Magnesium in PDB 8ojm: Galectin-3 in Complex with 2,6-Anhydro-3-Deoxy-3-S-(Beta-D- Galactopyranosyl)-3-Thio-D-Glycero-D-Galacto-Heptonamide

The structure of Galectin-3 in Complex with 2,6-Anhydro-3-Deoxy-3-S-(Beta-D- Galactopyranosyl)-3-Thio-D-Glycero-D-Galacto-Heptonamide, PDB code: 8ojm 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)	36.05 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.05, 57.42, 62.35, 90, 90, 90
R / Rfree (%)	14.9 / 19.1

The binding sites of Magnesium atom in the Galectin-3 in Complex with 2,6-Anhydro-3-Deoxy-3-S-(Beta-D- Galactopyranosyl)-3-Thio-D-Glycero-D-Galacto-Heptonamide (pdb code 8ojm). 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-3-Deoxy-3-S-(Beta-D- Galactopyranosyl)-3-Thio-D-Glycero-D-Galacto-Heptonamide, PDB code: 8ojm:
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-3-Deoxy-3-S-(Beta-D- Galactopyranosyl)-3-Thio-D-Glycero-D-Galacto-Heptonamide


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-3-Deoxy-3-S-(Beta-D- Galactopyranosyl)-3-Thio-D-Glycero-D-Galacto-Heptonamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:27.5 occ:1.00 O A:HOH455 3.5 24.8 1.0 O A:HOH571 3.9 24.7 1.0 O A:HOH561 4.7 17.3 1.0

Magnesium binding site 2 out of 3 in the Galectin-3 in Complex with 2,6-Anhydro-3-Deoxy-3-S-(Beta-D- Galactopyranosyl)-3-Thio-D-Glycero-D-Galacto-Heptonamide


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-3-Deoxy-3-S-(Beta-D- Galactopyranosyl)-3-Thio-D-Glycero-D-Galacto-Heptonamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:16.9 occ:1.00 O A:HOH572 2.7 11.7 1.0 O A:HOH652 2.7 16.1 1.0 O A:HOH544 3.0 11.3 1.0 NH1 A:ARG224 3.1 8.1 1.0 CD A:ARG224 3.5 7.5 1.0 CA A:GLY182 3.7 9.6 1.0 CB A:THR175 3.7 7.0 1.0 CG2 A:THR175 3.9 6.4 1.0 O A:HOH657 4.0 19.3 1.0 O A:THR175 4.0 7.5 1.0 CZ A:ARG224 4.1 8.2 1.0 CD1 A:LEU177 4.3 8.9 1.0 NE A:ARG224 4.3 8.1 1.0 N A:GLY182 4.3 9.8 1.0 O A:HOH602 4.4 19.6 1.0 C A:THR175 4.6 7.5 1.0 OG1 A:THR175 4.6 7.1 1.0 CA A:THR175 4.7 7.3 1.0 N A:ARG183 4.7 11.0 1.0 O A:HOH615 4.7 26.6 1.0 OD1 A:ASN174 4.7 8.0 1.0 CG A:LEU177 4.7 8.6 1.0 C A:GLY182 4.7 9.8 1.0 CG A:ARG224 4.7 7.2 1.0 O A:HOH633 4.7 28.7 1.0 CB A:ARG224 4.8 6.9 1.0 N A:THR175 4.8 7.2 1.0

Magnesium binding site 3 out of 3 in the Galectin-3 in Complex with 2,6-Anhydro-3-Deoxy-3-S-(Beta-D- Galactopyranosyl)-3-Thio-D-Glycero-D-Galacto-Heptonamide


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-3-Deoxy-3-S-(Beta-D- Galactopyranosyl)-3-Thio-D-Glycero-D-Galacto-Heptonamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:6.8 occ:1.00 O A:HOH608 3.1 8.9 1.0 N A:LYS226 3.1 8.2 1.0 N A:LYS227 3.4 7.7 1.0 CG A:LYS227 3.8 10.8 1.0 CG1 A:VAL225 3.9 7.1 1.0 CA A:LYS226 3.9 8.2 1.0 CB A:LYS226 3.9 8.4 1.0 CD A:LYS227 4.0 13.8 1.0 CB A:LYS227 4.0 9.3 1.0 C A:VAL225 4.1 8.1 1.0 CA A:VAL225 4.1 7.4 1.0 C A:LYS226 4.1 7.6 1.0 NH1 A:ARG151 4.1 7.9 1.0 CA A:LYS227 4.3 7.9 1.0 CG A:LYS226 4.4 8.9 1.0 CZ A:ARG151 4.5 8.8 1.0 O A:HOH463 4.5 8.8 1.0 CE A:LYS227 4.6 16.4 1.0 CB A:VAL225 4.6 7.3 1.0 NE A:ARG151 4.7 8.2 1.0 O A:HOH496 4.7 9.6 1.0 CD A:ARG151 4.9 8.1 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