Chlorine in PDB 5t0a: Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate

The structure of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate, PDB code: 5t0a 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)	37.84 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.775, 128.291, 178.929, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.3

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

Sodium

(Na)

6 atoms

The binding sites of Chlorine atom in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate (pdb code 5t0a). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate, PDB code: 5t0a:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide 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 Heptasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2030 b:27.5 occ:0.90 O A:HOH2243 3.0 26.0 1.0 O A:HOH2432 3.1 49.3 1.0 N A:LYS1305 3.3 22.0 1.0 CA A:PHE1302 3.5 23.6 1.0 CG A:LYS1305 3.5 24.2 1.0 NZ A:LYS1305 3.6 33.0 1.0 C A:PHE1302 3.6 22.4 1.0 N A:ARG1304 3.6 21.6 1.0 CB A:PHE1302 3.7 22.8 1.0 CB A:ARG1304 3.8 29.4 1.0 CB A:LYS1305 3.9 21.8 1.0 CD1 A:PHE1302 3.9 25.6 1.0 CD A:LYS1305 3.9 29.7 1.0 O A:PHE1302 4.0 21.6 1.0 N A:GLN1303 4.0 23.7 1.0 CA A:ARG1304 4.0 23.6 1.0 CA B:ALA239 4.1 35.2 1.0 C A:ARG1304 4.1 27.3 1.0 CA A:LYS1305 4.2 22.1 1.0 CG A:PHE1302 4.3 27.2 1.0 O B:HOH1642 4.4 38.4 1.0 CE A:LYS1305 4.4 33.3 1.0 CB B:ALA239 4.4 31.7 1.0 O B:SER238 4.5 30.5 1.0 O B:ALA239 4.6 32.3 1.0 C A:GLN1303 4.6 25.3 1.0 C B:ALA239 4.7 36.0 1.0 CG A:ARG1304 4.8 37.8 1.0 O A:GLU1301 4.8 23.1 1.0 N A:PHE1302 4.8 17.7 1.0 OE1 A:GLN1324 4.9 25.5 1.0 CA A:GLN1303 4.9 18.7 1.0 NE A:ARG1304 4.9 51.6 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide 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 Heptasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2031 b:40.3 occ:0.85 O A:HOH2534 2.5 50.3 1.0 NZ A:LYS1132 3.0 44.0 1.0 O3 A:GNS2003 3.1 38.4 1.0 O A:HOH2237 3.3 34.0 1.0 N A:TRP1153 3.3 27.7 1.0 CE A:LYS1132 3.6 45.9 1.0 CA A:GLY1152 3.7 25.2 1.0 C3 A:GNS2003 3.9 38.2 1.0 CD1 A:TRP1153 4.0 30.4 1.0 C A:GLY1152 4.0 32.6 1.0 CB A:TRP1153 4.2 26.4 1.0 CA A:TRP1153 4.3 25.8 1.0 CG A:TRP1153 4.4 34.8 1.0 N A:GNS2003 4.5 45.7 1.0 O3S A:IDS2004 4.6 51.0 1.0 O4 A:GNS2003 4.7 40.4 1.0 C2 A:GNS2003 4.9 40.5 1.0 C A:TRP1153 4.9 25.3 1.0 CD A:LYS1132 4.9 42.1 1.0 C4 A:GNS2003 5.0 35.7 1.0 NZ A:LYS1131 5.0 36.0 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide 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 Heptasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1421 b:37.1 occ:0.80 O B:HOH1752 3.0 29.5 1.0 N B:GLU1276 3.2 23.8 1.0 O B:HOH1843 3.6 35.1 1.0 CB B:GLU1276 3.7 31.9 1.0 CA B:ASN1275 3.8 31.6 1.0 C B:ASN1275 4.0 29.4 1.0 CA B:GLU1276 4.1 26.5 1.0 CB B:ASN1275 4.4 30.5 1.0 OD1 B:ASN1275 4.6 41.1 1.0 NH2 B:ARG1279 4.7 23.2 1.0 O B:MET1274 4.7 27.0 1.0 N B:ASN1275 5.0 24.0 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