Calcium in PDB 5zce: Crystal Structure of Alpha-Glucosidase in Complex with Maltotetraose

The structure of Crystal Structure of Alpha-Glucosidase in Complex with Maltotetraose, PDB code: 5zce 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)	46.10 / 1.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.989, 84.549, 128.715, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.1

The binding sites of Calcium atom in the Crystal Structure of Alpha-Glucosidase in Complex with Maltotetraose (pdb code 5zce). 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 Maltotetraose, PDB code: 5zce:
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 Maltotetraose


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 Maltotetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:15.7 occ:1.00 O A:HOH781 2.3 22.1 1.0 OD1 A:ASP21 2.3 15.4 1.0 OD2 A:ASP29 2.3 15.6 1.0 O A:ILE27 2.3 13.9 1.0 OD1 A:ASN23 2.4 16.4 1.0 OD1 A:ASP25 2.4 16.3 1.0 CG A:ASP25 3.3 16.5 1.0 CG A:ASP21 3.3 14.6 1.0 CG A:ASN23 3.4 17.6 1.0 CG A:ASP29 3.5 14.4 1.0 C A:ILE27 3.5 13.8 1.0 OD2 A:ASP25 3.5 19.9 1.0 ND2 A:ASN23 3.9 22.6 1.0 CB A:ASP29 4.0 13.6 1.0 OD2 A:ASP21 4.0 14.4 1.0 CB A:ASP21 4.1 15.8 1.0 N A:ILE27 4.1 16.1 1.0 N A:ASN23 4.1 17.0 1.0 CA A:ILE27 4.2 14.5 1.0 CA A:ASP21 4.2 14.8 1.0 N A:SER22 4.3 17.0 1.0 CB A:ILE27 4.3 14.7 1.0 C A:GLY28 4.4 12.4 1.0 N A:ASP25 4.5 15.5 1.0 O A:GLY28 4.5 14.3 1.0 OD1 A:ASP29 4.5 14.6 1.0 O A:ASP74 4.6 16.3 1.0 N A:GLY28 4.6 11.9 1.0 N A:ASP29 4.6 12.6 1.0 CB A:ASP25 4.6 15.9 1.0 N A:GLY24 4.6 16.3 1.0 C A:ASP21 4.6 15.0 1.0 CB A:ASN23 4.6 18.5 1.0 CA A:ASN23 4.7 17.0 1.0 CA A:GLY28 4.7 12.2 1.0 C A:ASN23 4.8 19.1 1.0 CA A:ASP29 4.9 11.2 1.0 CA A:ASP25 5.0 14.4 1.0

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


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 Maltotetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:15.7 occ:1.00 O A:HOH1226 2.3 19.1 1.0 OD2 A:ASP534 2.3 21.7 1.0 OE2 A:GLU537 2.4 17.5 1.0 O A:THR543 2.4 14.4 1.0 O A:HOH930 2.4 15.1 1.0 O A:HOH1107 2.5 19.7 1.0 OG1 A:THR543 2.5 17.0 1.0 CD A:GLU537 3.3 18.3 1.0 CB A:THR543 3.4 17.6 1.0 C A:THR543 3.4 15.1 1.0 CG A:ASP534 3.5 24.1 1.0 OE1 A:GLU537 3.8 17.3 1.0 CA A:THR543 3.9 17.7 1.0 CB A:ASP534 4.1 21.8 1.0 NH2 A:ARG550 4.2 15.5 1.0 O A:HOH998 4.3 18.3 1.0 N A:THR543 4.3 16.5 1.0 CG A:GLU537 4.4 21.2 1.0 NE2 A:HIS545 4.4 16.7 1.0 O A:HOH972 4.5 26.1 1.0 O A:HOH994 4.5 19.0 1.0 OD1 A:ASP534 4.5 26.2 1.0 N A:LEU544 4.6 13.8 1.0 CB A:GLU537 4.7 22.6 1.0 CG2 A:THR543 4.7 19.9 1.0 O A:HOH979 4.8 23.5 1.0 O A:HOH809 4.8 19.6 1.0 CE1 A:HIS545 4.8 17.6 1.0 CD2 A:HIS545 4.8 16.2 1.0 OE1 A:GLU548 5.0 13.2 1.0

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


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 Maltotetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:29.9 occ:1.00 OE1 A:GLU173 2.3 19.4 1.0 O A:HOH1454 2.4 31.0 1.0 O A:HOH1127 2.4 31.9 1.0 O A:HOH1134 2.4 31.2 1.0 O A:HOH1295 2.4 28.6 1.0 O A:HOH1268 2.4 30.6 1.0 O A:HOH1097 2.5 28.2 1.0 CD A:GLU173 3.5 19.5 1.0 CG A:GLU173 4.2 18.1 1.0 CB A:GLU173 4.2 15.4 1.0 OE2 A:GLU173 4.4 21.1 1.0 CA A:GLU173 4.4 16.7 1.0 O A:HOH1326 4.5 31.5 1.0 NZ A:LYS205 4.6 22.4 1.0 CE1 A:HIS237 4.6 19.1 1.0 O A:GLU173 4.6 19.9 1.0 O A:HOH991 4.7 22.7 1.0 O A:HOH836 4.7 37.3 1.0 O A:HOH1490 4.7 49.4 1.0 OE2 A:GLU236 4.8 35.1 1.0 O A:HOH1122 4.9 25.8 1.0 O A:HOH1447 4.9 36.6 1.0 NE2 A:HIS237 4.9 18.0 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