Sodium in PDB 6xkg: Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with 6S Sulfation

All present enzymatic activity of Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with 6S Sulfation:
2.8.2.30;

The structure of Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with 6S Sulfation, PDB code: 6xkg was solved by L.C.Pedersen, J.Liu, R.Wander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.86 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.76, 65.012, 92.235, 90, 124.74, 90
R / Rfree (%)	16.4 / 18.3

The binding sites of Sodium atom in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with 6S Sulfation (pdb code 6xkg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with 6S Sulfation, PDB code: 6xkg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with 6S Sulfation


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 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with 6S Sulfation within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:19.1 occ:1.00 OD1 B:ASP252 2.3 19.6 1.0 O3 E:SGN2 2.4 17.9 1.0 OG1 B:THR256 2.4 19.3 1.0 O B:ASP252 2.4 17.2 1.0 O3S E:SGN2 2.6 21.9 1.0 O6A E:IDS3 2.7 18.1 1.0 C B:ASP252 3.2 16.8 1.0 CG B:ASP252 3.4 17.3 1.0 S1 E:SGN2 3.6 20.7 1.0 CB B:THR256 3.6 17.4 1.0 N2 E:SGN2 3.6 19.8 1.0 C3 E:SGN2 3.7 19.3 1.0 NZ B:LYS161 3.7 18.3 1.0 N B:THR256 3.7 18.6 1.0 C6 E:IDS3 3.8 17.9 1.0 CA B:ASP252 3.9 15.6 1.0 C2 E:SGN2 4.0 16.1 1.0 CB B:ASP252 4.1 14.3 1.0 N B:TYR253 4.2 15.5 1.0 CA B:THR256 4.2 19.0 1.0 O1S E:SGN2 4.2 21.4 1.0 O B:HOH817 4.2 23.7 1.0 O B:HOH698 4.2 21.6 1.0 CB B:GLN255 4.3 17.3 1.0 O5 E:IDS3 4.3 15.9 1.0 OD2 B:ASP252 4.4 17.2 1.0 CE B:LYS161 4.4 25.1 1.0 O6B E:IDS3 4.5 18.2 1.0 CA B:TYR253 4.5 16.2 1.0 C5 E:IDS3 4.6 16.3 1.0 C B:GLN255 4.6 22.8 1.0 CG B:GLN255 4.7 18.1 1.0 O2S E:SGN2 4.8 22.4 1.0 CG2 B:THR256 4.8 21.2 1.0 C4 E:SGN2 4.8 16.7 1.0 CA B:GLN255 4.9 17.9 1.0 C B:TYR253 5.0 21.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with 6S Sulfation


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 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with 6S Sulfation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:38.6 occ:1.00 O A:HOH732 2.2 47.1 1.0 O A:HOH637 2.3 40.1 1.0 O A:TRP404 2.7 33.4 1.0 OH A:TYR395 2.9 25.9 1.0 O A:HOH762 3.2 30.4 1.0 N A:TRP404 3.2 24.6 1.0 CE2 A:TYR395 3.4 24.5 1.0 CZ A:TYR395 3.6 26.8 1.0 C A:GLY403 3.6 25.8 1.0 C A:TRP404 3.6 34.0 1.0 CA A:GLY403 3.7 27.4 1.0 OD1 A:ASP401 3.7 28.7 1.0 N A:GLY403 3.9 26.1 1.0 CA A:TRP404 4.0 27.8 1.0 O A:HOH825 4.0 36.4 1.0 O A:HOH798 4.2 42.6 1.0 O A:GLY403 4.4 31.0 1.0 CB A:TRP404 4.6 25.9 1.0 CG A:ASP401 4.7 34.1 1.0 CD2 A:TYR395 4.7 24.2 1.0 OD2 A:ASP401 4.8 45.1 1.0 N A:ASP405 4.8 40.6 1.0 CE1 A:TYR395 4.9 22.6 1.0

R.Wander, A.M.Kaminski, Y.Xu, V.Pagadala, J.M.Krahn, T.Q.Pham, J.Liu, L.C.Pedersen. Deciphering the Substrate Recognition Mechanisms of the Heparan Sulfate 3-O-Sulfotransferase-3 Rsc Chem Biol 2021.
ISSN: ESSN 2633-0679
DOI: 10.1039/D1CB00079A