Magnesium in PDB 3wy1: Crystal Structure of Alpha-Glucosidase

All present enzymatic activity of Crystal Structure of Alpha-Glucosidase:
3.2.1.20;

The structure of Crystal Structure of Alpha-Glucosidase, PDB code: 3wy1 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)	44.49 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.540, 119.590, 177.970, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.9

The binding sites of Magnesium atom in the Crystal Structure of Alpha-Glucosidase (pdb code 3wy1). 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, PDB code: 3wy1:
Jump to Magnesium binding site number: 1; 2;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg600 b:43.0 occ:1.00 O A:HOH934 2.1 37.8 1.0 O A:VAL29 2.2 39.3 1.0 OD1 A:ASP23 2.4 41.1 1.0 OD1 A:ASP27 2.4 42.6 1.0 OD2 A:ASP31 2.4 44.9 1.0 CG A:ASP27 3.2 40.8 1.0 OD2 A:ASP27 3.3 44.8 1.0 CG A:ASP23 3.4 42.3 1.0 CG A:ASP31 3.4 42.8 1.0 C A:VAL29 3.4 38.7 1.0 CB A:ASP31 3.8 45.6 1.0 CB A:ASP23 4.0 42.4 1.0 CA A:ASP23 4.0 41.4 1.0 N A:ARG25 4.1 47.0 1.0 CB A:ARG25 4.2 50.7 1.0 N A:VAL29 4.2 35.4 1.0 C A:GLY30 4.2 40.5 1.0 N A:ASP31 4.2 40.3 1.0 CA A:VAL29 4.3 40.3 1.0 OD2 A:ASP23 4.3 45.2 1.0 N A:SER24 4.3 45.2 1.0 N A:GLY30 4.4 39.9 1.0 N A:ASP27 4.4 44.0 1.0 N A:GLY26 4.4 45.4 1.0 CB A:VAL29 4.4 36.7 1.0 O A:GLY30 4.5 40.9 1.0 CA A:GLY30 4.5 37.0 1.0 CA A:ARG25 4.5 52.2 1.0 C A:ASP23 4.5 43.2 1.0 OD1 A:ASP31 4.6 45.7 1.0 CA A:ASP31 4.6 42.2 1.0 CB A:ASP27 4.6 44.0 1.0 O A:MET76 4.6 38.8 1.0 N A:GLY28 4.9 42.6 1.0 C A:ARG25 4.9 48.4 1.0 CA A:ASP27 5.0 42.3 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:42.3 occ:1.00 O B:VAL29 2.1 36.4 1.0 O B:HOH705 2.2 37.0 1.0 OD1 B:ASP31 2.2 37.5 1.0 OD1 B:ASP23 2.4 39.2 1.0 OD1 B:ASP27 2.4 43.7 1.0 CG B:ASP31 3.2 38.0 1.0 CG B:ASP27 3.3 43.7 1.0 C B:VAL29 3.3 37.6 1.0 CG B:ASP23 3.4 40.2 1.0 OD2 B:ASP27 3.4 44.8 1.0 CB B:ASP31 3.6 33.4 1.0 CB B:ARG25 3.8 44.6 1.0 CB B:ASP23 4.0 38.7 1.0 N B:ASP31 4.0 26.9 1.0 N B:ARG25 4.0 39.7 1.0 C B:GLY30 4.0 34.0 1.0 CA B:ASP23 4.0 36.9 1.0 N B:VAL29 4.1 39.0 1.0 CA B:VAL29 4.2 37.5 1.0 OD2 B:ASP23 4.3 41.5 1.0 O B:GLY30 4.3 33.0 1.0 N B:GLY30 4.3 35.0 1.0 CB B:VAL29 4.3 40.9 1.0 N B:SER24 4.3 38.7 1.0 CA B:ASP31 4.4 30.9 1.0 OD2 B:ASP31 4.4 34.1 1.0 CA B:ARG25 4.4 44.5 1.0 CA B:GLY30 4.4 30.0 1.0 N B:GLY26 4.4 45.5 1.0 N B:ASP27 4.5 49.4 1.0 O B:MET76 4.5 35.6 1.0 C B:ASP23 4.5 40.0 1.0 CB B:ASP27 4.7 40.1 1.0 NE B:ARG25 4.8 54.5 1.0 C B:ARG25 4.9 46.8 1.0 N B:GLY28 4.9 45.1 1.0 CG B:ARG25 4.9 53.2 1.0 CD B:ARG25 4.9 52.7 1.0 CG1 B:VAL29 4.9 36.5 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