Magnesium in PDB 3wy2: Crystal Structure of Alpha-Glucosidase in Complex with Glucose

All present enzymatic activity of Crystal Structure of Alpha-Glucosidase in Complex with Glucose:
3.2.1.20;

The structure of Crystal Structure of Alpha-Glucosidase in Complex with Glucose, PDB code: 3wy2 was solved by X.Shen, Z.Gai, K.Kato, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.09 / 1.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.219, 103.809, 176.890, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 17.9

The binding sites of Magnesium atom in the Crystal Structure of Alpha-Glucosidase in Complex with Glucose (pdb code 3wy2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Alpha-Glucosidase in Complex with Glucose, PDB code: 3wy2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Alpha-Glucosidase in Complex with Glucose


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 Alpha-Glucosidase in Complex with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg600 b:19.5 occ:0.46 O A:HOH779 1.9 20.0 1.0 OD1 A:ASP23 2.0 15.1 1.0 OD2 A:ASP31 2.0 15.0 1.0 O A:VAL29 2.1 11.0 1.0 OD1 A:ASP27 3.0 23.9 1.0 CG A:ASP23 3.0 14.0 1.0 CG A:ASP31 3.1 11.4 1.0 C A:VAL29 3.3 9.8 1.0 CB A:ASP31 3.6 11.4 1.0 CB A:ARG25 3.6 19.8 1.0 CA A:ASP23 3.7 10.6 1.0 CB A:ASP23 3.7 11.5 1.0 N A:ARG25 3.7 18.8 1.0 CG A:ASP27 4.0 31.3 1.0 OD2 A:ASP23 4.0 13.2 1.0 C A:GLY30 4.0 13.0 1.0 N A:SER24 4.1 15.2 1.0 CG A:ARG25 4.1 22.7 1.0 N A:ASP31 4.1 10.4 1.0 N A:GLY26 4.1 19.3 1.0 CA A:ARG25 4.1 20.3 1.0 C A:ASP23 4.2 10.8 1.0 N A:VAL29 4.2 10.2 1.0 OD1 A:ASP31 4.2 14.2 1.0 CA A:VAL29 4.2 10.6 1.0 N A:GLY30 4.2 9.8 1.0 CA A:GLY30 4.3 12.3 1.0 OD2 A:ASP27 4.3 42.0 1.0 O A:MET76 4.3 14.2 1.0 O A:GLY30 4.4 11.3 1.0 CD A:ARG25 4.4 41.1 1.0 CA A:ASP31 4.5 11.4 1.0 N A:ASP27 4.5 13.6 1.0 CB A:VAL29 4.6 13.1 1.0 C A:ARG25 4.6 23.7 1.0 C A:SER24 4.9 22.2 1.0 N A:ASP23 5.0 10.9 1.0 N A:GLY28 5.0 12.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Alpha-Glucosidase in Complex with Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Alpha-Glucosidase in Complex with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:34.1 occ:0.47 O B:HOH816 2.0 24.1 1.0 OD1 B:ASP23 2.0 25.8 1.0 O B:VAL29 2.2 21.2 1.0 OD2 B:ASP31 2.4 24.3 1.0 OD1 B:ASP27 2.5 39.9 1.0 CG B:ASP23 3.0 27.6 1.0 C B:VAL29 3.4 20.8 1.0 CG B:ASP31 3.5 20.6 1.0 CB B:ARG25 3.5 34.4 1.0 CG B:ASP27 3.7 36.0 1.0 N B:ARG25 3.7 28.6 1.0 CB B:ASP23 3.8 21.8 1.0 N B:GLY26 3.9 30.0 1.0 CA B:ASP23 3.9 20.8 1.0 OD2 B:ASP23 3.9 27.7 1.0 CB B:ASP31 3.9 18.7 1.0 N B:VAL29 4.0 22.7 1.0 CA B:ARG25 4.0 34.1 1.0 N B:ASP27 4.1 28.1 1.0 CA B:VAL29 4.2 20.8 1.0 CG B:ARG25 4.2 37.0 1.0 N B:SER24 4.2 22.4 1.0 CD B:ARG25 4.2 37.1 1.0 C B:GLY30 4.3 21.9 1.0 C B:ASP23 4.3 26.9 1.0 OD2 B:ASP27 4.4 33.5 1.0 N B:GLY30 4.4 17.7 1.0 O B:MET76 4.4 24.4 1.0 C B:ARG25 4.4 36.6 1.0 N B:ASP31 4.4 17.6 1.0 CA B:GLY30 4.5 18.8 1.0 CB B:VAL29 4.5 21.9 1.0 O B:GLY30 4.6 22.1 1.0 OD1 B:ASP31 4.6 22.9 1.0 NH2 B:ARG25 4.6 48.3 1.0 N B:GLY28 4.7 24.9 1.0 CB B:ASP27 4.8 28.2 1.0 CA B:ASP31 4.8 19.5 1.0 CA B:ASP27 4.8 26.4 1.0 C B:SER24 4.9 30.8 1.0 CA B:GLY26 4.9 31.0 1.0

X.Shen, W.Saburi, Z.Gai, K.Kato, T.Ojima-Kato, J.Yu, K.Komoda, Y.Kido, H.Matsui, H.Mori, M.Yao. Structural Analysis of the Alpha-Glucosidase Hag Provides New Insights Into Substrate Specificity and Catalytic Mechanism Acta Crystallogr. D Biol. V. 71 1382 2015CRYSTALLOGR..
ISSN: ESSN 1399-0047
PubMed: 26057678
DOI: 10.1107/S139900471500721X