Sodium in PDB 6ej9: Human Xylosyltransferase 1 in Complex with Peptide Qepegsgggqgg

All present enzymatic activity of Human Xylosyltransferase 1 in Complex with Peptide Qepegsgggqgg:
2.4.2.26;

The structure of Human Xylosyltransferase 1 in Complex with Peptide Qepegsgggqgg, PDB code: 6ej9 was solved by D.C.Briggs, E.Hohenester, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.53 / 2.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.380, 86.820, 153.200, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 22.5

The binding sites of Sodium atom in the Human Xylosyltransferase 1 in Complex with Peptide Qepegsgggqgg (pdb code 6ej9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human Xylosyltransferase 1 in Complex with Peptide Qepegsgggqgg, PDB code: 6ej9:

Sodium binding site 1 out of 1 in the Human Xylosyltransferase 1 in Complex with Peptide Qepegsgggqgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Xylosyltransferase 1 in Complex with Peptide Qepegsgggqgg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1003 b:34.7 occ:1.00 O A:SER375 2.3 36.5 1.0 O A:TYR378 2.3 27.4 1.0 O A:VAL381 2.4 31.1 1.0 O A:HOH1226 2.8 48.1 1.0 HA A:SER379 3.3 48.1 1.0 H A:VAL381 3.3 34.0 1.0 C A:SER375 3.4 37.5 1.0 C A:TYR378 3.5 32.3 1.0 C A:VAL381 3.5 28.6 1.0 HB2 A:SER375 3.6 45.0 1.0 HA A:SER375 3.6 43.2 1.0 HB A:VAL381 3.8 35.0 1.0 CA A:SER375 4.0 36.0 1.0 H A:TYR378 4.0 37.2 1.0 CA A:SER379 4.0 40.1 1.0 N A:VAL381 4.0 28.3 1.0 C A:SER379 4.2 34.7 1.0 N A:SER379 4.2 36.4 1.0 HA A:ARG382 4.2 31.1 1.0 O A:SER379 4.2 36.2 1.0 HG2 A:ARG382 4.2 34.5 1.0 HG3 A:ARG382 4.2 34.5 1.0 CA A:VAL381 4.3 28.9 1.0 CB A:SER375 4.3 37.5 1.0 HA A:ARG376 4.3 55.1 1.0 N A:ARG376 4.5 39.5 1.0 N A:TYR378 4.5 31.0 1.0 CB A:VAL381 4.5 29.1 1.0 CA A:TYR378 4.6 31.8 1.0 N A:ARG382 4.6 25.8 1.0 CG A:ARG382 4.7 28.8 1.0 CA A:ARG376 4.8 45.9 1.0 N A:ASN380 4.8 32.1 1.0 CA A:ARG382 4.9 25.9 1.0 HB2 A:TYR378 4.9 35.1 1.0 HB3 A:SER375 5.0 45.0 1.0 C A:ARG376 5.0 41.1 1.0

D.C.Briggs, E.Hohenester. Structural Basis For the Initiation of Glycosaminoglycan Biosynthesis By Human Xylosyltransferase 1. Structure V. 26 801 2018.
ISSN: ISSN 1878-4186
PubMed: 29681470
DOI: 10.1016/J.STR.2018.03.014