Magnesium in PDB 6lgf: Bombyx Mori GH13 Sucrose Hydrolase Mutant D247N Complexed with Sucrose

The structure of Bombyx Mori GH13 Sucrose Hydrolase Mutant D247N Complexed with Sucrose, PDB code: 6lgf was solved by T.Miyazaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.76 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.850, 128.280, 154.789, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 21.6

The structure of Bombyx Mori GH13 Sucrose Hydrolase Mutant D247N Complexed with Sucrose also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Bombyx Mori GH13 Sucrose Hydrolase Mutant D247N Complexed with Sucrose (pdb code 6lgf). 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 Mutant D247N Complexed with Sucrose, PDB code: 6lgf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Bombyx Mori GH13 Sucrose Hydrolase Mutant D247N Complexed with Sucrose


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 Mutant D247N Complexed with Sucrose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:29.9 occ:1.00 O A:HOH865 2.0 30.2 1.0 O A:ILE69 2.1 27.9 1.0 OD1 A:ASP63 2.1 28.6 1.0 OD1 A:ASP67 2.1 34.0 1.0 OD2 A:ASP71 2.3 29.6 1.0 OD1 A:ASP65 2.3 38.9 1.0 CG A:ASP63 3.1 26.4 1.0 CG A:ASP67 3.1 35.2 1.0 CG A:ASP65 3.2 36.2 1.0 C A:ILE69 3.3 28.3 1.0 CG A:ASP71 3.5 27.8 1.0 OD2 A:ASP67 3.5 33.0 1.0 OD2 A:ASP65 3.6 36.6 1.0 CB A:ASP63 3.9 27.0 1.0 OD2 A:ASP63 3.9 26.8 1.0 CB A:ASP71 4.0 25.4 1.0 CA A:ASP63 4.0 26.6 1.0 CA A:ILE69 4.0 27.0 1.0 N A:ILE69 4.0 26.7 1.0 N A:ASP65 4.1 30.4 1.0 CB A:ILE69 4.2 27.8 1.0 N A:SER64 4.3 30.7 1.0 N A:GLY70 4.3 27.5 1.0 C A:GLY70 4.4 25.9 1.0 N A:ASP67 4.4 36.3 1.0 CB A:ASP67 4.4 33.9 1.0 CB A:ASP65 4.5 34.0 1.0 C A:ASP63 4.5 28.7 1.0 N A:ASP71 4.5 25.4 1.0 OD1 A:ASP71 4.5 26.2 1.0 CA A:GLY70 4.5 26.2 1.0 O A:GLU116 4.6 31.7 1.0 CA A:ASP65 4.6 31.3 1.0 O A:GLY70 4.6 27.7 1.0 C A:ASP65 4.7 32.7 1.0 CG2 A:ILE69 4.7 27.6 1.0 CA A:ASP67 4.9 33.5 1.0 N A:GLY66 4.9 31.7 1.0 CA A:ASP71 4.9 24.8 1.0 N A:GLY68 4.9 32.1 1.0

Magnesium binding site 2 out of 4 in the Bombyx Mori GH13 Sucrose Hydrolase Mutant D247N Complexed with Sucrose


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 Mutant D247N Complexed with Sucrose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:31.7 occ:1.00 O A:HOH1020 1.9 22.7 1.0 O A:HOH900 2.0 30.8 1.0 O A:HOH825 2.0 28.0 1.0 O A:HOH935 2.0 25.7 1.0 O A:HOH985 2.1 24.6 1.0 O A:HOH1006 2.1 35.8 1.0 O A:ASP389 4.1 21.4 1.0 OE2 A:GLU440 4.1 25.5 1.0 O A:HOH855 4.2 27.5 1.0 O6 A:FRU705 4.3 19.7 1.0 OE1 A:GLU440 4.4 28.3 1.0 O A:TYR453 4.6 28.5 1.0 CD A:GLU440 4.6 24.3 1.0 O A:HOH986 4.7 19.8 1.0 ND2 A:ASN390 5.0 16.9 1.0 CG A:ARG455 5.0 26.4 1.0

Magnesium binding site 3 out of 4 in the Bombyx Mori GH13 Sucrose Hydrolase Mutant D247N Complexed with Sucrose


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 Mutant D247N Complexed with Sucrose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:14.6 occ:1.00 O B:HOH850 2.0 16.5 1.0 O B:ILE69 2.1 18.0 1.0 OD1 B:ASP65 2.1 23.9 1.0 OD1 B:ASP67 2.1 17.8 1.0 OD2 B:ASP71 2.1 16.1 1.0 OD1 B:ASP63 2.2 22.6 1.0 CG B:ASP67 3.1 21.5 1.0 CG B:ASP63 3.2 22.8 1.0 CG B:ASP65 3.2 29.5 1.0 C B:ILE69 3.3 16.0 1.0 CG B:ASP71 3.3 16.5 1.0 OD2 B:ASP67 3.4 19.3 1.0 OD2 B:ASP65 3.7 35.1 1.0 CB B:ASP71 3.9 16.9 1.0 CB B:ASP63 4.0 19.2 1.0 N B:ILE69 4.0 16.7 1.0 CA B:ASP63 4.0 18.9 1.0 CA B:ILE69 4.0 15.9 1.0 OD2 B:ASP63 4.0 22.4 1.0 N B:ASP65 4.2 23.5 1.0 N B:SER64 4.2 20.5 1.0 CB B:ILE69 4.2 15.9 1.0 N B:GLY70 4.3 15.2 1.0 OD1 B:ASP71 4.3 15.8 1.0 C B:GLY70 4.4 17.4 1.0 CB B:ASP67 4.4 19.9 1.0 N B:ASP67 4.4 22.9 1.0 CB B:ASP65 4.4 25.1 1.0 C B:ASP63 4.5 20.0 1.0 CA B:GLY70 4.5 15.2 1.0 O B:GLY70 4.6 16.8 1.0 N B:ASP71 4.6 17.3 1.0 O B:GLU116 4.6 18.2 1.0 CA B:ASP65 4.7 25.9 1.0 N B:GLY66 4.7 24.4 1.0 C B:ASP65 4.8 27.6 1.0 CA B:ASP67 4.8 19.2 1.0 N B:GLY68 4.8 17.3 1.0 CG2 B:ILE69 4.8 16.0 1.0 CA B:ASP71 4.9 16.4 1.0 C B:ASP67 4.9 18.0 1.0

Magnesium binding site 4 out of 4 in the Bombyx Mori GH13 Sucrose Hydrolase Mutant D247N Complexed with Sucrose


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 Mutant D247N Complexed with Sucrose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:36.4 occ:1.00 O B:HOH919 2.1 22.2 1.0 O B:HOH956 2.1 25.2 1.0 O B:HOH1132 2.1 34.0 1.0 O B:HOH983 2.2 32.7 1.0 O B:HOH1106 2.2 32.1 1.0 O B:HOH1061 2.3 22.9 1.0 O B:ASP389 4.0 17.7 1.0 O6 B:FRU705 4.1 22.1 1.0 OE2 B:GLU440 4.2 23.4 1.0 O B:TYR453 4.2 19.0 1.0 OE1 B:GLU440 4.3 21.3 1.0 CD B:GLU440 4.6 21.9 1.0 O B:HOH1039 4.7 16.9 1.0 CG B:ARG455 4.8 17.4 1.0 O B:HOH931 4.8 32.0 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