Calcium 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:

Magnesium

(Mg)

5 atoms

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

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


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 Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:13.0 occ:1.00 OD2 A:ASP217 2.3 12.0 1.0 OE2 A:GLU254 2.3 14.1 1.0 O A:TYR251 2.4 11.7 1.0 O A:HOH891 2.4 11.4 1.0 O A:HOH832 2.4 13.3 1.0 O A:LEU252 2.4 13.7 1.0 OD1 A:ASN144 2.5 11.3 1.0 C A:LEU252 3.1 13.2 1.0 CD A:GLU254 3.4 14.4 1.0 CG A:ASP217 3.4 13.0 1.0 C A:TYR251 3.5 12.6 1.0 CG A:ASN144 3.5 11.7 1.0 CA A:LEU252 3.5 13.6 1.0 OE1 A:GLU254 3.8 14.3 1.0 CB A:ASP217 3.8 13.2 1.0 ND2 A:ASN144 3.9 12.3 1.0 N A:LEU252 4.0 12.8 1.0 N A:ILE253 4.1 13.0 1.0 O A:PHE218 4.3 14.7 1.0 O A:ASN144 4.4 13.7 1.0 O A:HOH1114 4.4 14.8 1.0 NE2 A:GLN210 4.5 12.0 1.0 OD1 A:ASP217 4.5 12.9 1.0 CA A:TYR251 4.7 11.7 1.0 CA A:ASP217 4.7 13.6 1.0 CG A:GLU254 4.7 14.0 1.0 CA A:ILE253 4.7 13.4 1.0 CB A:ASN144 4.8 12.4 1.0 CB A:TYR251 4.8 12.1 1.0 CG A:GLN210 4.9 11.6 1.0 CD2 A:LEU208 4.9 13.8 1.0 CB A:LEU252 4.9 14.7 1.0

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


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 Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:10.3 occ:1.00 OD2 B:ASP217 2.4 9.6 1.0 O B:TYR251 2.4 9.3 1.0 OE2 B:GLU254 2.4 10.6 1.0 O B:HOH902 2.4 10.1 1.0 O B:LEU252 2.4 10.7 1.0 O B:HOH899 2.4 9.8 1.0 OD1 B:ASN144 2.5 9.3 1.0 C B:LEU252 3.1 11.3 1.0 CD B:GLU254 3.4 10.8 1.0 CG B:ASP217 3.4 10.5 1.0 C B:TYR251 3.5 9.9 1.0 CG B:ASN144 3.5 9.8 1.0 CA B:LEU252 3.6 11.2 1.0 OE1 B:GLU254 3.8 10.3 1.0 CB B:ASP217 3.8 9.9 1.0 ND2 B:ASN144 3.9 9.0 1.0 N B:LEU252 4.0 10.1 1.0 N B:ILE253 4.1 10.5 1.0 O B:PHE218 4.3 11.2 1.0 NE2 B:GLN210 4.3 10.3 1.0 O B:ASN144 4.4 9.2 1.0 O B:HOH1132 4.4 13.1 1.0 OD1 B:ASP217 4.6 10.7 1.0 CA B:TYR251 4.7 9.5 1.0 CA B:ASP217 4.7 9.8 1.0 CG B:GLU254 4.7 10.8 1.0 CA B:ILE253 4.8 11.3 1.0 CB B:TYR251 4.8 9.5 1.0 CB B:ASN144 4.8 9.5 1.0 CD2 B:LEU208 4.9 11.7 1.0 CG B:GLN210 4.9 10.4 1.0 CB B:LEU252 5.0 12.1 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