Chlorine in PDB 5t05: Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide Substrate

The structure of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide Substrate, PDB code: 5t05 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)	38.49 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.785, 128.161, 178.711, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.2

The structure of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide Substrate also contains other interesting chemical elements:

Sodium

(Na)

7 atoms

The binding sites of Chlorine atom in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide Substrate (pdb code 5t05). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide Substrate, PDB code: 5t05:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S 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 IDOA2S Containing Hexasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1422 b:31.0 occ:1.00 O A:HOH1644 2.9 27.4 1.0 O A:HOH1568 3.2 46.9 1.0 N A:LYS1305 3.2 22.3 1.0 CA A:PHE1302 3.5 24.1 1.0 CG A:LYS1305 3.5 26.3 1.0 C A:PHE1302 3.6 22.9 1.0 N A:ARG1304 3.6 22.8 1.0 CB A:PHE1302 3.6 24.2 1.0 NZ A:LYS1305 3.7 35.3 1.0 CB A:ARG1304 3.8 30.5 1.0 CB A:LYS1305 3.8 27.1 1.0 CD A:LYS1305 3.9 30.5 1.0 O A:PHE1302 3.9 23.7 1.0 CD1 A:PHE1302 3.9 25.1 1.0 N A:GLN1303 4.0 24.6 1.0 CA A:ARG1304 4.0 25.1 1.0 C A:ARG1304 4.1 25.6 1.0 CA B:ALA239 4.1 35.2 1.0 CA A:LYS1305 4.1 24.8 1.0 CG A:PHE1302 4.3 27.9 1.0 O B:HOH1701 4.4 43.0 1.0 CB B:ALA239 4.4 32.5 1.0 CE A:LYS1305 4.4 32.5 1.0 C A:GLN1303 4.5 26.3 1.0 O B:SER238 4.6 31.0 1.0 O A:HOH1821 4.6 47.5 1.0 O B:ALA239 4.6 35.1 1.0 C B:ALA239 4.7 35.9 1.0 CG A:ARG1304 4.8 39.2 1.0 N A:PHE1302 4.8 20.8 1.0 CA A:GLN1303 4.9 20.3 1.0 OE1 A:GLN1324 4.9 26.9 1.0 O A:GLU1301 4.9 24.2 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S 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 IDOA2S Containing Hexasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1423 b:41.6 occ:1.00 O A:HOH1972 2.6 45.6 1.0 NZ A:LYS1132 3.1 38.5 1.0 O3 A:GNS1404 3.2 32.2 1.0 O A:HOH1781 3.3 31.9 1.0 N A:TRP1153 3.4 26.9 1.0 CE A:LYS1132 3.6 37.1 1.0 CA A:GLY1152 3.8 27.1 1.0 C3 A:GNS1404 3.8 29.1 1.0 CD1 A:TRP1153 4.0 28.1 1.0 C A:GLY1152 4.1 30.4 1.0 CB A:TRP1153 4.3 25.2 1.0 CA A:TRP1153 4.3 27.6 1.0 CG A:TRP1153 4.5 31.2 1.0 N A:GNS1404 4.5 32.3 1.0 O4 A:GNS1404 4.6 32.3 1.0 O3S A:IDS1405 4.7 41.9 1.0 C2 A:GNS1404 4.8 29.0 1.0 O A:HOH1672 4.9 44.9 1.0 C4 A:GNS1404 4.9 29.9 1.0 C A:TRP1153 4.9 27.2 1.0 CD A:LYS1132 5.0 35.1 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S 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 IDOA2S Containing Hexasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1424 b:47.5 occ:1.00 O A:HOH1794 2.7 42.3 1.0 NH1 A:ARG1317 3.2 34.5 1.0 NH2 A:ARG1317 3.2 38.9 1.0 ND1 A:HIS1315 3.5 46.7 1.0 CZ A:ARG1317 3.7 38.4 1.0 O A:GLU1311 3.8 31.9 1.0 CA A:ARG1312 3.9 29.7 1.0 CA A:HIS1315 3.9 32.5 1.0 CG A:HIS1315 4.2 41.9 1.0 CG A:ARG1312 4.2 36.3 1.0 CE1 A:HIS1315 4.3 46.6 1.0 CB A:HIS1315 4.3 32.7 1.0 O A:ARG1312 4.3 30.3 1.0 C A:GLU1311 4.5 30.7 1.0 C A:ARG1312 4.6 31.8 1.0 CD A:ARG1312 4.6 40.1 1.0 N A:HIS1315 4.6 32.3 1.0 N A:ARG1312 4.6 29.9 1.0 CB A:ARG1312 4.6 31.5 1.0 NE A:ARG1312 4.7 37.6 1.0 C A:HIS1315 4.8 35.9 1.0 O A:HOH1989 4.8 44.4 1.0 NE A:ARG1317 5.0 34.6 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S 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 IDOA2S Containing Hexasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1419 b:43.1 occ:1.00 O B:HOH1784 3.1 30.2 1.0 N B:GLU1276 3.1 25.9 1.0 O B:HOH1839 3.5 37.2 1.0 CB B:GLU1276 3.6 31.9 1.0 CA B:ASN1275 3.9 29.8 1.0 C B:ASN1275 4.0 30.2 1.0 CA B:GLU1276 4.0 27.1 1.0 CB B:ASN1275 4.4 29.9 1.0 OD1 B:ASN1275 4.7 39.7 1.0 NH2 B:ARG1279 4.7 24.6 1.0 O B:MET1274 4.8 28.3 1.0

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