Calcium in PDB 2zic: Crystal Structure of Streptococcus Mutans Dextran Glucosidase

All present enzymatic activity of Crystal Structure of Streptococcus Mutans Dextran Glucosidase:
3.2.1.70;

The structure of Crystal Structure of Streptococcus Mutans Dextran Glucosidase, PDB code: 2zic 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)	9.99 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.720, 86.470, 104.300, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 22.2

The binding sites of Calcium atom in the Crystal Structure of Streptococcus Mutans Dextran Glucosidase (pdb code 2zic). 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 Streptococcus Mutans Dextran Glucosidase, PDB code: 2zic:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Streptococcus Mutans Dextran 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 Streptococcus Mutans Dextran Glucosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca944 b:11.8 occ:1.00 OD1 A:ASN23 2.3 10.7 1.0 OD1 A:ASP21 2.3 13.7 1.0 O A:HOH1321 2.4 24.2 1.0 OD1 A:ASP25 2.5 12.6 1.0 O A:HOH1196 2.5 8.3 1.0 OD2 A:ASP29 2.5 8.0 1.0 O A:ILE27 2.5 10.1 1.0 OD2 A:ASP25 2.8 16.4 1.0 CG A:ASP25 2.9 13.2 1.0 CG A:ASP21 3.3 13.7 1.0 CG A:ASN23 3.4 13.8 1.0 CG A:ASP29 3.6 8.3 1.0 C A:ILE27 3.7 9.5 1.0 CB A:ASP29 3.9 6.6 1.0 ND2 A:ASN23 3.9 14.4 1.0 OD2 A:ASP21 4.1 15.2 1.0 CB A:ASP21 4.2 13.3 1.0 N A:THR22 4.2 10.2 1.0 N A:ASN23 4.2 12.7 1.0 CA A:ASP21 4.3 11.4 1.0 N A:ILE27 4.4 9.2 1.0 C A:GLY28 4.4 8.3 1.0 CB A:ASP25 4.4 12.5 1.0 O A:ILE74 4.4 13.1 1.0 O A:GLY28 4.4 7.2 1.0 CA A:ILE27 4.4 9.4 1.0 N A:ASP25 4.5 12.1 1.0 N A:ASP29 4.5 6.9 1.0 CB A:ASN23 4.6 13.2 1.0 N A:GLY28 4.6 10.0 1.0 CB A:ILE27 4.7 9.3 1.0 OD1 A:ASP29 4.7 9.9 1.0 C A:ASP21 4.7 11.4 1.0 O A:HOH1235 4.8 24.2 1.0 CA A:GLY28 4.8 7.1 1.0 CA A:ASN23 4.8 13.4 1.0 CA A:ASP29 4.8 7.7 1.0 CA A:ASP25 4.9 11.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Streptococcus Mutans Dextran 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 Streptococcus Mutans Dextran Glucosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca945 b:34.5 occ:1.00 OD1 A:ASP151 2.3 29.6 1.0 O A:ASP148 2.3 26.4 1.0 CG A:ASP151 3.2 27.8 1.0 C A:ASP148 3.4 27.1 1.0 OD2 A:ASP151 3.5 31.7 1.0 CA A:ASP148 4.0 26.9 1.0 CB A:ASP148 4.2 29.8 1.0 OH A:TYR146 4.4 20.7 1.0 N A:LYS149 4.6 27.8 1.0 CB A:ASP151 4.6 25.7 1.0 O A:LYS149 4.8 29.1 1.0 CA A:LYS149 4.9 29.5 1.0 C A:LYS149 4.9 28.1 1.0 N A:ASP151 5.0 24.2 1.0 CA A:ASP151 5.0 22.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Streptococcus Mutans Dextran 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 Streptococcus Mutans Dextran Glucosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca946 b:28.8 occ:1.00 O A:HOH1227 2.5 12.1 1.0 O A:HOH1228 2.5 20.0 1.0 O A:HOH1314 2.6 24.8 1.0 O A:THR417 2.6 15.5 1.0 C A:THR417 3.7 15.5 1.0 CB A:THR417 4.3 14.8 1.0 OD1 A:ASP419 4.4 23.9 1.0 OG1 A:THR417 4.5 13.1 1.0 CA A:ALA418 4.6 13.9 1.0 N A:ALA418 4.6 13.9 1.0 CA A:THR417 4.6 14.9 1.0 OE1 A:GLN411 4.8 29.0 1.0 C A:ALA418 4.8 15.0 1.0 O A:HOH1294 4.9 25.9 1.0 N A:ASP419 4.9 16.7 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