Sodium 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:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium 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 Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate, PDB code: 5t0a:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 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 Sodium with other atoms in the Na 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:Na2026 b:53.1 occ:0.97 O3S A:GNS2003 2.3 44.1 1.0 O A:HOH2199 2.4 55.5 1.0 O1S A:IDS2004 2.7 50.4 1.0 S1 A:GNS2003 3.5 49.1 1.0 O2S A:GNS2003 3.7 40.7 1.0 S A:IDS2004 3.9 55.5 1.0 O3S A:IDS2004 3.9 51.0 1.0 O A:HOH2313 4.1 43.6 1.0 O1S A:GNS2003 4.3 46.4 1.0 O2 A:IDS2004 4.5 50.3 1.0 N A:GNS2003 4.6 45.7 1.0 NZ A:LYS1132 4.6 44.0 1.0 CD A:LYS1132 4.8 42.1 1.0

Sodium binding site 2 out of 6 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 Sodium with other atoms in the Na 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:Na2027 b:41.6 occ:0.91 O A:ASN1232 2.3 44.5 1.0 O A:HOH2552 2.3 53.5 1.0 O A:ASP1235 2.3 31.6 1.0 O A:HOH2548 2.3 47.6 1.0 O A:HOH2440 2.7 45.4 1.0 C A:ASP1235 3.5 29.0 1.0 C A:ASN1232 3.5 48.1 1.0 O A:HOH2622 4.0 46.2 1.0 N A:ASP1235 4.1 30.6 1.0 CB A:TYR1231 4.3 26.9 1.0 CA A:GLY1233 4.3 44.0 1.0 N A:ASN1232 4.3 42.6 1.0 OD1 A:ASP1235 4.4 28.8 1.0 N A:GLY1233 4.4 45.0 1.0 CA A:TRP1236 4.4 28.6 1.0 N A:TRP1236 4.4 26.9 1.0 CA A:ASP1235 4.5 26.1 1.0 CA A:ASN1232 4.5 47.2 1.0 C A:GLY1233 4.5 38.7 1.0 N A:ASP1234 4.6 38.5 1.0 CD1 A:TYR1231 4.7 31.2 1.0 CG A:TYR1231 4.9 31.4 1.0 C A:TYR1231 5.0 33.9 1.0 CB A:ASN1232 5.0 49.1 1.0

Sodium binding site 3 out of 6 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 Sodium with other atoms in the Na 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 A:Na2028 b:48.8 occ:0.95 O4 A:TLA2025 2.4 48.3 0.7 O6B A:BDP2002 2.8 27.5 1.0 O A:HOH2516 3.4 34.9 1.0 C4 A:TLA2025 3.4 41.1 0.7 C5 A:BDP2002 3.7 27.4 1.0 C6 A:BDP2002 3.7 35.5 1.0 O41 A:TLA2025 3.7 48.6 0.7 O4 A:BDP2002 3.7 28.1 1.0 O A:HOH2513 3.7 38.4 1.0 C3 A:GNS2001 4.1 33.5 1.0 O4 A:GNS2001 4.3 36.7 1.0 C4 A:BDP2002 4.3 26.3 1.0 C4 A:GNS2001 4.6 30.4 1.0 C5 A:GNS2001 4.6 26.0 1.0 C3 A:TLA2025 4.7 36.5 0.7 O5 A:BDP2002 4.7 34.9 1.0 O3 A:GNS2001 4.8 25.6 1.0 NH2 A:ARG1148 4.8 30.0 1.0 C1 A:GNS2001 4.9 26.3 1.0 O6A A:BDP2002 4.9 26.2 1.0 O3 A:TLA2025 4.9 38.6 0.7 C2 A:GNS2001 4.9 32.8 1.0 O6 A:GNS2003 5.0 41.5 1.0

Sodium binding site 4 out of 6 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 Sodium with other atoms in the Na binding site number 4 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:Na2029 b:55.0 occ:0.94 O A:ALA1331 2.4 32.7 1.0 O A:HOH2518 2.9 40.9 1.0 O A:VAL1333 3.0 41.5 1.0 C A:ALA1331 3.4 34.9 1.0 CA A:ALA1331 4.1 30.9 1.0 C A:VAL1333 4.1 38.9 1.0 N A:VAL1333 4.4 30.8 1.0 N A:ASN1332 4.5 31.9 1.0 O A:ALA1330 4.5 23.9 1.0 C A:ASN1332 4.7 39.3 1.0 O A:HOH2160 4.7 50.4 1.0 CA A:ASN1332 4.8 33.4 1.0 CA A:VAL1333 4.9 34.7 1.0 O A:HOH2519 4.9 39.7 1.0 N A:GLU1334 4.9 41.2 1.0 CB A:ALA1331 4.9 31.8 1.0 CA A:GLU1334 5.0 38.3 1.0

Sodium binding site 5 out of 6 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 Sodium with other atoms in the Na binding site number 5 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:Na1419 b:37.0 occ:0.77 O B:HOH1915 2.2 38.3 1.0 O B:ASP1235 2.3 25.2 1.0 O B:HOH1918 2.4 39.0 1.0 O B:ASN1232 2.4 35.2 1.0 O B:HOH1877 2.6 43.2 1.0 O B:HOH1715 2.8 39.9 1.0 C B:ASP1235 3.5 24.5 1.0 C B:ASN1232 3.6 36.3 1.0 O B:HOH1678 3.8 33.3 1.0 OD1 B:ASP1235 4.1 26.3 1.0 N B:ASP1235 4.2 28.1 1.0 N B:TRP1236 4.3 23.0 1.0 CA B:TRP1236 4.3 25.5 1.0 N B:ASN1232 4.4 36.7 1.0 CA B:ASP1235 4.4 24.2 1.0 CB B:TYR1231 4.4 23.6 1.0 CA B:ASN1232 4.5 42.6 1.0 N B:GLY1233 4.6 38.3 1.0 CA B:GLY1233 4.6 39.6 1.0 O B:HOH1862 4.7 50.5 1.0 CD2 B:TYR1231 4.8 27.7 1.0 N B:SER1237 4.8 24.8 0.5 C B:GLY1233 4.8 37.4 1.0 O B:HOH1641 4.8 36.7 1.0 N B:SER1237 4.8 24.8 0.6 N B:ASP1234 4.8 30.8 1.0 C B:TRP1236 4.9 23.8 1.0

Sodium binding site 6 out of 6 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 Sodium with other atoms in the Na binding site number 6 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:Na1420 b:53.2 occ:0.83 O B:HOH1577 2.4 54.8 1.0 O B:GLN325 2.4 35.8 1.0 O B:HOH1891 2.5 52.2 1.0 O B:GLY327 2.5 39.7 1.0 O B:HOH1908 3.0 47.1 1.0 C B:GLN325 3.5 41.2 1.0 C B:GLY327 3.7 46.5 1.0 OE1 B:GLU328 3.8 64.2 1.0 O B:ALA324 4.1 41.5 1.0 CA B:GLN325 4.1 42.8 1.0 N B:GLY327 4.3 35.8 1.0 C B:LYS326 4.3 41.8 1.0 N B:LYS326 4.5 34.9 1.0 O B:LYS326 4.5 37.0 1.0 CA B:GLY327 4.6 36.6 1.0 N B:GLU328 4.6 35.0 1.0 CA B:GLU328 4.7 47.0 1.0 CA B:LYS326 4.7 38.9 1.0 CD B:GLU328 4.9 61.3 1.0 C B:ALA324 5.0 38.0 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