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

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

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:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium 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 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 Glucuronic Acid Containing Hexasaccharide Substrate, PDB code: 5t03:
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 Glucuronic Acid Containing Hexasaccharide 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 Glucuronic Acid Containing Hexasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1427 b:54.6 occ:1.00 O A:ASP1235 2.4 35.0 1.0 O A:HOH1947 2.4 48.8 1.0 O A:ASN1232 2.5 41.6 1.0 O A:HOH1913 3.1 44.9 1.0 C A:ASP1235 3.6 33.3 1.0 C A:ASN1232 3.6 40.1 1.0 CA A:TRP1236 4.2 26.4 1.0 CB A:TYR1231 4.3 33.9 1.0 N A:ASN1232 4.3 39.7 1.0 N A:TRP1236 4.4 30.1 1.0 N A:ASP1235 4.5 28.0 1.0 CA A:ASN1232 4.5 47.2 1.0 N A:GLY1233 4.6 36.9 1.0 OD1 A:ASP1235 4.6 31.9 1.0 CA A:GLY1233 4.6 37.9 1.0 CA A:ASP1235 4.7 25.0 1.0 C A:TRP1236 4.9 26.5 1.0 CD1 A:TYR1231 4.9 31.3 1.0 C A:GLY1233 4.9 36.0 1.0 N A:SER1237 4.9 27.3 1.0 CB A:ASN1232 4.9 50.9 1.0 CD1 A:TRP1236 5.0 29.3 1.0 C A:TYR1231 5.0 35.1 1.0

Sodium binding site 2 out of 6 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 Sodium with other atoms in the Na 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:Na1428 b:38.6 occ:0.75 O11 A:TLA1431 2.3 42.5 1.0 O A:HOH1828 2.4 34.8 1.0 C1 A:TLA1431 3.3 38.4 1.0 O2 A:EDO1420 3.4 32.6 1.0 O A:HOH1751 3.6 19.6 1.0 NZ A:LYS1104 3.6 17.4 1.0 CE1 A:HIS1203 3.7 23.6 1.0 NH2 A:ARG1206 3.7 17.1 1.0 C3 A:TLA1431 3.7 37.0 1.0 C2 A:TLA1431 3.7 40.0 1.0 O A:HOH1703 3.9 33.6 1.0 ND1 A:HIS1203 4.2 17.3 1.0 NE2 A:HIS1203 4.3 16.4 1.0 O4 A:GNS1402 4.4 20.7 1.0 O4P A:A3P1401 4.4 16.2 1.0 C2 A:EDO1420 4.4 41.9 1.0 O1 A:TLA1431 4.4 36.5 1.0 O3 A:TLA1431 4.5 33.3 1.0 O41 A:TLA1431 4.8 50.4 1.0 C4 A:TLA1431 4.8 42.2 1.0 CZ A:ARG1206 4.9 21.2 1.0

Sodium binding site 3 out of 6 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 Sodium with other atoms in the Na 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:Na1429 b:40.8 occ:0.93 O4 A:TLA1431 2.3 43.0 1.0 O6B A:BDP1403 2.7 21.5 1.0 C4 A:TLA1431 3.2 42.2 1.0 O A:HOH1886 3.3 31.1 1.0 O41 A:TLA1431 3.4 50.4 1.0 C6 A:BDP1403 3.6 24.4 1.0 O A:HOH1893 3.6 40.2 1.0 C5 A:BDP1403 3.7 25.3 1.0 O4 A:BDP1403 3.7 26.5 1.0 C3 A:GNS1402 4.0 24.2 1.0 O A:HOH1666 4.1 50.9 1.0 O4 A:GNS1402 4.3 20.7 1.0 C4 A:BDP1403 4.4 23.4 1.0 C5 A:GNS1402 4.5 18.9 1.0 O A:HOH1917 4.5 58.7 1.0 C3 A:TLA1431 4.5 37.0 1.0 C4 A:GNS1402 4.5 21.7 1.0 O3 A:GNS1402 4.7 26.5 1.0 O3 A:TLA1431 4.8 33.3 1.0 C1 A:GNS1402 4.8 25.4 1.0 O6A A:BDP1403 4.8 23.9 1.0 NH2 A:ARG1148 4.8 19.4 1.0 O5 A:BDP1403 4.8 25.8 1.0 C2 A:GNS1402 4.9 25.6 1.0 N A:GNS1402 5.0 26.9 1.0

