Sodium in PDB 1t8u: Crystal Structure of Human 3-O-Sulfotransferase-3 with Bound Pap and Tetrasaccharide Substrate

The structure of Crystal Structure of Human 3-O-Sulfotransferase-3 with Bound Pap and Tetrasaccharide Substrate, PDB code: 1t8u was solved by A.F.Moon, S.C.Edavettal, J.M.Krahn, E.M.Munoz, M.Negishi, R.J.Linhardt, J.Liu, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	80.806, 154.525, 91.931, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 22.2

The binding sites of Sodium atom in the Crystal Structure of Human 3-O-Sulfotransferase-3 with Bound Pap and Tetrasaccharide Substrate (pdb code 1t8u). 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 Human 3-O-Sulfotransferase-3 with Bound Pap and Tetrasaccharide Substrate, PDB code: 1t8u:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human 3-O-Sulfotransferase-3 with Bound Pap and Tetrasaccharide 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 Human 3-O-Sulfotransferase-3 with Bound Pap and Tetrasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:39.1 occ:1.00 OD1 A:ASP252 2.2 22.1 1.0 OG1 A:THR256 2.2 18.6 1.0 O A:ASP252 2.6 16.8 1.0 CG A:ASP252 3.3 20.8 1.0 C A:ASP252 3.3 16.4 1.0 NZ A:LYS161 3.4 24.7 1.0 CB A:THR256 3.6 19.1 1.0 O A:HOH733 3.9 27.7 1.0 CA A:ASP252 3.9 16.8 1.0 N A:THR256 4.0 17.5 1.0 CB A:ASP252 4.1 18.2 1.0 OD2 A:ASP252 4.2 19.1 1.0 CE A:LYS161 4.2 24.8 1.0 CA A:THR256 4.2 17.7 1.0 N A:TYR253 4.2 15.4 1.0 CA A:TYR253 4.6 15.9 1.0 CG2 A:THR256 4.6 17.8 1.0 CB A:GLN255 4.6 17.2 1.0 C A:GLN255 4.8 17.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human 3-O-Sulfotransferase-3 with Bound Pap and Tetrasaccharide 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 Human 3-O-Sulfotransferase-3 with Bound Pap and Tetrasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:35.4 occ:1.00 OG1 B:THR256 2.3 21.4 1.0 OD1 B:ASP252 2.4 19.4 1.0 O3S B:SGN4 2.4 47.1 1.0 O3 B:SGN4 2.5 46.1 1.0 O B:ASP252 2.5 17.8 1.0 O62 B:IDS3 2.7 33.4 1.0 C B:ASP252 3.3 17.9 1.0 CG B:ASP252 3.4 20.4 1.0 S1 B:SGN4 3.5 47.7 1.0 N B:SGN4 3.5 48.6 1.0 CB B:THR256 3.5 23.8 1.0 NZ B:LYS161 3.6 27.3 1.0 N B:THR256 3.7 22.0 1.0 C3 B:SGN4 3.7 48.4 1.0 C6 B:IDS3 3.8 36.1 1.0 CA B:ASP252 3.9 17.6 1.0 C2 B:SGN4 4.0 48.6 1.0 CA B:THR256 4.0 23.0 1.0 CE B:LYS161 4.1 27.0 1.0 CB B:ASP252 4.1 19.4 1.0 O B:HOH748 4.2 31.5 1.0 O2S B:SGN4 4.2 48.5 1.0 N B:TYR253 4.3 17.8 1.0 CB B:GLN255 4.3 20.7 1.0 OD2 B:ASP252 4.4 20.1 1.0 O5 B:IDS3 4.5 39.0 1.0 O B:HOH806 4.5 26.6 1.0 O61 B:IDS3 4.5 32.4 1.0 C B:GLN255 4.6 22.4 1.0 CA B:TYR253 4.6 19.6 1.0 O1S B:SGN4 4.7 47.6 1.0 CG2 B:THR256 4.7 21.1 1.0 C5 B:IDS3 4.7 36.0 1.0 CG B:GLN255 4.8 21.5 1.0 CA B:GLN255 4.9 21.3 1.0 C4 B:SGN4 4.9 48.2 1.0 C B:TYR253 5.0 19.7 1.0

A.F.Moon, S.C.Edavettal, J.M.Krahn, E.M.Munoz, M.Negishi, R.J.Linhardt, J.Liu, L.C.Pedersen. Structural Analysis of the Sulfotransferase (3-O-Sulfotransferase Isoform 3) Involved in the Biosynthesis of An Entry Receptor For Herpes Simplex Virus 1 J.Biol.Chem. V. 279 45185 2004.
ISSN: ISSN 0021-9258
PubMed: 15304505
DOI: 10.1074/JBC.M405013200