Magnesium in PDB 6lgd: Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol

The structure of Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol, PDB code: 6lgd was solved by T.Miyazaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.29 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.054, 146.444, 153.291, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 18.4

The structure of Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol 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 1,4-Dideoxy-1,4- Imino-D-Arabinitol (pdb code 6lgd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol, PDB code: 6lgd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol


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 1,4-Dideoxy-1,4- Imino-D-Arabinitol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:28.5 occ:1.00 O A:HOH837 2.1 32.4 1.0 OD1 A:ASP63 2.1 28.4 1.0 OD1 A:ASP65 2.1 34.6 1.0 OD1 A:ASP67 2.2 32.0 1.0 O A:ILE69 2.2 26.6 1.0 OD2 A:ASP71 2.2 29.3 1.0 CG A:ASP67 3.0 31.8 1.0 CG A:ASP63 3.1 27.4 1.0 CG A:ASP65 3.2 41.9 1.0 OD2 A:ASP67 3.3 33.2 1.0 CG A:ASP71 3.3 28.2 1.0 C A:ILE69 3.4 27.2 1.0 OD2 A:ASP65 3.7 43.1 1.0 CB A:ASP71 3.9 27.3 1.0 CB A:ASP63 4.0 29.3 1.0 OD2 A:ASP63 4.0 29.9 1.0 N A:ILE69 4.0 26.2 1.0 CA A:ILE69 4.0 28.1 1.0 CA A:ASP63 4.1 27.8 1.0 N A:ASP65 4.1 34.4 1.0 CB A:ILE69 4.2 27.9 1.0 N A:SER64 4.2 30.6 1.0 CB A:ASP67 4.3 32.0 1.0 N A:ASP67 4.3 30.9 1.0 OD1 A:ASP71 4.4 29.4 1.0 N A:GLY70 4.4 26.9 1.0 CB A:ASP65 4.4 37.8 1.0 C A:GLY70 4.5 26.8 1.0 C A:ASP63 4.5 31.3 1.0 CA A:ASP65 4.6 36.2 1.0 N A:GLY66 4.6 34.8 1.0 N A:ASP71 4.6 26.3 1.0 O A:GLY70 4.6 28.7 1.0 O A:GLU116 4.7 33.2 1.0 CA A:GLY70 4.7 27.0 1.0 C A:ASP65 4.7 36.0 1.0 CA A:ASP67 4.7 32.0 1.0 CG2 A:ILE69 4.8 29.2 1.0 N A:GLY68 4.9 30.1 1.0 C A:ASP67 4.9 31.4 1.0 CA A:ASP71 5.0 27.7 1.0

Magnesium binding site 2 out of 4 in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol


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 1,4-Dideoxy-1,4- Imino-D-Arabinitol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:28.4 occ:1.00 O B:HOH925 2.0 23.8 1.0 O A:HOH946 2.1 25.1 1.0 O B:HOH1258 2.1 23.8 1.0 O A:HOH1220 2.1 24.8 1.0 O B:HOH919 2.1 22.9 1.0 O A:HOH1219 2.1 25.4 1.0 NE2 A:HIS564 4.0 30.1 1.0 NE2 B:HIS564 4.1 26.3 1.0 OD1 B:ASP523 4.1 25.8 1.0 OD1 A:ASP523 4.1 26.8 1.0 O B:HOH1308 4.1 26.3 1.0 O B:HOH1277 4.1 39.4 1.0 OD2 A:ASP523 4.1 27.9 1.0 O A:HOH1260 4.2 32.3 1.0 OD2 B:ASP523 4.2 26.5 1.0 O A:HOH1243 4.2 30.3 1.0 O A:HOH1263 4.3 32.5 1.0 O B:HOH1281 4.3 31.2 1.0 O B:HOH1303 4.3 26.9 1.0 O B:HOH1301 4.3 31.2 1.0 CG A:ASP523 4.5 26.6 1.0 CG B:ASP523 4.5 25.1 1.0 O A:HOH1184 4.5 30.8 1.0 O B:HOH1206 4.6 29.5 1.0 CE1 A:HIS564 4.6 31.1 1.0 CE1 B:HIS564 4.6 26.8 1.0

Magnesium binding site 3 out of 4 in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol


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 1,4-Dideoxy-1,4- Imino-D-Arabinitol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:41.9 occ:1.00 O A:HOH815 2.0 42.4 1.0 O A:HOH1200 2.0 48.5 1.0 O A:HOH1180 2.1 49.6 1.0 O A:HOH1057 2.1 54.2 1.0 O A:HOH859 2.4 33.9 1.0 O A:HOH1055 4.1 42.1 1.0 O A:ASP389 4.1 25.6 1.0 O A:TYR453 4.2 31.5 1.0 OE2 A:GLU440 4.2 35.2 1.0 O A:HOH1197 4.3 38.4 1.0 OE1 A:GLU440 4.4 32.6 1.0 O2 A:GOL707 4.5 42.7 1.0 CD A:GLU440 4.6 33.3 1.0 O3 A:GOL707 4.9 39.0 1.0 C3 A:GOL707 4.9 43.8 1.0 CG A:ARG455 5.0 25.9 1.0 O A:LEU452 5.0 41.0 1.0

Magnesium binding site 4 out of 4 in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:25.4 occ:1.00 O B:HOH867 2.1 28.1 1.0 OD1 B:ASP63 2.1 27.1 1.0 OD1 B:ASP65 2.1 32.7 1.0 O B:ILE69 2.1 25.1 1.0 OD2 B:ASP71 2.2 26.8 1.0 OD1 B:ASP67 2.3 26.2 1.0 CG B:ASP67 3.2 29.5 1.0 CG B:ASP63 3.2 28.6 1.0 CG B:ASP65 3.3 34.5 1.0 CG B:ASP71 3.3 25.4 1.0 C B:ILE69 3.4 25.3 1.0 OD2 B:ASP67 3.5 29.7 1.0 OD2 B:ASP65 3.8 40.4 1.0 CB B:ASP71 3.8 26.0 1.0 CB B:ASP63 3.9 28.2 1.0 OD2 B:ASP63 4.0 26.9 1.0 CA B:ASP63 4.0 27.2 1.0 N B:ILE69 4.1 26.4 1.0 CA B:ILE69 4.1 27.0 1.0 N B:ASP65 4.1 29.9 1.0 N B:SER64 4.2 28.6 1.0 CB B:ILE69 4.2 27.6 1.0 O B:HOH1077 4.4 47.1 1.0 OD1 B:ASP71 4.4 26.7 1.0 C B:GLY70 4.4 23.6 1.0 N B:GLY70 4.4 23.8 1.0 N B:ASP67 4.4 30.8 1.0 CB B:ASP65 4.5 32.0 1.0 CB B:ASP67 4.5 30.1 1.0 C B:ASP63 4.5 28.7 1.0 O B:GLY70 4.5 23.8 1.0 CA B:ASP65 4.6 31.8 1.0 O B:GLU116 4.6 28.5 1.0 N B:ASP71 4.6 24.7 1.0 N B:GLY66 4.7 32.2 1.0 CA B:GLY70 4.7 23.1 1.0 C B:ASP65 4.7 31.5 1.0 CG2 B:ILE69 4.8 28.0 1.0 CA B:ASP67 4.9 29.8 1.0 CA B:ASP71 4.9 25.8 1.0 N B:GLY68 4.9 26.9 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