Magnesium in PDB 5ysd: Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Complex with Sophorotriose

The structure of Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Complex with Sophorotriose, PDB code: 5ysd was solved by K.Abe, M.Nakajima, H.Taguchi, T.Arakawa, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.95 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.082, 125.561, 91.780, 90.00, 101.61, 90.00
R / Rfree (%)	16.9 / 20.7

The binding sites of Magnesium atom in the Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Complex with Sophorotriose (pdb code 5ysd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Complex with Sophorotriose, PDB code: 5ysd:

Magnesium binding site 1 out of 1 in the Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Complex with Sophorotriose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Complex with Sophorotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:33.4 occ:1.00 O A:HOH755 2.2 44.8 1.0 O A:SER181 2.3 37.2 1.0 O A:HOH722 2.3 45.8 1.0 O A:MET187 2.4 39.0 1.0 O A:GLY184 2.4 46.5 1.0 C A:SER181 3.3 35.8 1.0 C A:MET187 3.5 40.5 1.0 C A:GLY184 3.5 49.8 1.0 CB A:SER181 3.7 35.0 1.0 CA A:SER181 3.7 34.6 1.0 N A:MET187 3.8 48.8 1.0 CA A:MET187 4.1 44.9 1.0 CA A:LYS185 4.2 60.0 1.0 CB A:MET187 4.2 46.0 1.0 N A:LYS185 4.3 55.2 1.0 N A:GLY184 4.4 44.1 1.0 N A:LYS182 4.4 35.8 1.0 N A:ASP186 4.5 59.0 1.0 OG A:SER181 4.5 35.8 1.0 O A:HOH635 4.5 24.7 1.0 C A:LYS185 4.5 59.7 1.0 CA A:GLY184 4.6 48.0 1.0 N A:TYR188 4.6 37.0 1.0 O A:GLY239 4.7 33.1 1.0 CA A:LYS182 4.8 38.1 1.0 CA A:TYR188 4.9 34.6 1.0 C A:ASP186 5.0 54.2 1.0

K.Abe, N.Sunagawa, T.Terada, Y.Takahashi, T.Arakawa, K.Igarashi, M.Samejima, H.Nakai, H.Taguchi, M.Nakajima, S.Fushinobu. Structural and Thermodynamic Insights Into Beta-1,2-Glucooligosaccharide Capture By A Solute-Binding Protein Inlisteria Innocua. J. Biol. Chem. V. 293 8812 2018.
ISSN: ESSN 1083-351X
PubMed: 29678880
DOI: 10.1074/JBC.RA117.001536