Calcium in PDB 2y4s: Barley Limit Dextrinase in Complex with Beta-Cyclodextrin

All present enzymatic activity of Barley Limit Dextrinase in Complex with Beta-Cyclodextrin:
3.2.1.41;

The structure of Barley Limit Dextrinase in Complex with Beta-Cyclodextrin, PDB code: 2y4s was solved by M.B.Vester-Christensen, M.A.Hachem, B.Svensson, A.Henriksen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.195 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	175.030, 82.390, 59.380, 90.00, 96.13, 90.00
R / Rfree (%)	16.54 / 20.4

The structure of Barley Limit Dextrinase in Complex with Beta-Cyclodextrin also contains other interesting chemical elements:

Iodine

(I)

5 atoms

The binding sites of Calcium atom in the Barley Limit Dextrinase in Complex with Beta-Cyclodextrin (pdb code 2y4s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Barley Limit Dextrinase in Complex with Beta-Cyclodextrin, PDB code: 2y4s:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Barley Limit Dextrinase in Complex with Beta-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Barley Limit Dextrinase in Complex with Beta-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1893 b:10.3 occ:1.00 O A:TYR353 2.4 2.2 1.0 O A:GLN348 2.4 3.9 1.0 OD1 A:ASN701 2.5 10.8 1.0 OD1 A:ASP351 2.6 6.7 1.0 O A:HOH2189 2.7 5.9 1.0 O A:HOH2232 2.7 5.5 1.0 O A:HOH2233 2.8 10.5 1.0 CG A:ASP351 3.5 10.2 1.0 C A:TYR353 3.5 7.8 1.0 C A:GLN348 3.6 8.4 1.0 CG A:ASN701 3.7 8.7 1.0 OD2 A:ASP351 3.9 5.5 1.0 N A:TYR353 4.2 6.3 1.0 O A:GLY314 4.2 7.3 1.0 CA A:TYR353 4.2 6.6 1.0 CA A:GLN348 4.2 9.3 1.0 ND2 A:ASN701 4.4 5.5 1.0 O A:HOH2227 4.5 24.0 1.0 O A:ASP351 4.5 6.0 1.0 CB A:TYR353 4.5 9.6 1.0 ND2 A:ASN354 4.5 7.2 1.0 CB A:GLN348 4.6 8.2 1.0 N A:ASN354 4.6 8.2 1.0 N A:GLU349 4.6 5.3 1.0 CB A:ASN354 4.6 5.9 1.0 O A:ASN701 4.7 13.1 1.0 N A:ASP351 4.7 8.5 1.0 CA A:ASN701 4.7 8.8 1.0 CB A:ASP351 4.8 5.2 1.0 C A:ASP351 4.8 8.5 1.0 CA A:GLU349 4.8 13.0 1.0 CB A:ASN701 4.8 7.5 1.0 CA A:ASN354 4.9 6.7 1.0 C A:GLU349 5.0 15.9 1.0 C A:ASN701 5.0 11.2 1.0 CA A:ASP351 5.0 6.2 1.0

Calcium binding site 2 out of 2 in the Barley Limit Dextrinase in Complex with Beta-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Barley Limit Dextrinase in Complex with Beta-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1894 b:29.0 occ:1.00 O A:LEU301 2.5 4.2 1.0 OG A:SER297 2.6 5.2 1.0 O A:GLY393 2.6 4.8 1.0 O A:HOH2015 2.7 8.4 1.0 O A:HOH2045 2.7 15.5 1.0 O A:SER297 2.8 4.3 1.0 C A:SER297 3.4 6.6 1.0 C A:GLY393 3.4 7.2 1.0 CA A:SER297 3.5 4.8 1.0 CB A:SER297 3.5 3.8 1.0 C A:LEU301 3.7 4.5 1.0 CA A:GLY393 3.9 4.2 1.0 CD2 A:LEU394 4.2 1.4 1.0 O A:HOH2257 4.2 11.4 1.0 CA A:THR302 4.3 3.2 1.0 C A:GLY300 4.4 7.8 1.0 O A:GLY300 4.5 2.9 1.0 N A:THR302 4.5 2.0 1.0 N A:LEU394 4.5 6.9 1.0 N A:LEU301 4.5 4.7 1.0 N A:ASP298 4.6 6.5 1.0 O A:ILE392 4.6 8.8 1.0 O A:HOH2184 4.6 12.1 1.0 CA A:LEU301 4.7 9.5 1.0 CG A:LEU394 4.7 7.2 1.0 CA A:LEU394 4.9 6.0 1.0 N A:SER297 4.9 3.7 1.0 CA A:GLY300 4.9 9.1 1.0

M.B.Vester-Christensen, M.Abou Hachem, B.Svensson, A.Henriksen. Crystal Structure of An Essential Enzyme in Seed Starch Degradation: Barley Limit Dextrinase in Complex with Cyclodextrins. J.Mol.Biol. V. 403 739 2010.
ISSN: ISSN 0022-2836
PubMed: 20863834
DOI: 10.1016/J.JMB.2010.09.031