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Iodine in PDB 6xl8: Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation

Enzymatic activity of Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation

All present enzymatic activity of Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation:
2.8.2.30;

Protein crystallography data

The structure of Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation, PDB code: 6xl8 was solved by L.C.Pedersen, J.Liu, R.Wander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.70 / 2.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.217, 147.469, 51.037, 90, 94.35, 90
R / Rfree (%) 21.6 / 27.1

Other elements in 6xl8:

The structure of Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation (pdb code 6xl8). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation, PDB code: 6xl8:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 6xl8

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Iodine binding site 1 out of 9 in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation


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 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:65.8
occ:0.57
 N A:PHE343 4.0 40.4 1.0
CB A:PRO350 4.1 39.2 1.0
C A:TYR342 4.1 38.9 1.0
CG A:PRO350 4.1 41.8 1.0
CB A:PHE343 4.1 43.2 1.0
CA A:PHE343 4.4 42.4 1.0
CA A:TYR342 4.4 38.7 1.0
N A:TYR342 4.5 39.6 1.0
O A:TYR342 4.5 41.7 1.0
CB A:PHE341 4.5 35.9 1.0
CA A:PRO350 4.5 40.5 1.0
CG A:PRO319 4.7 36.9 1.0
CD1 A:PHE343 4.9 39.8 1.0
C A:PHE341 4.9 35.5 1.0
CD A:PRO319 4.9 39.7 1.0
CG A:PHE343 4.9 42.4 1.0

Iodine binding site 2 out of 9 in 6xl8

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Iodine binding site 2 out of 9 in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation


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 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:59.7
occ:0.54
 O3 C:GNS1 3.8 49.5 1.0
O6A C:IDS2 3.9 41.4 1.0
C6 C:IDS2 4.0 48.8 1.0
C5 C:IDS2 4.0 47.8 1.0
CG2 A:THR256 4.1 47.0 1.0
C3 C:GNS1 4.3 48.1 1.0
O4 C:GNS1 4.4 49.4 1.0
OG1 A:THR256 4.5 48.7 1.0
O6B C:IDS2 4.6 48.7 1.0
O5 C:IDS2 4.7 46.7 1.0
CB A:THR256 4.7 46.5 1.0
CA A:THR256 4.8 43.4 1.0
NA A:NA501 4.9 43.1 1.0
CB A:LYS259 5.0 45.0 1.0

Iodine binding site 3 out of 9 in 6xl8

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Iodine binding site 3 out of 9 in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation


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 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I505

b:75.3
occ:0.53
 NH1 A:ARG200 3.4 61.9 1.0
N A:LEU152 3.5 47.6 1.0
CG A:LEU152 3.9 45.5 1.0
CA A:GLN151 3.9 50.8 1.0
CZ A:ARG200 4.0 60.2 1.0
CD A:ARG200 4.1 49.0 1.0
C A:GLN151 4.2 45.5 1.0
CB A:LEU152 4.2 44.4 1.0
NE A:ARG200 4.3 55.5 1.0
CD1 A:LEU152 4.3 35.3 1.0
O A:LYS150 4.5 49.4 1.0
CA A:LEU152 4.5 39.9 1.0
CB A:GLN151 4.5 40.4 1.0
CG A:GLN151 4.7 46.5 1.0
NH2 A:ARG200 4.8 53.0 1.0

Iodine binding site 4 out of 9 in 6xl8

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Iodine binding site 4 out of 9 in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation


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 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I504

b:49.1
occ:0.79
 CE B:LYS259 3.8 41.9 1.0
OG1 B:THR256 3.9 42.0 1.0
NZ B:LYS259 4.0 43.8 1.0
CG2 B:THR256 4.0 40.6 1.0
C3 D:GNS2 4.0 42.4 1.0
O3 D:GNS2 4.1 43.5 1.0
CA B:THR256 4.2 36.5 1.0
CB B:THR256 4.3 40.6 1.0
C6 D:IDS3 4.3 45.5 1.0
O6B D:IDS3 4.4 40.0 1.0
O4 D:GNS2 4.4 46.2 1.0
C5 D:IDS3 4.5 42.1 1.0
O4 D:BDP1 4.7 43.9 1.0
O6A D:IDS3 4.7 46.2 1.0
CD B:LYS259 4.7 42.7 1.0
NE B:ARG260 4.7 65.2 1.0
CB B:LYS259 4.8 40.9 1.0
C4 D:GNS2 4.9 44.7 1.0
CD B:ARG260 4.9 55.6 1.0
O5 D:IDS3 4.9 39.5 1.0

