.3 1.0
CB A:GLU132 4.3 16.5 1.0
I A:IOD1392 4.5 28.0 0.3
CB A:PRO87 4.5 11.4 1.0
CA A:GLY282 4.7 11.5 1.0
N A:PRO283 4.8 11.1 1.0
O A:HOH2158 4.9 30.0 1.0

Iodine binding site 5 out of 29 in 1gw9

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Iodine binding site 5 out of 29 in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1395

b:16.3
occ:0.53
I A:IOD1396 3.3 46.3 0.3
NE2 A:GLN234 3.6 12.4 1.0
CB A:ALA238 3.9 11.9 1.0
CE3 A:TRP237 3.9 11.1 1.0
CZ3 A:TRP237 4.0 12.7 1.0
CG A:GLN234 4.0 11.6 1.0
CD A:GLN234 4.3 17.5 1.0
CD1 A:LEU200 4.4 10.4 1.0
O A:GLN234 4.5 10.0 1.0
CA A:ALA238 4.7 11.3 1.0
OE1 A:GLU204 4.8 24.0 0.5
CB A:LEU200 5.0 8.7 1.0

Iodine binding site 6 out of 29 in 1gw9

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Iodine binding site 6 out of 29 in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1396

b:46.3
occ:0.26
OE1 A:GLU204 2.8 24.0 0.5
I A:IOD1397 2.8 30.8 0.2
I A:IOD1395 3.3 16.3 0.5
CB A:ALA238 3.7 11.9 1.0
CD A:GLU204 3.8 34.9 0.5
CG A:GLU204 4.0 23.8 0.6
CG A:GLU204 4.1 21.2 0.5
O A:LEU200 4.4 12.4 1.0
CB A:LEU200 4.4 8.7 1.0
CD A:GLU204 4.5 44.6 0.6
I A:IOD1398 4.5 37.1 0.3
OE1 A:GLU204 4.6 40.0 0.6
CA A:ALA238 4.7 11.3 1.0
CD2 A:LEU200 4.8 12.6 1.0
C A:LEU200 4.9 12.3 1.0
OE2 A:GLU204 4.9 21.5 0.5

Iodine binding site 7 out of 29 in 1gw9

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Iodine binding site 7 out of 29 in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1397

b:30.8
occ:0.24
I A:IOD1396 2.8 46.3 0.3
O A:LEU200 3.0 12.4 1.0
I A:IOD1398 3.1 37.1 0.3
CG A:GLU204 3.4 23.8 0.6
CG A:GLU204 3.6 21.2 0.5
CE A:LYS240 3.7 16.5 1.0
CG2 A:ILE203 3.8 12.6 1.0
C A:LEU200 3.9 12.3 1.0
CG A:LYS240 3.9 11.7 1.0
CB A:ILE203 3.9 11.1 1.0
CD A:GLU204 4.0 44.6 0.6
CA A:LEU200 4.0 8.8 1.0
OE1 A:GLU204 4.1 24.0 0.5
CD2 A:LEU200 4.2 12.6 1.0
CB A:LEU200 4.2 8.7 1.0
CD A:GLU204 4.2 34.9 0.5
OE2 A:GLU204 4.3 39.9 0.6
N A:GLU204 4.3 11.5 0.5
N A:GLU204 4.3 12.1 0.6
CD A:LYS240 4.4 14.5 1.0
CB A:GLU204 4.5 14.5 0.6
CD1 A:ILE203 4.7 14.2 1.0
CB A:GLU204 4.8 13.4 0.5
CA A:GLU204 4.8 11.8 0.5
CA A:GLU204 4.8 12.6 0.6
C A:ILE203 4.8 14.0 1.0
NZ A:LYS240 4.8 12.5 1.0
OE1 A:GLU204 4.9 40.0 0.6
CG A:LEU200 4.9 11.4 1.0
CA A:ILE203 4.9 8.7 1.0
CG1 A:ILE203 5.0 10.3 1.0
CB A:ALA238 5.0 11.9 1.0

