Magnesium in PDB 8ojo: Galectin-3 in Complex with 2,6-Anhydro-5-S-(Beta-D-Galactopyranosyl)- 5-Thio-D-Altritol

The structure of Galectin-3 in Complex with 2,6-Anhydro-5-S-(Beta-D-Galactopyranosyl)- 5-Thio-D-Altritol, PDB code: 8ojo was solved by A.S.Tsagkarakou, D.D.Leonidas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.16 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	35.92, 58.09, 62.48, 90, 90, 90
R / Rfree (%)	13.6 / 17.6

The binding sites of Magnesium atom in the Galectin-3 in Complex with 2,6-Anhydro-5-S-(Beta-D-Galactopyranosyl)- 5-Thio-D-Altritol (pdb code 8ojo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Galectin-3 in Complex with 2,6-Anhydro-5-S-(Beta-D-Galactopyranosyl)- 5-Thio-D-Altritol, PDB code: 8ojo:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Galectin-3 in Complex with 2,6-Anhydro-5-S-(Beta-D-Galactopyranosyl)- 5-Thio-D-Altritol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Galectin-3 in Complex with 2,6-Anhydro-5-S-(Beta-D-Galactopyranosyl)- 5-Thio-D-Altritol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:19.2 occ:1.00 OE1 A:GLN201 2.7 17.6 1.0 N A:ASP215 2.9 10.6 1.0 O A:ALA212 3.1 8.4 1.0 N A:ASN214 3.2 7.9 1.0 CD A:GLN201 3.4 13.9 1.0 C A:ALA212 3.4 8.1 1.0 O A:LYS199 3.5 9.0 1.0 CA A:ASP215 3.6 12.1 1.0 C A:VAL213 3.6 8.0 1.0 CG A:GLN201 3.6 12.3 1.0 CE A:LYS199 3.7 11.7 1.0 CA A:VAL213 3.7 7.8 1.0 N A:VAL213 3.7 7.4 1.0 CB A:ALA212 3.8 7.9 1.0 CB A:GLN201 3.8 9.9 1.0 C A:ASN214 3.9 9.8 1.0 CA A:ASN214 4.0 9.2 1.0 N A:GLN201 4.0 8.2 1.0 CG A:LYS199 4.0 10.3 1.0 OD1 A:ASP215 4.1 14.6 1.0 C A:LYS199 4.2 8.5 1.0 CA A:ALA212 4.2 7.4 1.0 O A:VAL213 4.3 8.0 1.0 CD A:LYS199 4.4 10.1 1.0 CB A:LYS199 4.4 10.0 1.0 NE2 A:GLN201 4.5 19.6 1.0 C A:ASP215 4.5 12.5 1.0 CA A:GLN201 4.6 8.7 1.0 C A:ILE200 4.6 8.9 1.0 CG A:ASP215 4.6 15.7 1.0 N A:ALA216 4.7 10.5 1.0 CA A:ILE200 4.7 8.1 1.0 CB A:ASP215 4.7 13.3 1.0 N A:ILE200 4.7 8.0 1.0 NZ A:LYS199 4.8 13.6 1.0 CA A:LYS199 5.0 8.4 1.0

Magnesium binding site 2 out of 3 in the Galectin-3 in Complex with 2,6-Anhydro-5-S-(Beta-D-Galactopyranosyl)- 5-Thio-D-Altritol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Galectin-3 in Complex with 2,6-Anhydro-5-S-(Beta-D-Galactopyranosyl)- 5-Thio-D-Altritol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:45.8 occ:1.00 O A:SER194 3.6 11.0 1.0 O A:HOH428 3.6 22.5 1.0 C A:SER194 3.8 10.7 1.0 CA A:GLY195 4.1 9.5 1.0 N A:GLY195 4.1 9.2 1.0 CA A:PRO140 4.1 17.3 1.0 CB A:PRO140 4.2 19.7 1.0 CB A:SER194 4.2 14.1 1.0 CA A:SER194 4.7 10.9 1.0 CG A:PRO140 4.9 20.9 1.0 N A:ASN141 4.9 18.2 1.0

Magnesium binding site 3 out of 3 in the Galectin-3 in Complex with 2,6-Anhydro-5-S-(Beta-D-Galactopyranosyl)- 5-Thio-D-Altritol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Galectin-3 in Complex with 2,6-Anhydro-5-S-(Beta-D-Galactopyranosyl)- 5-Thio-D-Altritol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:5.5 occ:1.00 O A:HOH572 3.1 9.1 1.0 N A:LYS226 3.2 8.4 1.0 N A:LYS227 3.4 7.7 1.0 CG A:LYS227 3.7 10.0 1.0 CG1 A:VAL225 3.9 8.5 1.0 CA A:LYS226 4.0 9.0 1.0 CB A:LYS226 4.0 9.1 1.0 CB A:LYS227 4.0 8.8 1.0 CD A:LYS227 4.0 10.8 1.0 CA A:VAL225 4.1 8.0 1.0 C A:VAL225 4.1 8.2 1.0 C A:LYS226 4.1 8.5 1.0 NH1 A:ARG151 4.3 9.8 1.0 CA A:LYS227 4.3 8.2 1.0 CG A:LYS226 4.4 9.9 1.0 CZ A:ARG151 4.5 10.5 1.0 CB A:VAL225 4.5 8.4 1.0 O A:HOH439 4.6 9.2 1.0 CE A:LYS227 4.7 11.9 1.0 O A:HOH498 4.7 8.6 1.0 NE A:ARG151 4.7 9.2 1.0 CD A:ARG151 4.9 9.2 1.0

L.Lazar, A.S.Tsagkarakou, G.Stravodimos, G.Kontopidis, H.Leffler, U.J.Nilsson, L.Somsak, D.D.Leonidas. Strong Binding of C -GLYCOSYLIC1,2-Thiodisaccharides to Galectin-3─Enthalpy-Driven Affinity Enhancement By Water-Mediated Hydrogen Bonds. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37658813
DOI: 10.1021/ACS.JMEDCHEM.3C00882