Magnesium in PDB 6lgc: Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1-Deoxynojirimycin

The structure of Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1-Deoxynojirimycin, PDB code: 6lgc was solved by T.Miyazaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.97 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.634, 146.750, 154.025, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 19.7

The structure of Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1-Deoxynojirimycin also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1-Deoxynojirimycin (pdb code 6lgc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1-Deoxynojirimycin, PDB code: 6lgc:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1-Deoxynojirimycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1-Deoxynojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:29.6 occ:1.00 O A:HOH842 2.1 32.6 1.0 OD2 A:ASP71 2.1 31.6 1.0 OD1 A:ASP65 2.1 34.4 1.0 OD1 A:ASP67 2.1 33.5 1.0 OD1 A:ASP63 2.2 31.6 1.0 O A:ILE69 2.2 28.6 1.0 CG A:ASP67 3.0 35.0 1.0 CG A:ASP65 3.1 43.5 1.0 CG A:ASP63 3.2 27.8 1.0 CG A:ASP71 3.2 27.6 1.0 OD2 A:ASP67 3.3 35.6 1.0 C A:ILE69 3.3 29.3 1.0 OD2 A:ASP65 3.5 44.2 1.0 CB A:ASP71 3.9 28.8 1.0 CB A:ASP63 3.9 30.0 1.0 OD2 A:ASP63 4.0 29.1 1.0 CA A:ASP63 4.0 28.4 1.0 N A:ILE69 4.0 27.8 1.0 N A:ASP65 4.0 31.2 1.0 CA A:ILE69 4.1 29.6 1.0 CB A:ILE69 4.2 30.5 1.0 N A:SER64 4.3 31.0 1.0 OD1 A:ASP71 4.3 27.4 1.0 CB A:ASP67 4.3 32.5 1.0 N A:ASP67 4.4 31.1 1.0 N A:GLY70 4.4 28.2 1.0 CB A:ASP65 4.4 35.9 1.0 C A:GLY70 4.5 27.1 1.0 C A:ASP63 4.5 32.4 1.0 CA A:ASP65 4.6 34.1 1.0 N A:ASP71 4.6 25.8 1.0 CA A:GLY70 4.6 28.5 1.0 O A:GLU116 4.6 31.8 1.0 N A:GLY66 4.6 29.3 1.0 O A:GLY70 4.7 29.7 1.0 C A:ASP65 4.8 33.5 1.0 CG2 A:ILE69 4.8 29.8 1.0 CA A:ASP67 4.8 33.2 1.0 CA A:ASP71 4.9 27.5 1.0 N A:GLY68 4.9 29.1 1.0

Magnesium binding site 2 out of 3 in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1-Deoxynojirimycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1-Deoxynojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg706 b:28.0 occ:1.00 O B:HOH882 2.0 22.8 1.0 O B:HOH1181 2.1 25.0 1.0 O A:HOH869 2.1 23.6 1.0 O B:HOH875 2.2 24.3 1.0 O A:HOH1157 2.2 21.9 1.0 O A:HOH1161 2.3 21.3 1.0 OD2 A:ASP523 4.0 24.4 1.0 OD1 B:ASP523 4.0 23.5 1.0 NE2 B:HIS564 4.1 23.8 1.0 NE2 A:HIS564 4.1 25.7 1.0 O B:HOH1221 4.1 22.9 1.0 O B:HOH1205 4.1 40.2 1.0 OD1 A:ASP523 4.2 26.2 1.0 OD2 B:ASP523 4.2 22.6 1.0 O A:HOH1194 4.2 30.7 1.0 O A:HOH1195 4.2 30.9 1.0 O A:HOH1197 4.3 25.9 1.0 O B:HOH1214 4.3 26.6 1.0 O A:HOH1183 4.3 29.0 1.0 CG A:ASP523 4.4 24.9 1.0 O B:HOH1207 4.4 26.1 1.0 CG B:ASP523 4.4 24.1 1.0 O A:HOH1113 4.6 26.2 1.0 O B:HOH1140 4.6 31.6 1.0 CE1 B:HIS564 4.6 27.2 1.0 CE1 A:HIS564 4.6 30.5 1.0

Magnesium binding site 3 out of 3 in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1-Deoxynojirimycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1-Deoxynojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:23.5 occ:1.00 OD1 B:ASP63 2.1 27.4 1.0 O B:HOH881 2.1 23.8 1.0 OD1 B:ASP65 2.1 32.1 1.0 OD2 B:ASP71 2.2 24.5 1.0 O B:ILE69 2.2 25.6 1.0 OD1 B:ASP67 2.2 25.6 1.0 CG B:ASP67 3.1 31.2 1.0 CG B:ASP63 3.1 30.3 1.0 CG B:ASP65 3.2 36.7 1.0 CG B:ASP71 3.3 24.8 1.0 C B:ILE69 3.4 25.9 1.0 OD2 B:ASP67 3.4 27.2 1.0 OD2 B:ASP65 3.8 44.4 1.0 CB B:ASP63 3.8 29.1 1.0 CB B:ASP71 3.9 25.1 1.0 OD2 B:ASP63 3.9 27.9 1.0 N B:ILE69 4.0 29.1 1.0 CA B:ASP63 4.0 27.2 1.0 CA B:ILE69 4.1 26.9 1.0 N B:ASP65 4.1 33.0 1.0 N B:SER64 4.2 29.1 1.0 CB B:ILE69 4.3 28.9 1.0 CB B:ASP67 4.4 33.3 1.0 N B:ASP67 4.4 31.4 1.0 OD1 B:ASP71 4.4 25.3 1.0 C B:GLY70 4.4 23.9 1.0 N B:GLY70 4.4 25.2 1.0 CB B:ASP65 4.4 33.0 1.0 C B:ASP63 4.5 31.3 1.0 O B:GLY70 4.5 27.5 1.0 CA B:ASP65 4.6 35.3 1.0 N B:GLY66 4.6 36.6 1.0 N B:ASP71 4.7 27.2 1.0 CA B:GLY70 4.7 24.6 1.0 O B:GLU116 4.7 30.7 1.0 C B:ASP65 4.7 37.0 1.0 CA B:ASP67 4.8 28.6 1.0 CG2 B:ILE69 4.9 27.1 1.0 CA B:ASP71 4.9 25.8 1.0 N B:GLY68 4.9 31.2 1.0 C B:ASP67 5.0 27.4 1.0

T.Miyazaki, E.Y.Park. Structure-Function Analysis of Silkworm Sucrose Hydrolase Uncovers the Mechanism of Substrate Specificity in GH13 Subfamily 17EXO-Alpha-Glucosidases. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32381508
DOI: 10.1074/JBC.RA120.013595