Calcium 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:

Magnesium

(Mg)

3 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1-Deoxynojirimycin, PDB code: 6lgc:
Jump to Calcium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca702 b:24.2 occ:1.00 OD2 A:ASP217 2.3 27.8 1.0 O A:LEU252 2.3 23.4 1.0 O A:HOH880 2.4 24.7 1.0 O A:HOH821 2.4 22.6 1.0 O A:TYR251 2.5 23.0 1.0 OE2 A:GLU254 2.5 26.0 1.0 OD1 A:ASN144 2.5 22.3 1.0 C A:LEU252 3.1 24.9 1.0 CG A:ASP217 3.4 24.7 1.0 CG A:ASN144 3.5 21.7 1.0 CD A:GLU254 3.5 28.2 1.0 C A:TYR251 3.6 23.9 1.0 CA A:LEU252 3.6 24.9 1.0 OE1 A:GLU254 3.8 26.6 1.0 CB A:ASP217 3.8 23.6 1.0 ND2 A:ASN144 3.8 22.9 1.0 N A:LEU252 4.1 25.8 1.0 N A:ILE253 4.1 26.9 1.0 O A:ASN144 4.3 22.0 1.0 O A:PHE218 4.3 26.4 1.0 OD1 A:ASP217 4.5 26.6 1.0 NE2 A:GLN210 4.5 19.9 1.0 O A:HOH1050 4.6 25.8 1.0 CA A:ILE253 4.7 26.5 1.0 CA A:ASP217 4.7 23.5 1.0 CB A:ASN144 4.7 24.2 1.0 CA A:TYR251 4.8 23.0 1.0 CG A:GLU254 4.8 28.3 1.0 CB A:TYR251 4.9 24.5 1.0 CG A:GLN210 5.0 23.4 1.0 CD2 A:LEU208 5.0 25.2 1.0 CB A:LEU252 5.0 27.7 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 B:Ca702 b:26.5 occ:1.00 OE2 B:GLU254 2.4 30.6 1.0 OD2 B:ASP217 2.4 26.4 1.0 O B:TYR251 2.4 23.9 1.0 O B:LEU252 2.4 25.7 1.0 O B:HOH979 2.5 22.1 1.0 O B:HOH936 2.5 24.1 1.0 OD1 B:ASN144 2.5 24.4 1.0 C B:LEU252 3.1 25.5 1.0 CD B:GLU254 3.4 29.9 1.0 CG B:ASP217 3.4 27.6 1.0 C B:TYR251 3.5 27.3 1.0 CG B:ASN144 3.5 23.7 1.0 CA B:LEU252 3.5 26.2 1.0 OE1 B:GLU254 3.7 30.1 1.0 CB B:ASP217 3.8 25.4 1.0 ND2 B:ASN144 3.9 26.3 1.0 N B:LEU252 3.9 24.7 1.0 N B:ILE253 4.1 26.6 1.0 O B:PHE218 4.4 25.6 1.0 O B:ASN144 4.4 23.1 1.0 O B:HOH1137 4.4 25.9 1.0 NE2 B:GLN210 4.5 30.2 1.0 OD1 B:ASP217 4.6 26.9 1.0 CA B:TYR251 4.7 25.8 1.0 CA B:ILE253 4.7 29.8 1.0 CG B:GLU254 4.7 29.1 1.0 CB B:ASN144 4.8 24.7 1.0 CA B:ASP217 4.8 25.6 1.0 CB B:TYR251 4.8 26.3 1.0 CB B:LEU252 4.9 25.4 1.0 CD2 B:LEU208 4.9 34.4 1.0 CG B:GLN210 5.0 28.2 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