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Chlorine in PDB 5t03: Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Glucuronic Acid Containing Hexasaccharide Substrate

Protein crystallography data

The structure of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Glucuronic Acid Containing Hexasaccharide Substrate, PDB code: 5t03 was solved by L.C.Pedersen, A.F.Moon, J.M.Krahn, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.65 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.778, 128.396, 179.722, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21.2

Other elements in 5t03:

The structure of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Glucuronic Acid Containing Hexasaccharide Substrate also contains other interesting chemical elements:

Sodium (Na) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Glucuronic Acid Containing Hexasaccharide Substrate (pdb code 5t03). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Glucuronic Acid Containing Hexasaccharide Substrate, PDB code: 5t03:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5t03

Go back to Chlorine Binding Sites List in 5t03
Chlorine binding site 1 out of 5 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Glucuronic Acid Containing Hexasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Glucuronic Acid Containing Hexasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1424

b:28.8
occ:1.00
 O A:HOH1594 2.9 23.1 1.0
N A:LYS1305 3.3 19.5 1.0
O A:HOH1582 3.4 63.2 1.0
CG A:LYS1305 3.4 22.1 1.0
CA A:PHE1302 3.5 26.6 1.0
C A:PHE1302 3.6 20.9 1.0
N A:ARG1304 3.6 23.9 1.0
NZ A:LYS1305 3.7 31.3 1.0
CB A:PHE1302 3.7 19.0 1.0
CB A:ARG1304 3.8 27.1 1.0
CD A:LYS1305 3.8 23.9 1.0
CD1 A:PHE1302 3.8 23.8 1.0
CB A:LYS1305 3.9 21.4 1.0
O A:PHE1302 4.0 24.6 1.0
N A:GLN1303 4.0 19.7 1.0
CA B:ALA239 4.0 28.8 1.0
CA A:ARG1304 4.0 25.2 1.0
C A:ARG1304 4.1 25.5 1.0
CA A:LYS1305 4.2 24.3 1.0
CG A:PHE1302 4.2 20.4 1.0
O B:HOH1570 4.2 37.9 1.0
CB B:ALA239 4.3 25.8 1.0
CE A:LYS1305 4.3 26.0 1.0
O B:SER238 4.5 29.6 1.0
C A:GLN1303 4.6 23.1 1.0
O B:ALA239 4.6 32.0 1.0
O A:HOH1862 4.6 45.5 1.0
C B:ALA239 4.7 31.6 1.0
N A:PHE1302 4.8 18.8 1.0
O A:GLU1301 4.8 21.7 1.0
CG A:ARG1304 4.8 36.5 1.0
OE1 A:GLN1324 4.9 24.1 1.0
CA A:GLN1303 4.9 21.2 1.0
N B:ALA239 4.9 29.6 1.0

Chlorine binding site 2 out of 5 in 5t03

Go back to Chlorine Binding Sites List in 5t03
Chlorine binding site 2 out of 5 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Glucuronic Acid Containing Hexasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Glucuronic Acid Containing Hexasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1425

b:45.7
occ:1.00
 NZ A:LYS1132 3.0 44.0 1.0
O3 A:GNS1404 3.1 41.5 1.0
N A:TRP1153 3.2 26.0 1.0
O A:HOH1578 3.3 38.5 1.0
O A:HOH1934 3.4 61.6 1.0
CE A:LYS1132 3.5 41.9 1.0
CA A:GLY1152 3.6 27.7 1.0
C3 A:GNS1404 3.7 37.6 1.0
C A:GLY1152 3.9 30.5 1.0
O A:HOH1717 3.9 46.3 1.0
CD1 A:TRP1153 4.0 21.2 1.0
CB A:TRP1153 4.1 28.0 1.0
CA A:TRP1153 4.2 22.7 1.0
N A:GNS1404 4.3 43.9 1.0
CG A:TRP1153 4.3 24.8 1.0
O4 A:GNS1404 4.5 33.9 1.0
C2 A:GNS1404 4.7 37.3 1.0
C4 A:GNS1404 4.8 36.7 1.0
C A:TRP1153 4.8 30.4 1.0
CD A:LYS1132 4.9 42.2 1.0
N A:GLY1152 4.9 29.3 1.0
NZ A:LYS1131 5.0 39.4 1.0
NE1 A:TRP1153 5.0 24.0 1.0

