Calcium in PDB 7d9b: Crystal Structure of Alpha-Glucosidase

The structure of Crystal Structure of Alpha-Glucosidase, PDB code: 7d9b was solved by K.Krusong, K.Wangpaiboon, S.Kim, T.Mori, T.Hakoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.31 / 1.58
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	116.503, 116.503, 106.638, 90, 90, 90
R / Rfree (%)	14.5 / 17.6

The binding sites of Calcium atom in the Crystal Structure of Alpha-Glucosidase (pdb code 7d9b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Alpha-Glucosidase, PDB code: 7d9b:

Calcium binding site 1 out of 1 in the Crystal Structure of Alpha-Glucosidase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:21.6 occ:1.00 OD1 A:ASP161 2.3 23.1 1.0 OD1 A:ASN160 2.3 24.0 1.0 OD2 A:ASP183 2.3 21.5 1.0 OD1 A:ASN155 2.4 21.1 1.0 O A:ASP157 2.4 24.5 1.0 O A:GLY181 2.5 21.7 1.0 O A:HOH1198 2.5 22.0 1.0 CG A:ASN155 3.3 22.3 1.0 CG A:ASP183 3.4 20.4 1.0 C A:ASP157 3.4 22.9 1.0 CG A:ASN160 3.5 23.3 1.0 C A:GLY181 3.5 20.9 1.0 CG A:ASP161 3.5 23.3 1.0 ND2 A:ASN155 3.9 23.0 1.0 CB A:ASP183 3.9 20.9 1.0 CA A:GLY181 3.9 21.4 1.0 ND2 A:ASN160 4.1 23.2 1.0 N A:ASP157 4.1 22.7 1.0 N A:ASP161 4.2 22.6 1.0 CA A:ASP157 4.2 22.7 1.0 CA A:ASP161 4.3 22.5 1.0 OD2 A:ASP161 4.3 23.2 1.0 N A:VAL158 4.3 23.1 1.0 O A:HIS227 4.3 22.9 1.0 OD1 A:ASP183 4.4 21.7 1.0 CA A:VAL158 4.4 24.4 1.0 C A:ASN160 4.4 23.6 1.0 CB A:ASN155 4.5 21.3 1.0 CB A:ASP161 4.5 23.4 1.0 CB A:ASP157 4.5 23.7 1.0 CA A:ASN155 4.6 20.4 1.0 C A:GLY182 4.7 20.0 1.0 N A:GLY182 4.7 20.4 1.0 N A:ASN160 4.7 24.8 1.0 O A:GLY182 4.7 21.5 1.0 C A:VAL158 4.7 24.4 1.0 CB A:ASN160 4.7 22.8 1.0 O A:ASN160 4.8 24.4 1.0 CA A:ASN160 4.8 23.6 1.0 N A:ASP183 4.9 20.0 1.0 N A:GLY156 4.9 21.6 1.0 O A:HOH1191 5.0 25.9 1.0 C A:ASN155 5.0 21.8 1.0 O A:VAL158 5.0 25.4 1.0

K.Wangpaiboon, P.Laohawutthichai, S.Kim, T.Mori, P.Nakapong, R.Pichayangkura, P.Pongsawasdi, T.Hakoshima, K.Krusong. A GH13 Alpha-Glucosidase From Weissella Cibaria Uncommonly Acts on Short-Chain Maltooligosaccharides Acta Crystallogr.,Sect.D V. 77 1064 2021.
ISSN: ESSN 1399-0047
DOI: 10.1107/S205979832100677X