Calcium in PDB 5zcd: Crystal Structure of Alpha-Glucosidase in Complex with Maltotriose

The structure of Crystal Structure of Alpha-Glucosidase in Complex with Maltotriose, PDB code: 5zcd was solved by K.Kato, W.Saburi, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.50 / 1.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.628, 84.745, 128.514, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.6

The binding sites of Calcium atom in the Crystal Structure of Alpha-Glucosidase in Complex with Maltotriose (pdb code 5zcd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Alpha-Glucosidase in Complex with Maltotriose, PDB code: 5zcd:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Alpha-Glucosidase in Complex with Maltotriose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Alpha-Glucosidase in Complex with Maltotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:21.2 occ:1.00 OD1 A:ASP21 2.3 20.1 1.0 O A:ILE27 2.3 21.3 1.0 OD2 A:ASP29 2.4 18.8 1.0 OD1 A:ASP25 2.4 20.8 1.0 OD1 A:ASN23 2.4 22.4 1.0 O A:HOH742 2.4 23.4 1.0 CG A:ASP25 3.3 23.6 1.0 CG A:ASP21 3.3 20.8 1.0 CG A:ASP29 3.5 17.5 1.0 CG A:ASN23 3.5 24.5 1.0 C A:ILE27 3.5 19.1 1.0 OD2 A:ASP25 3.5 24.0 1.0 CB A:ASP29 4.0 17.7 1.0 ND2 A:ASN23 4.0 26.7 1.0 OD2 A:ASP21 4.0 22.6 1.0 N A:ILE27 4.1 18.9 1.0 CB A:ASP21 4.2 20.4 1.0 N A:ASN23 4.2 23.0 1.0 CA A:ILE27 4.2 19.3 1.0 N A:SER22 4.2 21.4 1.0 CA A:ASP21 4.3 18.9 1.0 CB A:ILE27 4.4 20.2 1.0 C A:GLY28 4.4 17.0 1.0 N A:ASP25 4.5 21.4 1.0 O A:GLY28 4.5 20.2 1.0 N A:GLY28 4.6 18.0 1.0 OD1 A:ASP29 4.6 20.5 1.0 O A:ASP74 4.6 20.2 1.0 CB A:ASP25 4.6 20.9 1.0 O A:HOH772 4.6 50.9 1.0 N A:ASP29 4.6 18.5 1.0 C A:ASP21 4.6 21.8 1.0 N A:GLY24 4.7 20.1 1.0 CB A:ASN23 4.7 28.8 1.0 CA A:GLY28 4.8 17.3 1.0 CA A:ASN23 4.8 24.5 1.0 C A:ASN23 4.8 25.6 1.0 CA A:ASP29 4.9 17.8 1.0 CA A:ASP25 5.0 21.2 1.0 N A:GLY26 5.0 21.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Alpha-Glucosidase in Complex with Maltotriose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Alpha-Glucosidase in Complex with Maltotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:16.9 occ:1.00 OD2 A:ASP534 2.3 23.3 1.0 O A:HOH1168 2.4 21.6 1.0 O A:THR543 2.4 16.7 1.0 OE2 A:GLU537 2.4 19.4 1.0 O A:HOH1080 2.4 19.2 1.0 OG1 A:THR543 2.4 18.9 1.0 O A:HOH844 2.5 16.3 1.0 CD A:GLU537 3.3 23.7 1.0 CB A:THR543 3.4 20.2 1.0 C A:THR543 3.4 18.5 1.0 CG A:ASP534 3.5 24.6 1.0 OE1 A:GLU537 3.8 19.9 1.0 CA A:THR543 3.9 20.8 1.0 CB A:ASP534 4.1 24.8 1.0 NH2 A:ARG550 4.2 16.6 1.0 N A:THR543 4.3 21.0 1.0 O A:HOH905 4.4 21.3 1.0 CG A:GLU537 4.4 23.5 1.0 NE2 A:HIS545 4.5 20.7 1.0 OD1 A:ASP534 4.5 28.3 1.0 O A:HOH1026 4.6 21.0 1.0 N A:LEU544 4.6 17.1 1.0 CB A:GLU537 4.7 22.4 1.0 CG2 A:THR543 4.7 19.2 1.0 O A:HOH921 4.7 24.0 1.0 O A:HOH851 4.8 20.4 1.0 CE1 A:HIS545 4.8 19.7 1.0 CD2 A:HIS545 4.9 16.5 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Alpha-Glucosidase in Complex with Maltotriose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Alpha-Glucosidase in Complex with Maltotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:52.2 occ:1.00 O A:HOH1217 2.2 35.7 1.0 OE1 A:GLU173 2.3 23.2 1.0 O A:HOH1353 2.4 46.7 1.0 O A:HOH1223 2.5 47.8 1.0 O A:HOH1203 2.6 40.6 1.0 O A:HOH972 2.6 36.6 1.0 O A:HOH729 2.7 39.0 1.0 CD A:GLU173 3.5 24.8 1.0 CB A:GLU173 4.1 21.2 1.0 CG A:GLU173 4.2 21.6 1.0 CA A:GLU173 4.4 20.4 1.0 OE2 A:GLU173 4.5 22.6 1.0 O A:GLU173 4.6 24.8 1.0 OE2 A:GLU236 4.6 37.2 1.0 CE1 A:HIS237 4.6 22.1 1.0 NZ A:LYS205 4.6 21.8 1.0 O A:HOH1227 4.7 32.6 1.0 O A:HOH874 4.7 27.6 1.0 O A:HOH993 4.8 29.4 1.0 NE2 A:HIS237 5.0 21.1 1.0 C A:GLU173 5.0 21.4 1.0

W.Auiewiriyanukul, W.Saburi, K.Kato, M.Yao, H.Mori. Function and Structure of GH13_31 Alpha-Glucosidase with High Alpha-(1→4)-Glucosidic Linkage Specificity and Transglucosylation Activity. Febs Lett. V. 592 2268 2018.
ISSN: ISSN 1873-3468
PubMed: 29870070
DOI: 10.1002/1873-3468.13126