Calcium in PDB 4xb3: Structure of Dextran Glucosidase

All present enzymatic activity of Structure of Dextran Glucosidase:
3.2.1.70;

The structure of Structure of Dextran Glucosidase, PDB code: 4xb3 was solved by M.Kobayashi, K.Kato, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.11 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.151, 82.550, 103.559, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.9

The binding sites of Calcium atom in the Structure of Dextran Glucosidase (pdb code 4xb3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Dextran Glucosidase, PDB code: 4xb3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of Dextran Glucosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Dextran Glucosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:32.4 occ:1.00 O A:ASP148 2.4 34.2 1.0 OD1 A:ASP151 2.4 34.7 1.0 OD2 A:ASP151 2.9 40.8 1.0 CG A:ASP151 2.9 32.4 1.0 C A:ASP148 3.5 32.5 1.0 CA A:ASP148 4.2 31.1 1.0 CB A:ASP151 4.4 33.1 1.0 O A:LYS149 4.4 34.2 1.0 N A:LYS149 4.6 39.3 1.0 OH A:TYR146 4.7 30.6 1.0 C A:LYS149 4.7 38.8 1.0 CB A:ASP148 4.8 33.6 1.0 N A:ASP151 4.8 27.1 1.0 CA A:LYS149 4.8 36.7 1.0 CA A:ASP151 4.8 25.8 1.0

Calcium binding site 2 out of 4 in the Structure of Dextran Glucosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Dextran Glucosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:21.0 occ:1.00 O A:ILE27 2.3 18.2 1.0 OD1 A:ASN23 2.3 23.4 1.0 OD1 A:ASP25 2.4 19.5 1.0 OD1 A:ASP21 2.4 19.2 1.0 O A:HOH1020 2.4 28.5 1.0 O A:HOH1018 2.4 24.8 1.0 OD1 A:ASP29 2.5 22.4 1.0 OD2 A:ASP25 3.0 27.1 1.0 CG A:ASP25 3.0 24.1 1.0 CG A:ASN23 3.3 30.3 1.0 CG A:ASP21 3.4 22.7 1.0 C A:ILE27 3.5 20.0 1.0 CG A:ASP29 3.6 22.4 1.0 ND2 A:ASN23 3.8 29.4 1.0 CB A:ASP29 4.0 18.9 1.0 OD2 A:ASP21 4.2 23.1 1.0 CB A:ASP21 4.2 18.1 1.0 N A:ILE27 4.3 20.2 1.0 N A:ASN23 4.3 19.2 1.0 CA A:ILE27 4.3 19.8 1.0 CA A:ASP21 4.3 20.7 1.0 N A:THR22 4.3 22.6 1.0 C A:GLY28 4.3 21.0 1.0 O A:ILE74 4.4 25.0 1.0 CB A:ASP25 4.4 21.2 1.0 O A:GLY28 4.4 21.0 1.0 CB A:ILE27 4.5 18.6 1.0 N A:ASP29 4.5 19.1 1.0 N A:GLY28 4.5 19.6 1.0 N A:ASP25 4.5 19.8 1.0 CB A:ASN23 4.6 23.6 1.0 CA A:GLY28 4.7 17.8 1.0 OD2 A:ASP29 4.7 20.3 1.0 C A:ASP21 4.7 24.1 1.0 CA A:ASN23 4.8 24.7 1.0 CA A:ASP29 4.8 20.7 1.0 N A:GLY24 4.9 21.0 1.0 C A:ASN23 4.9 24.8 1.0 CA A:ASP25 4.9 20.1 1.0

Calcium binding site 3 out of 4 in the Structure of Dextran Glucosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Dextran Glucosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:32.0 occ:1.00 O A:HOH720 2.4 24.2 1.0 O A:HOH726 2.5 27.8 1.0 O A:THR417 2.5 24.0 1.0 O A:HOH729 2.5 31.7 1.0 O A:HOH727 2.7 22.4 1.0 C A:THR417 3.6 21.8 1.0 OD1 A:ASP419 4.1 38.2 1.0 CB A:THR417 4.2 21.6 1.0 CA A:THR417 4.4 27.2 1.0 N A:ALA418 4.4 24.6 1.0 OG1 A:THR417 4.4 21.2 1.0 CA A:ALA418 4.5 24.2 1.0 NE2 A:GLN411 4.6 31.2 1.0 OE1 A:GLN411 4.7 30.9 1.0 C A:ALA418 4.7 26.1 1.0 O A:HOH703 4.8 34.7 1.0 N A:ASP419 4.8 29.0 1.0 O A:HOH766 5.0 32.3 1.0

Calcium binding site 4 out of 4 in the Structure of Dextran Glucosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Dextran Glucosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:33.2 occ:1.00 O A:HOH736 2.4 23.8 1.0 O A:LYS439 2.4 21.7 1.0 OG A:SER441 2.7 27.3 1.0 C A:LYS439 3.5 20.4 1.0 N A:SER441 3.6 18.8 1.0 CB A:SER441 3.8 21.4 1.0 CA A:SER441 4.0 19.9 1.0 C A:ASN440 4.3 22.2 1.0 CA A:LYS439 4.4 25.9 1.0 N A:ASN440 4.4 20.5 1.0 CA A:ASN440 4.5 21.7 1.0 O A:HOH761 4.5 24.3 1.0 O A:LEU438 4.5 25.4 1.0

M.Kobayashi, W.Saburi, D.Nakatsuka, H.Hondoh, K.Kato, M.Okuyama, H.Mori, A.Kimura, M.Yao. Structural Insights Into the Catalytic Reaction That Is Involved in the Reorientation of TRP238 at the Substrate-Binding Site in GH13 Dextran Glucosidase Febs Lett. V. 589 484 2015.
ISSN: ISSN 0014-5793
PubMed: 25595454
DOI: 10.1016/J.FEBSLET.2015.01.005