Chlorine in PDB 5dkx: Crystal Structure of Glucosidase II Alpha Subunit (Tris-Bound From)

The structure of Crystal Structure of Glucosidase II Alpha Subunit (Tris-Bound From), PDB code: 5dkx was solved by T.Satoh, T.Toshimori, G.Yan, T.Yamaguchi, K.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.40
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	189.026, 189.026, 157.181, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 17.5

The binding sites of Chlorine atom in the Crystal Structure of Glucosidase II Alpha Subunit (Tris-Bound From) (pdb code 5dkx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Glucosidase II Alpha Subunit (Tris-Bound From), PDB code: 5dkx:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Glucosidase II Alpha Subunit (Tris-Bound From)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Glucosidase II Alpha Subunit (Tris-Bound From) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1002 b:29.5 occ:1.00 O A:HOH1899 3.0 37.2 1.0 O A:HOH1399 3.0 18.2 1.0 N A:ARG95 3.0 17.5 1.0 O A:HOH1941 3.1 36.4 1.0 CA A:VAL94 3.5 19.8 1.0 CB A:VAL94 3.8 20.1 1.0 C A:VAL94 3.8 17.8 1.0 CB A:ARG95 3.9 18.4 1.0 CA A:ARG95 4.0 18.1 1.0 CG A:ARG95 4.1 18.7 1.0 CE A:LYS116 4.2 27.2 1.0 CG1 A:VAL94 4.3 21.2 1.0 CD A:ARG95 4.3 19.8 1.0 O A:ARG95 4.4 17.3 1.0 CB A:LYS116 4.5 21.4 1.0 O A:HOH1416 4.6 19.4 1.0 O A:THR93 4.6 22.8 1.0 C A:ARG95 4.7 17.2 1.0 N A:LYS116 4.7 17.5 1.0 N A:VAL94 4.8 20.1 1.0 OE1 A:GLU115 4.9 28.4 1.0 NZ A:LYS116 5.0 28.1 1.0 O A:VAL94 5.0 18.2 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Glucosidase II Alpha Subunit (Tris-Bound From)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Glucosidase II Alpha Subunit (Tris-Bound From) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1003 b:20.1 occ:1.00 NZ A:LYS742 3.2 10.4 1.0 O A:HOH2014 3.2 19.6 1.0 CE1 A:TYR746 3.6 8.8 1.0 CD A:LYS742 3.8 8.7 1.0 CE A:LYS742 3.8 9.6 1.0 NZ A:LYS387 3.8 24.8 1.0 CE A:LYS387 3.9 22.0 1.0 CD1 A:TYR746 4.1 8.6 1.0 CG2 A:THR747 4.3 8.4 1.0 CA A:THR747 4.7 8.2 1.0 CZ A:TYR746 4.8 9.2 1.0 CB A:THR747 4.9 8.6 1.0

T.Satoh, T.Toshimori, G.Yan, T.Yamaguchi, K.Kato. Structural Basis For Two-Step Glucose Trimming By Glucosidase II Involved in Er Glycoprotein Quality Control. Sci Rep V. 6 20575 2016.
ISSN: ESSN 2045-2322
PubMed: 26847925
DOI: 10.1038/SREP20575