Iodine binding site 5 out of 9 in 6xl8

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Iodine binding site 5 out of 9 in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation


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 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I505

b:54.1
occ:0.62
 NE B:ARG274 3.5 41.8 1.0
OE1 B:GLU378 3.5 69.8 1.0
CD B:GLU378 3.5 57.4 1.0
CG B:GLU378 3.6 46.9 1.0
NH2 B:ARG274 3.7 44.0 1.0
CZ B:ARG274 4.1 43.7 1.0
OE2 B:GLU378 4.1 60.7 1.0
CG2 B:VAL379 4.2 34.3 1.0
NE B:ARG382 4.2 51.0 1.0
CD B:ARG382 4.2 43.3 1.0
CB B:GLU378 4.3 41.6 1.0
CE2 B:PHE271 4.5 40.8 1.0
CG B:ARG274 4.5 45.3 1.0
CZ B:PHE271 4.5 40.5 1.0
CD B:ARG274 4.6 44.5 1.0
N B:VAL379 4.7 34.7 1.0
C B:GLU378 4.7 35.9 1.0
O B:GLU378 5.0 38.9 1.0
CA B:VAL379 5.0 40.0 1.0

Iodine binding site 6 out of 9 in 6xl8

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Iodine binding site 6 out of 9 in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation


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 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I506

b:65.7
occ:0.61
 N B:PHE343 3.8 41.4 1.0
C B:TYR342 3.8 43.1 1.0
CB B:PRO350 3.9 37.8 1.0
CG B:PRO350 4.1 39.6 1.0
CA B:TYR342 4.2 39.9 1.0
O B:TYR342 4.2 42.2 1.0
N B:TYR342 4.2 36.5 1.0
CB B:PHE341 4.3 34.0 1.0
CA B:PHE343 4.3 40.7 1.0
CB B:PHE343 4.3 42.3 1.0
CA B:PRO350 4.4 44.8 1.0
CG B:PRO319 4.6 39.4 1.0
C B:PHE341 4.6 36.3 1.0
CD B:PRO319 4.7 43.6 1.0
CD1 B:PHE343 4.9 45.5 1.0

Iodine binding site 7 out of 9 in 6xl8

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Iodine binding site 7 out of 9 in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation


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 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I507

b:63.3
occ:0.71
 N B:LYS293 3.7 39.6 1.0
CA B:LYS293 3.8 39.4 1.0
CB B:LYS293 3.9 36.5 1.0
CD1 B:PHE390 4.1 34.1 1.0
CE1 B:PHE390 4.2 34.8 1.0
CB B:ALA292 4.2 34.8 1.0
C B:ALA292 4.4 35.4 1.0
CG2 B:ILE290 4.6 33.5 1.0
CG B:LYS293 4.6 46.3 1.0
CE B:LYS293 4.7 55.5 1.0
OE1 B:GLU296 4.7 61.1 1.0
CA B:ALA292 4.9 36.6 1.0
O B:ALA292 5.0 36.3 1.0

Iodine binding site 8 out of 9 in 6xl8

Go back to Iodine Binding Sites List in 6xl8
Iodine binding site 8 out of 9 in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation


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 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I508

b:59.5
occ:0.73
 CD B:ARG274 3.9 44.5 1.0
CB B:SER268 4.1 32.1 1.0
NH1 B:ARG274 4.2 45.3 1.0
CA B:SER268 4.2 34.2 1.0
CB B:ARG274 4.5 46.3 1.0
CG B:ARG274 4.8 45.3 1.0
NE B:ARG274 5.0 41.8 1.0

Iodine binding site 9 out of 9 in 6xl8

Go back to Iodine Binding Sites List in 6xl8
Iodine binding site 9 out of 9 in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation


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 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I509

b:79.3
occ:0.71
 CD B:PRO264 4.1 38.3 1.0
OH B:NPO502 4.2 43.2 1.0
O2 D:BDP1 4.2 52.0 1.0
CG B:PRO264 4.6 35.4 1.0
C2 D:BDP1 4.8 45.5 1.0

Reference:

R.Wander, A.M.Kaminski, Y.Xu, V.Pagadala, J.M.Krahn, T.Q.Pham, J.Liu, L.C.Pedersen. Deciphering the Substrate Recognition Mechanisms of the Heparan Sulfate 3-O-Sulfotransferase-3 Rsc Chem Biol 2021.
ISSN: ESSN 2633-0679
DOI: 10.1039/D1CB00079A
Page generated: Mon Aug 12 00:32:38 2024

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