Calcium in PDB 4wlc: Structure of Dextran Glucosidase with Glucose

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

The structure of Structure of Dextran Glucosidase with Glucose, PDB code: 4wlc 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)	44.11 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.989, 83.736, 103.790, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 26.3

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

Calcium binding site 1 out of 3 in the Structure of Dextran Glucosidase with Glucose


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 with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:46.3 occ:1.00 O A:ASP148 2.4 40.4 1.0 OD1 A:ASP151 2.5 41.0 1.0 O A:HOH721 2.9 37.6 1.0 CG A:ASP151 3.3 41.3 1.0 OD2 A:ASP151 3.5 43.7 1.0 C A:ASP148 3.6 41.8 1.0 CA A:ASP148 4.2 41.5 1.0 CB A:ASP148 4.3 40.0 1.0 N A:LYS149 4.7 45.0 1.0 CB A:ASP151 4.7 38.2 1.0 OH A:TYR146 4.8 41.6 1.0 CA A:LYS149 5.0 45.0 1.0 N A:ASP151 5.0 40.2 1.0

Calcium binding site 2 out of 3 in the Structure of Dextran Glucosidase with Glucose


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 with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:45.3 occ:1.00 OD1 A:ASP29 2.2 43.4 1.0 OD1 A:ASP25 2.3 44.3 1.0 O A:ILE27 2.4 36.6 1.0 OD1 A:ASN23 2.4 42.3 1.0 OD1 A:ASP21 2.8 40.0 1.0 OD2 A:ASP25 2.8 41.0 1.0 CG A:ASP25 2.9 41.3 1.0 CG A:ASN23 3.3 44.4 1.0 CG A:ASP29 3.3 42.0 1.0 C A:ILE27 3.4 38.1 1.0 ND2 A:ASN23 3.6 44.0 1.0 CG A:ASP21 3.8 42.1 1.0 OD2 A:ASP29 3.8 42.1 1.0 O A:ILE74 4.0 36.3 1.0 CA A:ILE27 4.1 39.1 1.0 CB A:ILE27 4.1 38.0 1.0 N A:ILE27 4.1 39.0 1.0 O A:GLY28 4.3 36.5 1.0 C A:GLY28 4.3 37.0 1.0 CB A:ASP25 4.3 42.3 1.0 N A:GLY28 4.4 37.8 1.0 OD2 A:ASP21 4.5 42.4 1.0 CB A:ASP29 4.5 40.4 1.0 N A:ASP29 4.6 38.5 1.0 CB A:ASP21 4.6 40.4 1.0 N A:ASP25 4.7 42.8 1.0 CB A:ASN23 4.7 42.9 1.0 CA A:GLY28 4.7 38.3 1.0 N A:ASN23 4.8 43.5 1.0 CA A:ASP29 4.9 41.3 1.0 N A:THR22 4.9 41.0 1.0 CA A:ASP21 4.9 40.0 1.0 CG2 A:ILE27 4.9 36.2 1.0 CA A:ASP25 5.0 42.9 1.0

Calcium binding site 3 out of 3 in the Structure of Dextran Glucosidase with Glucose


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 with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:52.7 occ:1.00 O A:THR417 2.4 48.4 1.0 O A:HOH720 2.6 42.3 1.0 O A:HOH719 2.6 45.8 1.0 OG1 A:THR417 3.5 62.5 1.0 C A:THR417 3.6 47.9 1.0 CA A:ALA418 4.4 46.0 1.0 OD2 A:ASP419 4.5 42.8 1.0 N A:ALA418 4.5 44.6 1.0 CB A:THR417 4.5 48.9 1.0 CA A:THR417 4.6 49.9 1.0 NE2 A:GLN411 4.7 47.8 1.0 O A:HOH725 4.8 43.6 1.0 CG2 A:THR417 4.9 46.5 1.0 C A:ALA418 4.9 41.6 1.0 OE1 A:GLN411 4.9 55.0 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