Calcium in PDB 8ibk: Crystal Structure of Bacillus Sp. AHU2216 GH13_31 Alpha-Glucosidase E256Q/N258G in Complex with Maltotriose

The structure of Crystal Structure of Bacillus Sp. AHU2216 GH13_31 Alpha-Glucosidase E256Q/N258G in Complex with Maltotriose, PDB code: 8ibk was solved by W.Auiewiriyanukul, W.Saburi, J.Yu, K.Kato, M.Yao, H.Mori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.98 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.965, 88.991, 128.373, 90, 90, 90
R / Rfree (%)	18.2 / 20.9

The binding sites of Calcium atom in the Crystal Structure of Bacillus Sp. AHU2216 GH13_31 Alpha-Glucosidase E256Q/N258G in Complex with Maltotriose (pdb code 8ibk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Bacillus Sp. AHU2216 GH13_31 Alpha-Glucosidase E256Q/N258G in Complex with Maltotriose, PDB code: 8ibk:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Bacillus Sp. AHU2216 GH13_31 Alpha-Glucosidase E256Q/N258G 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 Bacillus Sp. AHU2216 GH13_31 Alpha-Glucosidase E256Q/N258G in Complex with Maltotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:22.0 occ:1.00 OD1 A:ASP21 2.3 22.2 1.0 O A:ILE27 2.3 20.5 1.0 OD1 A:ASN23 2.3 23.6 1.0 OD2 A:ASP29 2.3 23.5 1.0 O A:HOH719 2.4 26.7 1.0 OD1 A:ASP25 2.4 24.5 1.0 CG A:ASP21 3.3 21.6 1.0 CG A:ASP25 3.3 26.4 1.0 CG A:ASN23 3.4 28.1 1.0 CG A:ASP29 3.4 22.6 1.0 C A:ILE27 3.5 19.2 1.0 OD2 A:ASP25 3.6 28.1 1.0 CB A:ASP29 3.9 21.5 1.0 ND2 A:ASN23 4.0 33.0 1.0 N A:ASN23 4.1 24.9 1.0 OD2 A:ASP21 4.1 22.5 1.0 N A:ILE27 4.1 20.3 1.0 CB A:ASP21 4.2 21.8 1.0 CA A:ILE27 4.2 20.9 1.0 N A:SER22 4.2 23.9 1.0 CA A:ASP21 4.2 21.4 1.0 CB A:ILE27 4.3 21.7 1.0 C A:GLY28 4.4 20.6 1.0 N A:ASP25 4.5 24.3 1.0 OD1 A:ASP29 4.5 23.5 1.0 N A:GLY28 4.5 18.9 1.0 O A:GLY28 4.5 20.7 1.0 O A:ASP74 4.6 24.6 1.0 C A:ASP21 4.6 23.3 1.0 CB A:ASP25 4.6 25.5 1.0 CB A:ASN23 4.6 26.7 1.0 N A:ASP29 4.6 17.8 1.0 CA A:ASN23 4.7 25.1 1.0 CA A:GLY28 4.7 18.4 1.0 N A:GLY24 4.8 23.1 1.0 C A:ASN23 4.8 25.9 1.0 CA A:ASP29 4.9 20.4 1.0 N A:GLY26 4.9 23.1 1.0 CA A:ASP25 4.9 27.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Bacillus Sp. AHU2216 GH13_31 Alpha-Glucosidase E256Q/N258G 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 Bacillus Sp. AHU2216 GH13_31 Alpha-Glucosidase E256Q/N258G in Complex with Maltotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:21.0 occ:1.00 O A:HOH1084 2.3 22.5 1.0 O A:HOH1156 2.3 27.3 1.0 OG1 A:THR543 2.4 21.8 1.0 O A:HOH897 2.4 21.5 1.0 O A:HOH782 2.4 20.8 1.0 O A:THR543 2.4 20.2 1.0 OE1 A:GLU537 2.5 23.9 1.0 CB A:THR543 3.4 22.5 1.0 CD A:GLU537 3.4 25.4 1.0 C A:THR543 3.5 21.3 1.0 CA A:THR543 3.9 22.3 1.0 OE2 A:GLU537 4.0 26.4 1.0 NH2 A:ARG550 4.2 22.4 1.0 N A:THR543 4.4 24.9 1.0 CB A:ASP534 4.4 31.5 1.0 NE2 A:HIS545 4.4 26.9 1.0 OD2 A:ASP534 4.5 34.0 1.0 CG A:GLU537 4.5 30.5 1.0 O A:HOH1016 4.6 24.2 1.0 O A:HOH1046 4.6 23.4 1.0 N A:LEU544 4.6 19.0 1.0 CG2 A:THR543 4.7 22.6 1.0 CD2 A:HIS545 4.7 25.0 1.0 O A:HOH853 4.9 29.6 1.0 O A:HOH743 4.9 25.2 1.0 CE1 A:HIS545 5.0 26.6 1.0 CG A:ASP534 5.0 35.6 1.0 CB A:GLU537 5.0 31.5 1.0 OE1 A:GLU548 5.0 20.1 1.0

W.Auiewiriyanukul, W.Saburi, T.Ota, J.Yu, K.Kato, M.Yao, H.Mori. Alteration of Substrate Specificity and Transglucosylation Activity of GH13_31 Alpha-Glucosidase From Bacillus Sp. AHU2216 Through Site-Directed Mutagenesis of ASN258 on Beta → Alpha Loop 5. Molecules V. 28 2023.
ISSN: ESSN 1420-3049
PubMed: 37049872
DOI: 10.3390/MOLECULES28073109