Calcium in PDB 5zcc: Crystal Structure of Alpha-Glucosidase in Complex with Maltose

The structure of Crystal Structure of Alpha-Glucosidase in Complex with Maltose, PDB code: 5zcc 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)	46.18 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.046, 84.840, 128.767, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 18.9

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


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 Maltose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:18.7 occ:1.00 OD1 A:ASP21 2.3 18.2 1.0 O A:ILE27 2.3 17.4 1.0 OD2 A:ASP29 2.4 17.1 1.0 OD1 A:ASN23 2.4 18.9 1.0 O A:HOH746 2.4 21.4 1.0 OD1 A:ASP25 2.4 19.0 1.0 CG A:ASP25 3.3 22.2 1.0 CG A:ASP21 3.3 18.4 1.0 CG A:ASN23 3.4 25.1 1.0 CG A:ASP29 3.5 18.7 1.0 C A:ILE27 3.5 18.8 1.0 OD2 A:ASP25 3.5 21.9 1.0 CB A:ASP29 3.9 16.4 1.0 ND2 A:ASN23 4.0 24.8 1.0 OD2 A:ASP21 4.0 20.6 1.0 CB A:ASP21 4.1 17.0 1.0 N A:ILE27 4.2 16.4 1.0 N A:ASN23 4.2 20.3 1.0 CA A:ILE27 4.2 16.0 1.0 CA A:ASP21 4.2 17.5 1.0 N A:SER22 4.3 19.1 1.0 CB A:ILE27 4.4 18.9 1.0 C A:GLY28 4.4 16.1 1.0 O A:GLY28 4.4 16.7 1.0 N A:ASP25 4.5 20.5 1.0 O A:ASP74 4.5 20.3 1.0 O A:HOH1150 4.5 40.6 1.0 OD1 A:ASP29 4.5 19.3 1.0 N A:GLY28 4.5 16.8 1.0 N A:ASP29 4.6 18.4 1.0 CB A:ASP25 4.6 23.4 1.0 C A:ASP21 4.6 19.8 1.0 CB A:ASN23 4.7 23.9 1.0 CA A:GLY28 4.7 16.1 1.0 CA A:ASN23 4.7 23.4 1.0 N A:GLY24 4.7 18.9 1.0 C A:ASN23 4.8 23.2 1.0 CA A:ASP29 4.9 17.5 1.0 CA A:ASP25 5.0 19.7 1.0 N A:GLY26 5.0 17.4 1.0

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


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 Maltose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:18.9 occ:1.00 O A:HOH1209 2.3 20.4 1.0 OD2 A:ASP534 2.4 23.9 1.0 OE2 A:GLU537 2.4 19.0 1.0 O A:THR543 2.4 17.4 1.0 O A:HOH937 2.4 16.6 1.0 O A:HOH1146 2.4 19.2 1.0 OG1 A:THR543 2.4 19.3 1.0 CD A:GLU537 3.3 22.4 1.0 CB A:THR543 3.4 19.0 1.0 C A:THR543 3.5 17.2 1.0 CG A:ASP534 3.5 26.2 1.0 OE1 A:GLU537 3.8 21.2 1.0 CA A:THR543 3.9 20.6 1.0 CB A:ASP534 4.1 24.7 1.0 NH2 A:ARG550 4.2 19.0 1.0 O A:HOH946 4.3 20.2 1.0 N A:THR543 4.3 20.5 1.0 CG A:GLU537 4.4 24.2 1.0 NE2 A:HIS545 4.4 20.2 1.0 O A:HOH916 4.4 25.1 1.0 O A:HOH1168 4.5 21.2 1.0 OD1 A:ASP534 4.6 26.8 1.0 N A:LEU544 4.6 14.7 1.0 O A:HOH872 4.7 25.3 1.0 CB A:GLU537 4.7 25.9 1.0 CG2 A:THR543 4.7 20.6 1.0 O A:HOH842 4.8 21.7 1.0 CD2 A:HIS545 4.8 17.5 1.0 CE1 A:HIS545 4.8 20.8 1.0 OE1 A:GLU548 5.0 15.4 1.0

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


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 Maltose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:49.8 occ:1.00 O A:HOH1263 2.1 35.0 1.0 O A:HOH1486 2.3 43.0 1.0 O A:HOH1298 2.3 36.4 1.0 OE1 A:GLU173 2.4 24.4 1.0 O A:HOH756 2.4 35.5 1.0 O A:HOH1174 2.4 46.0 1.0 O A:HOH1178 2.5 37.6 1.0 CD A:GLU173 3.6 26.4 1.0 CB A:GLU173 4.3 18.5 1.0 CG A:GLU173 4.3 24.8 1.0 CA A:GLU173 4.5 22.6 1.0 OE2 A:GLU236 4.5 41.0 1.0 OE2 A:GLU173 4.5 23.8 1.0 CE1 A:HIS237 4.6 21.4 1.0 O A:GLU173 4.6 23.8 1.0 O A:HOH857 4.6 30.0 1.0 NZ A:LYS205 4.7 25.3 1.0 O A:HOH1448 4.7 45.7 1.0 O A:HOH1122 4.8 32.4 1.0 O A:HOH1434 4.9 40.5 1.0 NE2 A:HIS237 5.0 22.1 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