Chlorine binding site 3 out of 5 in 5t03

Go back to Chlorine Binding Sites List in 5t03
Chlorine binding site 3 out of 5 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Glucuronic Acid Containing Hexasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Glucuronic Acid Containing Hexasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1426

b:52.4
occ:1.00
 NH2 A:ARG1317 3.1 35.0 1.0
O A:HOH1556 3.1 40.6 1.0
NH1 A:ARG1317 3.3 30.9 1.0
ND1 A:HIS1315 3.5 47.3 1.0
CZ A:ARG1317 3.6 32.8 1.0
O A:GLU1311 3.9 27.9 1.0
CA A:HIS1315 4.0 30.3 1.0
CA A:ARG1312 4.0 25.2 1.0
CE1 A:HIS1315 4.2 46.8 1.0
CG A:HIS1315 4.2 44.2 1.0
CG A:ARG1312 4.3 31.3 1.0
CB A:HIS1315 4.4 32.3 1.0
O A:ARG1312 4.4 29.4 1.0
CD A:ARG1312 4.5 37.8 1.0
C A:GLU1311 4.6 25.6 1.0
O A:HOH1928 4.6 52.5 1.0
C A:ARG1312 4.6 27.8 1.0
N A:ARG1312 4.6 28.9 1.0
NE A:ARG1312 4.7 30.5 1.0
N A:HIS1315 4.7 31.2 1.0
CB A:ARG1312 4.7 32.1 1.0
C A:HIS1315 4.8 32.9 1.0
NE A:ARG1317 5.0 32.8 1.0

Chlorine binding site 4 out of 5 in 5t03

Go back to Chlorine Binding Sites List in 5t03
Chlorine binding site 4 out of 5 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Glucuronic Acid Containing Hexasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Glucuronic Acid Containing Hexasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1418

b:47.9
occ:1.00
 N B:GLU1276 3.2 26.6 1.0
O B:HOH1834 3.4 31.3 1.0
CB B:GLU1276 3.7 27.6 1.0
CA B:ASN1275 3.9 24.9 1.0
C B:ASN1275 4.0 26.9 1.0
CA B:GLU1276 4.1 26.1 1.0
CB B:ASN1275 4.4 32.4 1.0
OD1 B:ASN1275 4.6 60.9 1.0
O B:MET1274 4.8 24.7 1.0
CG B:ASN1275 4.8 53.9 1.0
NH2 B:ARG1279 4.9 21.8 1.0

Chlorine binding site 5 out of 5 in 5t03

Go back to Chlorine Binding Sites List in 5t03
Chlorine binding site 5 out of 5 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Glucuronic Acid Containing Hexasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Glucuronic Acid Containing Hexasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1419

b:35.1
occ:1.00
 O B:HOH1613 2.9 24.6 1.0
N B:LYS1305 3.1 22.5 1.0
CA B:PHE1302 3.3 22.2 1.0
C B:PHE1302 3.3 22.0 1.0
N B:ARG1304 3.4 26.8 1.0
CG B:LYS1305 3.4 24.1 1.0
CB B:PHE1302 3.5 17.7 1.0
N B:GLN1303 3.7 23.5 1.0
O B:PHE1302 3.7 19.7 1.0
CB B:LYS1305 3.8 20.2 1.0
CA B:ARG1304 3.9 25.7 1.0
CB B:ARG1304 4.0 21.8 1.0
C B:ARG1304 4.0 26.3 1.0
NZ B:LYS1305 4.0 48.5 1.0
CD1 B:PHE1302 4.0 22.6 1.0
CA B:LYS1305 4.1 19.2 1.0
CD B:LYS1305 4.1 29.4 1.0
CG B:PHE1302 4.2 23.4 1.0
C B:GLN1303 4.3 17.0 1.0
OE1 B:GLN1324 4.5 23.6 1.0
CA B:GLN1303 4.6 18.6 1.0
N B:PHE1302 4.6 19.5 1.0
CE B:LYS1305 4.7 34.4 1.0
O B:GLU1301 4.8 19.8 1.0
O B:HOH1923 4.8 40.0 1.0

Reference:

Y.Xu, A.F.Moon, S.Xu, J.M.Krahn, J.Liu, L.C.Pedersen. Structure Based Substrate Specificity Analysis of Heparan Sulfate 6-O-Sulfotransferases. Acs Chem. Biol. V. 12 73 2017.
ISSN: ESSN 1554-8937
PubMed: 28103688
DOI: 10.1021/ACSCHEMBIO.6B00841
Page generated: Sat Jul 12 08:44:43 2025

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