Calcium in PDB 2zid: Crystal Structure of Dextran Glucosidase E236Q Complex with Isomaltotriose

All present enzymatic activity of Crystal Structure of Dextran Glucosidase E236Q Complex with Isomaltotriose:
3.2.1.70;

The structure of Crystal Structure of Dextran Glucosidase E236Q Complex with Isomaltotriose, PDB code: 2zid was solved by H.Hondoh, W.Saburi, H.Mori, M.Okuyama, T.Nakada, Y.Matsuura, A.Kimura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.490, 82.530, 104.300, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.4

The binding sites of Calcium atom in the Crystal Structure of Dextran Glucosidase E236Q Complex with Isomaltotriose (pdb code 2zid). 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 Dextran Glucosidase E236Q Complex with Isomaltotriose, PDB code: 2zid:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Dextran Glucosidase E236Q Complex with Isomaltotriose


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 Dextran Glucosidase E236Q Complex with Isomaltotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca880 b:32.7 occ:1.00 OD2 A:ASP151 2.2 23.3 1.0 O A:ASP148 2.6 25.1 1.0 CG A:ASP151 3.1 22.8 1.0 OD1 A:ASP151 3.3 25.1 1.0 C A:ASP148 3.6 24.4 1.0 CA A:ASP148 4.0 24.3 1.0 CB A:ASP148 4.3 26.8 1.0 CB A:ASP151 4.5 20.2 1.0 OH A:TYR146 4.6 18.3 1.0 N A:LYS149 4.8 26.3 1.0 CA A:ASP151 4.9 17.8 1.0 N A:ASP151 4.9 18.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Dextran Glucosidase E236Q Complex with Isomaltotriose


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 Dextran Glucosidase E236Q Complex with Isomaltotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca881 b:17.7 occ:1.00 O A:THR417 2.4 12.3 1.0 O A:HOH1160 2.5 14.6 1.0 O A:HOH1159 2.5 14.6 1.0 O A:HOH1161 2.5 19.6 1.0 O A:HOH1066 2.6 15.8 1.0 C A:THR417 3.6 12.2 1.0 CB A:THR417 4.2 13.6 1.0 OD1 A:ASP419 4.4 17.9 1.0 N A:ALA418 4.4 11.5 1.0 OG1 A:THR417 4.4 13.6 1.0 CA A:THR417 4.5 12.6 1.0 CA A:ALA418 4.5 12.6 1.0 C A:ALA418 4.7 12.8 1.0 OE1 A:GLN411 4.8 20.0 1.0 O A:HOH1128 4.8 15.6 1.0 N A:ASP419 4.8 12.5 1.0 NE2 A:GLN411 4.9 20.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Dextran Glucosidase E236Q Complex with Isomaltotriose


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 Dextran Glucosidase E236Q Complex with Isomaltotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca882 b:11.1 occ:1.00 OD1 A:ASN23 2.2 14.0 1.0 OD1 A:ASP21 2.2 11.0 1.0 OD1 A:ASP25 2.3 6.6 1.0 O A:ILE27 2.3 9.8 1.0 OD2 A:ASP29 2.5 7.2 1.0 CG A:ASP25 3.0 11.3 1.0 OD2 A:ASP25 3.1 13.0 1.0 CG A:ASP21 3.3 11.8 1.0 CG A:ASN23 3.3 12.2 1.0 C A:ILE27 3.5 11.0 1.0 CG A:ASP29 3.6 9.6 1.0 ND2 A:ASN23 3.9 14.3 1.0 CB A:ASP29 4.0 6.4 1.0 OD2 A:ASP21 4.1 12.1 1.0 CB A:ASP21 4.1 9.0 1.0 N A:ASN23 4.2 9.2 1.0 N A:ILE27 4.2 10.9 1.0 CA A:ASP21 4.2 9.1 1.0 N A:THR22 4.3 10.2 1.0 CA A:ILE27 4.3 11.7 1.0 C A:GLY28 4.3 7.4 1.0 CB A:ASP25 4.3 8.6 1.0 O A:GLY28 4.4 8.8 1.0 N A:ASP25 4.4 10.9 1.0 CB A:ILE27 4.5 10.8 1.0 CB A:ASN23 4.5 9.6 1.0 O A:ILE74 4.5 11.7 1.0 N A:GLY28 4.6 10.7 1.0 N A:ASP29 4.6 6.9 1.0 CA A:GLY28 4.7 9.1 1.0 OD1 A:ASP29 4.7 9.4 1.0 C A:ASP21 4.7 9.8 1.0 CA A:ASN23 4.7 10.4 1.0 CA A:ASP25 4.8 10.1 1.0 C A:ASN23 4.9 10.0 1.0 CA A:ASP29 4.9 7.2 1.0 N A:GLY24 4.9 10.6 1.0

H.Hondoh, W.Saburi, H.Mori, M.Okuyama, T.Nakada, Y.Matsuura, A.Kimura. Substrate Recognition Mechanism of Alpha-1,6-Glucosidic Linkage Hydrolyzing Enzyme, Dextran Glucosidase From Streptococcus Mutans. J.Mol.Biol. V. 378 911 2008.
ISSN: ISSN 0022-2836
PubMed: 18395742
DOI: 10.1016/J.JMB.2008.03.016