Sodium binding site 4 out of 6 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 Sodium with other atoms in the Na 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 A:Na1430 b:69.2 occ:1.00 O A:HOH1905 2.4 53.0 1.0 O A:ALA1331 2.5 34.0 1.0 O A:VAL1333 3.0 45.3 1.0 O A:HOH1890 3.3 36.1 1.0 C A:ALA1331 3.6 29.1 1.0 C A:VAL1333 4.0 37.9 1.0 OE2 A:GLU1334 4.1 83.7 1.0 CA A:ALA1331 4.3 28.4 1.0 N A:VAL1333 4.6 27.8 1.0 N A:ASN1332 4.6 28.7 1.0 C A:ASN1332 4.6 35.5 1.0 O A:ALA1330 4.7 25.7 1.0 CA A:GLU1334 4.8 43.9 1.0 N A:GLU1334 4.8 38.2 1.0 CA A:ASN1332 4.9 30.4 1.0 CA A:VAL1333 4.9 31.2 1.0

Sodium binding site 5 out of 6 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 Sodium with other atoms in the Na 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:Na1420 b:43.0 occ:1.00 O B:ASP1235 2.4 23.5 1.0 O B:HOH1880 2.4 36.4 1.0 O B:ASN1232 2.4 29.9 1.0 O B:HOH1889 2.5 44.4 1.0 O B:HOH1864 2.5 45.0 1.0 O B:HOH1851 2.5 38.3 1.0 C B:ASP1235 3.5 22.4 1.0 C B:ASN1232 3.6 31.8 1.0 O B:HOH1705 3.8 37.6 1.0 N B:ASP1235 4.2 22.5 1.0 OD1 B:ASP1235 4.2 29.6 1.0 N B:TRP1236 4.4 21.8 1.0 N B:ASN1232 4.4 35.2 1.0 CA B:TRP1236 4.4 23.6 1.0 CA B:GLY1233 4.4 34.9 1.0 N B:GLY1233 4.5 35.7 1.0 CA B:ASP1235 4.5 21.7 1.0 CB B:TYR1231 4.5 21.0 1.0 CA B:ASN1232 4.6 46.2 1.0 C B:GLY1233 4.7 32.4 1.0 N B:ASP1234 4.7 26.4 1.0 O B:HOH1718 4.7 34.0 1.0 CD1 B:TYR1231 4.9 27.6 1.0 N B:SER1237 4.9 22.2 0.4 N B:SER1237 5.0 23.3 0.6

Sodium binding site 6 out of 6 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 Sodium with other atoms in the Na binding site number 6 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:Na1421 b:56.9 occ:0.75 O B:HOH1878 2.3 45.2 0.8 O11 B:TLA1422 2.4 46.4 1.0 O2 B:TLA1422 2.4 40.0 1.0 O3 B:TLA1422 2.9 47.3 1.0 C1 B:TLA1422 3.1 49.9 1.0 C2 B:TLA1422 3.2 39.1 1.0 O B:HOH1754 3.3 45.6 1.0 O B:HOH1803 3.5 34.3 1.0 C3 B:TLA1422 3.6 44.6 1.0 O3 B:GNS1402 3.8 22.3 1.0 O1 B:TLA1422 4.2 51.8 1.0 O B:HOH1556 4.3 34.0 1.0 O B:HOH1837 4.3 33.6 1.0 C3 B:GNS1402 4.5 20.2 1.0 C4 B:TLA1422 4.6 43.7 1.0 O41 B:TLA1422 4.6 42.1 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