Magnesium in PDB 3wy3: Crystal Structure of Alpha-Glucosidase Mutant D202N in Complex with Glucose and Glycerol

All present enzymatic activity of Crystal Structure of Alpha-Glucosidase Mutant D202N in Complex with Glucose and Glycerol:
3.2.1.20;

The structure of Crystal Structure of Alpha-Glucosidase Mutant D202N in Complex with Glucose and Glycerol, PDB code: 3wy3 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)	42.54 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.530, 119.570, 177.940, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.4

The binding sites of Magnesium atom in the Crystal Structure of Alpha-Glucosidase Mutant D202N in Complex with Glucose and Glycerol (pdb code 3wy3). 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 Mutant D202N in Complex with Glucose and Glycerol, PDB code: 3wy3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Alpha-Glucosidase Mutant D202N in Complex with Glucose and Glycerol


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 Mutant D202N in Complex with Glucose and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg600 b:76.8 occ:1.00 OD1 A:ASP27 2.5 63.8 1.0 OD2 A:ASP31 2.7 66.6 1.0 OD2 A:ASP27 2.8 61.6 1.0 O A:VAL29 2.8 37.1 1.0 CG A:ASP27 2.9 62.3 1.0 OD1 A:ASP23 3.1 60.7 1.0 CG A:ASP31 3.6 64.6 1.0 O A:MET76 3.7 49.7 1.0 CB A:ASP31 3.7 60.4 1.0 CB A:ARG25 3.9 72.2 1.0 C A:VAL29 3.9 36.9 1.0 CG A:ASP23 4.2 64.7 1.0 CB A:ASP27 4.4 51.9 1.0 N A:ARG25 4.5 63.7 1.0 N A:ASP31 4.6 60.7 1.0 C A:GLY30 4.6 40.1 1.0 N A:ASP27 4.6 62.6 1.0 N A:VAL29 4.6 29.6 1.0 CA A:VAL29 4.6 31.9 1.0 CB A:VAL29 4.6 34.5 1.0 O A:GLY30 4.7 39.3 1.0 CA A:ARG25 4.7 74.0 1.0 OD1 A:ASP31 4.7 66.7 1.0 CA A:ASP31 4.7 60.4 1.0 CD A:ARG25 4.7 94.1 1.0 N A:GLY26 4.8 53.5 1.0 CG A:ARG25 4.8 80.5 1.0 N A:GLY30 4.9 35.9 1.0 C A:MET76 4.9 50.8 1.0 CB A:ASP23 5.0 56.4 1.0 N A:SER24 5.0 45.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Alpha-Glucosidase Mutant D202N in Complex with Glucose and Glycerol


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 Mutant D202N in Complex with Glucose and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg600 b:53.0 occ:1.00 OD1 B:ASP27 2.5 52.8 1.0 O B:VAL29 2.7 43.2 1.0 OD2 B:ASP27 2.7 46.6 1.0 OD2 B:ASP31 2.7 56.7 1.0 CG B:ASP27 3.0 47.7 1.0 OD1 B:ASP23 3.3 49.3 1.0 O B:MET76 3.3 41.0 1.0 CG B:ASP31 3.6 49.0 1.0 CB B:ASP31 3.7 43.2 1.0 C B:VAL29 3.7 41.4 1.0 CB B:ARG25 3.8 53.5 1.0 CD B:ARG25 4.2 64.2 1.0 NE B:ARG25 4.2 71.6 1.0 CB B:VAL29 4.3 40.3 1.0 CG B:ASP23 4.3 57.7 1.0 C B:GLY30 4.4 35.5 1.0 CA B:VAL29 4.4 40.3 1.0 O B:GLY30 4.4 32.6 1.0 N B:ASP31 4.5 46.2 1.0 CB B:ASP27 4.5 47.0 1.0 N B:VAL29 4.5 45.1 1.0 C B:MET76 4.5 40.9 1.0 CG B:ARG25 4.6 61.2 1.0 CZ B:ARG25 4.6 67.7 1.0 CA B:ASP31 4.6 41.7 1.0 N B:ARG25 4.7 47.3 1.0 N B:GLY30 4.7 36.4 1.0 OD1 B:ASP31 4.8 51.1 1.0 CA B:ARG25 4.8 47.3 1.0 N B:ASP27 4.8 50.2 1.0 NH1 B:ARG25 4.9 54.0 1.0 CG1 B:VAL29 4.9 41.9 1.0 CA B:GLY30 4.9 36.1 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