Iodine binding site 8 out of 29 in 1gw9

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Iodine binding site 8 out of 29 in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1398

b:37.1
occ:0.35
OE2 A:GLU204 1.5 39.9 0.6
CD A:GLU204 2.1 44.6 0.6
CG A:GLU204 2.7 23.8 0.6
I A:IOD1399 3.0 48.2 0.3
OE1 A:GLU204 3.0 40.0 0.6
I A:IOD1397 3.1 30.8 0.2
CG A:GLU204 3.5 21.2 0.5
CB A:PRO209 3.8 14.1 1.0
CB A:GLU204 3.8 14.5 0.6
CA A:GLU204 3.8 12.6 0.6
CA A:GLU204 3.8 11.8 0.5
CE A:LYS240 3.8 16.5 1.0
CG2 A:ILE203 4.2 12.6 1.0
N A:GLU204 4.2 12.1 0.6
N A:GLU204 4.2 11.5 0.5
CB A:GLU204 4.2 13.4 0.5
NZ A:LYS240 4.2 12.5 1.0
I A:IOD1396 4.5 46.3 0.3
C A:ILE203 4.6 14.0 1.0
CG A:PRO209 4.7 19.2 1.0
CD A:GLU204 4.7 34.9 0.5
O A:ILE203 4.8 13.7 1.0
OE1 A:GLU204 4.8 24.0 0.5
CA A:PRO209 5.0 12.2 1.0
O A:PRO209 5.0 14.8 1.0

Iodine binding site 9 out of 29 in 1gw9

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Iodine binding site 9 out of 29 in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1399

b:48.2
occ:0.35
NZ A:LYS240 3.0 12.5 1.0
I A:IOD1398 3.0 37.1 0.3
CE A:LYS240 3.5 16.5 1.0
CB A:PRO209 3.6 14.1 1.0
OE2 A:GLU204 3.7 39.9 0.6
C A:PRO209 3.8 16.0 1.0
O A:PRO209 3.8 14.8 1.0
N A:GLU210 3.9 13.5 1.0
CA A:GLU210 4.1 13.6 1.0
O A:HOH2232 4.2 26.9 1.0
CA A:PRO209 4.4 12.2 1.0
O A:HOH2231 4.5 33.5 1.0
CD A:GLU204 4.6 44.6 0.6
CG A:PRO209 4.7 19.2 1.0
CB A:GLU210 4.7 15.2 1.0
CD A:LYS240 4.9 14.5 1.0

Iodine binding site 10 out of 29 in 1gw9

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Iodine binding site 10 out of 29 in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1400

b:25.5
occ:0.29
I A:IOD1401 2.6 21.3 0.2
O A:HOH2163 2.8 31.6 1.0
SD A:MET158 3.1 16.7 0.6
CA A:GLY138 3.7 9.4 1.0
CZ A:PHE162 3.7 14.9 1.0
CD2 A:PHE104 3.8 12.5 1.0
I A:IOD1404 3.9 26.5 0.2
CE A:MET158 3.9 13.4 0.6
CE2 A:PHE162 3.9 16.8 1.0
N A:GLY138 4.0 9.0 1.0
CG A:GLU141 4.1 10.0 1.0
CE2 A:PHE104 4.3 14.4 1.0
I A:IOD1414 4.4 23.6 0.3
CG A:MET158 4.5 13.4 0.6
CG A:MET158 4.6 13.3 0.4
CG A:PHE104 4.6 10.3 1.0
SD A:MET158 4.6 16.4 0.4
CB A:ALA136 4.7 11.0 1.0
O A:HOH2202 4.7 18.5 1.0
CD A:GLU141 4.7 17.3 1.0
C A:TRP137 4.8 11.1 1.0
CB A:PHE104 4.8 9.3 1.0
CE1 A:PHE162 4.9 16.3 1.0
OE2 A:GLU141 5.0 14.3 1.0

Reference:

G.Evans, G.Bricogne. Triiodide Derivatization and Combinatorial Counter-Ion Replacement: Two Methods For Enhancing Phasing Signal Using Laboratory Cu Kalpha X-Ray Equipment Acta Crystallogr.,Sect.D V. 58 976 2002.
ISSN: ISSN 0907-4449
PubMed: 12037300
DOI: 10.1107/S0907444902005486
Page generated: Sun Dec 13 19:19:38 2020

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