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Calcium in PDB 2y5e: Barley Limit Dextrinase in Complex with Alpha-Cyclodextrin

Enzymatic activity of Barley Limit Dextrinase in Complex with Alpha-Cyclodextrin

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

Protein crystallography data

The structure of Barley Limit Dextrinase in Complex with Alpha-Cyclodextrin, PDB code: 2y5e 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) 33.47 / 2.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 174.840, 85.610, 61.120, 90.00, 96.83, 90.00
R / Rfree (%) 17.5 / 22.6

Other elements in 2y5e:

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

Iodine (I) 9 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Barley Limit Dextrinase in Complex with Alpha-Cyclodextrin (pdb code 2y5e). 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 Alpha-Cyclodextrin, PDB code: 2y5e:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2y5e

Go back to Calcium Binding Sites List in 2y5e
Calcium binding site 1 out of 2 in the Barley Limit Dextrinase in Complex with Alpha-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 Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1887

b:36.0
occ:1.00
O A:TYR353 2.5 27.9 1.0
O A:GLN348 2.6 47.6 1.0
OD1 A:ASN701 2.6 23.1 1.0
OD1 A:ASP351 2.7 32.2 1.0
O A:HOH2080 2.7 21.8 1.0
O A:HOH2196 2.9 31.5 1.0
CG A:ASP351 3.6 30.1 1.0
C A:GLN348 3.6 44.4 1.0
C A:TYR353 3.6 27.3 1.0
OD2 A:ASP351 3.7 32.4 1.0
CG A:ASN701 3.8 30.9 1.0
CA A:GLN348 4.3 38.5 1.0
ND2 A:ASN354 4.4 19.4 1.0
O A:GLY314 4.4 38.4 1.0
CA A:TYR353 4.4 28.2 1.0
N A:TYR353 4.4 32.1 1.0
CB A:ASN354 4.5 25.1 1.0
CB A:GLN348 4.5 33.0 1.0
ND2 A:ASN701 4.6 35.9 1.0
O A:HOH2095 4.6 23.1 1.0
CB A:TYR353 4.6 23.8 1.0
CA A:ASN701 4.6 27.7 1.0
O A:ASN701 4.6 29.6 1.0
N A:GLU349 4.6 45.8 1.0
N A:ASN354 4.6 28.7 1.0
O A:ASP351 4.7 29.7 1.0
CA A:ASN354 4.8 25.7 1.0
CB A:ASN701 4.8 28.1 1.0
CA A:GLU349 4.8 44.2 1.0
C A:ASN701 4.9 26.3 1.0
N A:ASP351 4.9 30.0 1.0
CB A:ASP351 4.9 23.1 1.0
CG A:ASN354 5.0 26.0 1.0

Calcium binding site 2 out of 2 in 2y5e

Go back to Calcium Binding Sites List in 2y5e
Calcium binding site 2 out of 2 in the Barley Limit Dextrinase in Complex with Alpha-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 Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1888

b:74.7
occ:1.00
O A:GLY393 2.9 31.5 1.0
O A:LEU301 2.9 31.2 1.0
O A:HOH2077 2.9 53.4 1.0
OG A:SER297 3.0 37.3 1.0
O A:HOH2075 3.0 47.3 1.0
O A:SER297 3.0 29.7 1.0
C A:SER297 3.7 28.5 1.0
C A:GLY393 3.7 27.2 1.0
CA A:SER297 3.9 29.5 1.0
C A:LEU301 3.9 23.2 1.0
CB A:SER297 4.0 33.0 1.0
CA A:GLY393 4.0 22.9 1.0
O A:HOH2078 4.3 25.9 1.0
CA A:THR302 4.5 23.0 1.0
C A:GLY300 4.5 23.3 1.0
O A:GLY300 4.6 22.4 1.0
N A:LEU301 4.6 23.9 1.0
N A:THR302 4.7 17.4 1.0
N A:ASP298 4.8 30.7 1.0
N A:LEU394 4.8 26.4 1.0
CD2 A:LEU394 4.9 19.7 1.0
O A:ILE392 4.9 37.3 1.0
CA A:LEU301 4.9 22.4 1.0
CA A:GLY300 4.9 26.4 1.0

Reference:

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
Page generated: Sat Dec 12 03:59:45 2020

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