Sodium in PDB 6ej7: Human Xylosyltransferase 1 in Complex with Udp-Xylose and Peptide Qeeegagggqgg

All present enzymatic activity of Human Xylosyltransferase 1 in Complex with Udp-Xylose and Peptide Qeeegagggqgg:
2.4.2.26;

The structure of Human Xylosyltransferase 1 in Complex with Udp-Xylose and Peptide Qeeegagggqgg, PDB code: 6ej7 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)	76.46 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.460, 86.890, 152.910, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23

The binding sites of Sodium atom in the Human Xylosyltransferase 1 in Complex with Udp-Xylose and Peptide Qeeegagggqgg (pdb code 6ej7). 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 Udp-Xylose and Peptide Qeeegagggqgg, PDB code: 6ej7:

Sodium binding site 1 out of 1 in the Human Xylosyltransferase 1 in Complex with Udp-Xylose and Peptide Qeeegagggqgg


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 Udp-Xylose and Peptide Qeeegagggqgg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1003 b:31.1 occ:1.00 O A:SER375 2.4 34.0 1.0 O A:VAL381 2.4 29.2 1.0 O A:TYR378 2.4 28.1 1.0 O A:HOH1395 2.4 34.3 1.0 O A:HOH1386 2.4 46.4 1.0 O A:HOH1233 2.4 50.9 1.0 HA A:SER379 3.3 45.1 1.0 H A:VAL381 3.3 31.1 1.0 C A:SER375 3.5 36.4 1.0 C A:TYR378 3.5 30.8 1.0 C A:VAL381 3.6 29.5 1.0 HB2 A:SER375 3.7 43.4 1.0 HA A:SER375 3.8 40.9 1.0 HB A:VAL381 4.0 36.2 1.0 HG3 A:ARG382 4.0 38.2 1.0 CA A:SER379 4.0 37.6 1.0 H A:TYR378 4.1 37.5 1.0 N A:VAL381 4.1 25.9 1.0 CA A:SER375 4.1 34.1 1.0 HA A:ARG382 4.2 35.7 1.0 C A:SER379 4.2 36.3 1.0 HG2 A:ARG382 4.2 38.2 1.0 N A:SER379 4.2 33.3 1.0 O A:SER379 4.3 37.5 1.0 CA A:VAL381 4.3 25.7 1.0 HA A:ARG376 4.3 46.0 1.0 CB A:SER375 4.4 36.2 1.0 CG A:ARG382 4.6 31.8 1.0 N A:ARG376 4.6 35.0 1.0 N A:TYR378 4.6 31.2 1.0 N A:ARG382 4.6 30.2 1.0 CB A:VAL381 4.6 30.1 1.0 CA A:TYR378 4.7 32.3 1.0 O2 A:PO41006 4.8 1.0 1.0 N A:ASN380 4.8 32.0 1.0 CA A:ARG382 4.8 29.8 1.0 CA A:ARG376 4.8 38.3 1.0 O3 A:PO41006 4.9 0.8 1.0 O4 A:PO41006 4.9 0.5 1.0 HE A:ARG382 4.9 46.7 1.0 HB2 A:TYR378 5.0 36.8 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