Calcium in PDB 5zcb: Crystal Structure of Alpha-Glucosidase

The structure of Crystal Structure of Alpha-Glucosidase, PDB code: 5zcb 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)	46.09 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.893, 84.856, 128.429, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.5

The binding sites of Calcium atom in the Crystal Structure of Alpha-Glucosidase (pdb code 5zcb). 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, PDB code: 5zcb:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 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:Ca601 b:30.7 occ:1.00 OD1 A:ASN23 2.4 27.2 1.0 O A:ILE27 2.4 20.6 1.0 OD1 A:ASP21 2.4 21.8 1.0 OD2 A:ASP29 2.4 23.6 1.0 O A:HOH721 2.4 23.1 1.0 OD1 A:ASP25 2.4 25.9 1.0 CG A:ASP25 3.2 24.1 1.0 CG A:ASN23 3.2 25.1 1.0 OD2 A:ASP25 3.3 21.1 1.0 CG A:ASP21 3.4 21.6 1.0 CG A:ASP29 3.5 23.3 1.0 ND2 A:ASN23 3.5 25.6 1.0 C A:ILE27 3.5 21.1 1.0 CB A:ASP29 3.9 19.6 1.0 OD2 A:ASP21 4.2 21.1 1.0 CB A:ASP21 4.3 20.4 1.0 CA A:ILE27 4.3 21.6 1.0 N A:ASN23 4.3 24.1 1.0 C A:GLY28 4.3 22.6 1.0 O A:ASP74 4.4 24.6 1.0 N A:SER22 4.4 21.8 1.0 N A:ILE27 4.4 20.5 1.0 CB A:ILE27 4.4 19.4 1.0 CA A:ASP21 4.4 20.4 1.0 O A:GLY28 4.5 20.5 1.0 N A:ASP29 4.5 20.4 1.0 N A:GLY28 4.5 20.6 1.0 OD1 A:ASP29 4.6 24.3 1.0 CB A:ASN23 4.6 25.9 1.0 CB A:ASP25 4.6 22.4 1.0 N A:ASP25 4.6 22.3 1.0 CA A:GLY28 4.7 19.8 1.0 CA A:ASP29 4.8 20.5 1.0 C A:ASP21 4.9 22.8 1.0 CA A:ASN23 4.9 26.0 1.0 N A:GLY24 4.9 24.5 1.0 CG2 A:ILE27 5.0 19.9 1.0

Calcium binding site 2 out of 3 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 2 of Crystal Structure of Alpha-Glucosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:31.2 occ:1.00 OD2 A:ASP534 2.3 31.8 1.0 O A:THR543 2.4 22.8 1.0 OG1 A:THR543 2.5 30.0 1.0 O A:HOH781 2.5 27.9 1.0 O A:HOH833 2.5 28.1 1.0 OE2 A:GLU537 2.6 33.1 1.0 CB A:THR543 3.4 28.8 1.0 C A:THR543 3.4 25.3 1.0 CG A:ASP534 3.6 34.9 1.0 CD A:GLU537 3.6 35.0 1.0 CA A:THR543 3.9 26.7 1.0 OE1 A:GLU537 4.1 32.1 1.0 NH2 A:ARG550 4.2 26.9 1.0 N A:THR543 4.3 28.9 1.0 CB A:ASP534 4.3 36.7 1.0 NE2 A:HIS545 4.4 29.3 1.0 OD1 A:ASP534 4.5 36.2 1.0 O A:HOH770 4.6 30.9 1.0 N A:LEU544 4.6 22.9 1.0 CG A:GLU537 4.6 36.2 1.0 O A:HOH808 4.6 35.4 1.0 CG2 A:THR543 4.7 26.3 1.0 CD2 A:HIS545 4.7 25.1 1.0 CE1 A:HIS545 4.8 25.2 1.0 OE1 A:GLU548 4.8 23.3 1.0 CB A:GLU537 4.9 37.3 1.0

Calcium binding site 3 out of 3 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 3 of Crystal Structure of Alpha-Glucosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:54.7 occ:1.00 OE1 A:GLU173 2.5 37.1 1.0 O A:HOH886 3.0 44.3 1.0 CD A:GLU173 3.7 32.0 1.0 OE2 A:GLU236 4.3 48.7 1.0 O A:HOH846 4.4 32.5 1.0 OE2 A:GLU173 4.5 32.6 1.0 CE1 A:HIS237 4.5 26.5 1.0 CB A:GLU173 4.7 26.4 1.0 CG A:GLU173 4.7 28.6 1.0 O A:HOH828 4.7 32.4 1.0 CA A:GLU173 4.7 25.8 1.0 O A:GLU173 4.8 30.2 1.0 NZ A:LYS205 4.9 29.3 1.0 NE2 A:HIS237 4.9 27.3 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