Magnesium in PDB 6lgb: Bombyx Mori GH13 Sucrose Hydrolase Complexed with Glucose

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

Resolution Low / High (Å)	49.58 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.700, 128.530, 153.980, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 18.2

The structure of Bombyx Mori GH13 Sucrose Hydrolase Complexed with Glucose 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 Glucose (pdb code 6lgb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with Glucose, PDB code: 6lgb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with Glucose


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 Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:19.5 occ:1.00 O A:ILE69 2.1 16.8 1.0 OD1 A:ASP63 2.1 21.6 1.0 OD2 A:ASP71 2.1 20.1 1.0 O A:HOH814 2.2 23.4 1.0 OD1 A:ASP67 2.2 23.5 1.0 OD1 A:ASP65 2.2 24.7 1.0 CG A:ASP67 3.1 23.3 1.0 CG A:ASP63 3.1 18.4 1.0 CG A:ASP65 3.2 27.6 1.0 C A:ILE69 3.3 20.1 1.0 CG A:ASP71 3.3 17.1 1.0 OD2 A:ASP67 3.4 22.4 1.0 OD2 A:ASP65 3.7 31.0 1.0 CB A:ASP71 3.8 17.7 1.0 OD2 A:ASP63 3.9 19.6 1.0 N A:ILE69 3.9 20.8 1.0 CB A:ASP63 4.0 19.8 1.0 CA A:ILE69 4.0 20.1 1.0 CA A:ASP63 4.0 18.6 1.0 N A:ASP65 4.1 25.2 1.0 CB A:ILE69 4.2 21.2 1.0 N A:SER64 4.2 21.8 1.0 N A:GLY70 4.3 20.1 1.0 OD1 A:ASP71 4.4 17.7 1.0 N A:ASP67 4.4 25.5 1.0 C A:GLY70 4.4 18.1 1.0 CB A:ASP67 4.4 23.3 1.0 CB A:ASP65 4.5 26.2 1.0 C A:ASP63 4.5 20.5 1.0 CA A:GLY70 4.6 18.8 1.0 N A:ASP71 4.6 16.8 1.0 O A:GLY70 4.6 17.1 1.0 CA A:ASP65 4.6 25.4 1.0 O A:GLU116 4.7 21.5 1.0 N A:GLY66 4.7 25.6 1.0 C A:ASP65 4.7 26.3 1.0 CG2 A:ILE69 4.8 20.8 1.0 CA A:ASP67 4.8 23.7 1.0 N A:GLY68 4.9 22.8 1.0 CA A:ASP71 4.9 17.6 1.0

Magnesium binding site 2 out of 5 in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with Glucose


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 Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:39.3 occ:1.00 O A:HOH1182 2.1 35.6 1.0 O A:HOH1256 2.2 32.0 1.0 OD2 A:ASP296 4.2 24.3 1.0 O A:HOH1066 4.2 19.0 1.0 O A:HOH876 4.3 37.3 1.0 OD1 A:ASP296 4.4 23.1 1.0 CG A:ASP296 4.7 21.4 1.0

Magnesium binding site 3 out of 5 in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with Glucose


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 Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:12.3 occ:1.00 OD1 B:ASP65 2.1 18.1 1.0 O B:HOH869 2.1 13.4 1.0 OD1 B:ASP63 2.1 15.2 1.0 OD1 B:ASP67 2.1 13.7 1.0 O B:ILE69 2.2 12.0 1.0 OD2 B:ASP71 2.2 13.7 1.0 CG B:ASP67 3.1 14.7 1.0 CG B:ASP63 3.2 14.4 1.0 CG B:ASP65 3.2 24.6 1.0 CG B:ASP71 3.4 13.6 1.0 C B:ILE69 3.4 12.5 1.0 OD2 B:ASP67 3.4 15.0 1.0 OD2 B:ASP65 3.8 31.8 1.0 CB B:ASP71 3.9 13.0 1.0 CB B:ASP63 4.0 14.5 1.0 CA B:ASP63 4.0 14.0 1.0 N B:ILE69 4.0 12.8 1.0 N B:ASP65 4.1 16.8 1.0 CA B:ILE69 4.1 12.8 1.0 OD2 B:ASP63 4.1 15.9 1.0 N B:SER64 4.1 15.4 1.0 CB B:ILE69 4.3 13.1 1.0 N B:ASP67 4.4 15.6 1.0 CB B:ASP67 4.4 14.5 1.0 OD1 B:ASP71 4.4 13.4 1.0 N B:GLY70 4.4 12.2 1.0 CB B:ASP65 4.4 21.5 1.0 C B:ASP63 4.4 15.4 1.0 C B:GLY70 4.5 12.2 1.0 CA B:ASP65 4.6 19.3 1.0 O B:GLY70 4.7 13.5 1.0 N B:ASP71 4.7 12.6 1.0 O B:HOH1226 4.7 40.8 1.0 CA B:GLY70 4.7 12.8 1.0 N B:GLY66 4.7 19.1 1.0 O B:GLU116 4.7 15.7 1.0 CA B:ASP67 4.8 15.0 1.0 C B:ASP65 4.8 19.1 1.0 N B:GLY68 4.8 13.7 1.0 CG2 B:ILE69 4.9 12.6 1.0 CA B:ASP71 4.9 12.3 1.0 C B:ASP67 5.0 14.7 1.0

Magnesium binding site 4 out of 5 in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with Glucose


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 Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:33.8 occ:1.00 O B:HOH1348 2.0 36.3 1.0 O B:HOH1324 2.1 27.9 1.0 O B:HOH842 2.1 19.2 1.0 O B:HOH976 2.2 25.0 1.0 O B:HOH910 2.3 21.3 1.0 O B:HOH853 2.4 27.6 1.0 OE1 B:GLU440 3.9 15.9 1.0 OE2 B:GLU440 3.9 16.7 1.0 O B:HOH1323 4.2 33.1 1.0 CD B:GLU440 4.3 16.1 1.0 O B:ASP389 4.4 10.4 1.0 O B:HOH1270 4.5 29.5 1.0 C2 B:GOL706 4.6 37.9 1.0 O B:HOH1228 4.6 17.5 1.0 O1 B:GOL706 4.7 22.8 1.0 O B:TYR453 4.7 15.8 1.0 O B:HOH937 4.7 18.2 1.0 C1 B:GOL706 4.8 31.4 1.0 O B:HOH1129 4.8 36.6 1.0 CD B:ARG455 4.8 10.4 1.0 CG B:ARG455 4.9 10.5 1.0

Magnesium binding site 5 out of 5 in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Bombyx Mori GH13 Sucrose Hydrolase Complexed with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:39.0 occ:1.00 O B:HOH1315 2.0 33.5 1.0 O B:HOH929 2.0 21.0 1.0 O B:HOH1361 2.5 40.9 1.0 OE2 B:GLU276 4.0 18.2 1.0 O B:HOH1267 4.1 36.3 1.0 O B:HOH1059 4.1 25.4 1.0 OE1 B:GLU276 4.1 18.0 1.0 CD B:GLU276 4.5 15.5 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