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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 2y4s:

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

Calcium (Ca) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine 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 Iodine atom.
In total 5 binding sites of Iodine where determined in the Barley Limit Dextrinase in Complex with Beta-Cyclodextrin, PDB code: 2y4s:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in 2y4s

Go back to Iodine Binding Sites List in 2y4s
Iodine binding site 1 out of 5 in the Barley Limit Dextrinase in Complex with Beta-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I 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:I1896

b:90.5
occ:1.00
 O A:HOH2319 3.4 22.7 1.0
N A:THR495 3.5 13.1 1.0
OG1 A:THR495 3.7 31.4 1.0
OD1 A:ASP501 3.8 29.4 1.0
CG2 A:THR495 3.8 18.7 1.0
CA A:THR494 3.9 11.5 1.0
CG A:ASP501 3.9 23.8 1.0
CB A:THR494 4.0 13.5 1.0
CB A:ASP501 4.1 16.8 1.0
CB A:THR495 4.2 22.6 1.0
C A:THR494 4.2 15.3 1.0
CA A:ASP501 4.3 15.1 1.0
CA A:THR495 4.4 18.8 1.0
OD2 A:ASP501 4.5 26.0 1.0
CG2 A:THR494 4.5 13.5 1.0
O A:HOH2317 4.6 23.8 1.0
O A:LEU493 5.0 11.2 1.0

Iodine binding site 2 out of 5 in 2y4s

Go back to Iodine Binding Sites List in 2y4s
Iodine binding site 2 out of 5 in the Barley Limit Dextrinase in Complex with Beta-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I 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:I1897

b:66.5
occ:1.00
 CE1 A:HIS142 3.8 18.6 1.0
OG A:SER140 4.0 27.5 1.0
CG A:PRO129 4.0 14.3 1.0
NE2 A:HIS142 4.6 19.4 1.0
CG2 A:VAL133 4.6 27.6 1.0
CB A:PRO129 4.6 11.8 1.0
CG1 A:VAL133 4.6 23.9 1.0
ND1 A:HIS142 4.6 17.3 1.0
O A:HOH2062 4.7 43.2 1.0
CB A:VAL133 4.7 24.4 1.0
CD A:PRO129 4.8 10.9 1.0
CB A:SER140 4.9 18.2 1.0

Iodine binding site 3 out of 5 in 2y4s

Go back to Iodine Binding Sites List in 2y4s
Iodine binding site 3 out of 5 in the Barley Limit Dextrinase in Complex with Beta-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Barley Limit Dextrinase in Complex with Beta-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1898

b:0.5
occ:1.00
 O A:HOH2181 3.7 48.5 1.0
CD A:LYS736 4.0 28.3 1.0
CB A:TRP732 4.2 16.0 1.0
O A:TRP732 4.2 15.1 1.0
C A:TRP732 4.2 16.3 1.0
N A:PRO733 4.3 17.1 1.0
CA A:PRO733 4.4 17.0 1.0
CB A:LYS736 4.7 19.0 1.0
CD1 A:LEU722 4.7 11.0 1.0
CG A:PRO733 4.8 21.1 1.0
CD A:PRO733 4.9 20.1 1.0
CA A:TRP732 4.9 17.1 1.0
CE3 A:TRP732 4.9 15.5 1.0
O A:HOH2467 4.9 35.0 1.0
CG A:LYS736 5.0 21.2 1.0

Iodine binding site 4 out of 5 in 2y4s

Go back to Iodine Binding Sites List in 2y4s
Iodine binding site 4 out of 5 in the Barley Limit Dextrinase in Complex with Beta-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Barley Limit Dextrinase in Complex with Beta-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1899

b:43.6
occ:0.50
 O A:HOH2345 3.2 19.9 1.0
NZ A:LYS487 3.4 31.5 1.0
CE A:LYS487 4.1 30.1 1.0
CA A:GLY535 4.2 9.8 1.0
CD1 A:ILE632 4.6 16.2 1.0
O A:THR534 4.7 13.2 1.0
NE2 A:GLN491 4.8 43.0 1.0

Iodine binding site 5 out of 5 in 2y4s

Go back to Iodine Binding Sites List in 2y4s
Iodine binding site 5 out of 5 in the Barley Limit Dextrinase in Complex with Beta-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Barley Limit Dextrinase in Complex with Beta-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1900

b:30.1
occ:0.50
 CE1 A:HIS847 3.8 10.6 1.0
CB A:SER767 4.2 6.2 1.0
CG A:PRO848 4.4 18.1 1.0
CB A:PRO848 4.4 12.5 1.0
NE2 A:HIS847 4.5 11.7 1.0
CZ A:PHE818 4.5 14.6 1.0
CG2 A:VAL849 4.6 6.6 1.0
ND1 A:HIS847 4.6 10.3 1.0
CD A:PRO848 4.8 13.8 1.0
OG A:SER767 4.9 5.5 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: Sun Aug 11 14:32:57 2024

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