Magnesium in PDB 9ena: Lysosomal Glucocerebrosidase in Complex with A Stabilizing Nanobody

All present enzymatic activity of Lysosomal Glucocerebrosidase in Complex with A Stabilizing Nanobody:
3.2.1.104; 3.2.1.45;

The structure of Lysosomal Glucocerebrosidase in Complex with A Stabilizing Nanobody, PDB code: 9ena was solved by T.Dal Maso, W.Versees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.86 / 1.70
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	113.209, 113.209, 257.373, 90, 90, 90
R / Rfree (%)	16.3 / 19.4

The binding sites of Magnesium atom in the Lysosomal Glucocerebrosidase in Complex with A Stabilizing Nanobody (pdb code 9ena). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Lysosomal Glucocerebrosidase in Complex with A Stabilizing Nanobody, PDB code: 9ena:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Lysosomal Glucocerebrosidase in Complex with A Stabilizing Nanobody


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Lysosomal Glucocerebrosidase in Complex with A Stabilizing Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:12.4 occ:1.00 O A:HOH836 2.0 20.6 1.0 O A:HOH704 2.1 16.0 1.0 O A:HOH752 2.1 11.1 1.0 O A:HOH653 2.1 13.5 1.0 OE2 A:GLU340 2.1 13.9 1.0 OE2 A:GLU235 2.1 18.3 1.0 CD A:GLU235 3.1 18.1 1.0 CD A:GLU340 3.1 13.7 1.0 OE1 A:GLU340 3.4 13.4 1.0 OE1 A:GLU235 3.4 21.6 1.0 O A:HOH716 3.8 11.2 1.0 O A:HOH778 3.9 18.3 1.0 ND1 A:HIS311 4.0 13.2 1.0 O A:HOH1091 4.1 30.9 1.0 O A:HOH1160 4.1 24.4 1.0 O A:HOH929 4.2 28.9 1.0 CE1 A:HIS311 4.3 10.6 1.0 CG A:GLU235 4.3 11.5 1.0 O A:HOH816 4.4 16.1 1.0 CG A:GLU340 4.4 13.6 1.0 O A:HOH1013 4.7 31.0 1.0 OD1 A:ASN234 4.8 12.9 1.0 ND2 A:ASN234 4.9 12.9 1.0 O A:HOH643 4.9 14.9 1.0

Magnesium binding site 2 out of 2 in the Lysosomal Glucocerebrosidase in Complex with A Stabilizing Nanobody


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Lysosomal Glucocerebrosidase in Complex with A Stabilizing Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:34.9 occ:1.00 O A:HOH663 2.2 29.2 1.0 O A:HOH660 2.2 24.4 1.0 O A:HOH777 2.3 28.8 1.0 NE2 A:HIS365 2.4 22.1 1.0 O A:HOH621 2.5 31.8 1.0 O A:HOH1103 2.5 35.5 1.0 CE1 A:HIS365 3.1 25.2 1.0 CD2 A:HIS365 3.5 19.1 1.0 O A:LEU317 3.8 19.4 1.0 O A:ALA318 4.1 17.9 1.0 OG1 A:THR369 4.1 14.5 1.0 O2 A:SO4505 4.2 35.0 1.0 C A:LEU317 4.2 22.6 1.0 ND1 A:HIS365 4.3 23.4 1.0 O A:HOH1124 4.4 32.6 1.0 CA A:LEU317 4.4 23.1 1.0 O3 A:SO4505 4.5 44.4 1.0 O A:HOH1025 4.5 40.2 1.0 CG A:HIS365 4.6 22.1 1.0 O A:HOH881 4.6 32.5 1.0 O A:PHE316 4.6 20.8 1.0 C A:ALA318 4.7 22.7 1.0 N A:ALA318 4.9 21.8 1.0

T.Dal Maso, C.Sinisgalli, G.Zilio, E.Franzin, I.Tessari, E.Pardon, J.Steyaert, S.Ballet, E.Greggio, W.Versees, N.Plotegher. Developing Nanobodies As Allosteric Molecular Chaperones of Glucocerebrosidase Function. Nat Commun V. 16 4890 2025.
ISSN: ESSN 2041-1723
PubMed: 40425544
DOI: 10.1038/S41467-025-60134-4