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Iodine 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:

Calcium (Ca) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine 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 Iodine atom.
In total 9 binding sites of Iodine where determined in the Barley Limit Dextrinase in Complex with Alpha-Cyclodextrin, PDB code: 2y5e:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 2y5e

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Iodine binding site 1 out of 9 in the Barley Limit Dextrinase in Complex with Alpha-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 Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1890

b:65.0
occ:1.00
 O A:HOH2120 3.7 42.1 1.0
CA A:GLY423 3.9 35.8 1.0
NE A:ARG428 3.9 46.0 1.0
CG A:PRO198 3.9 50.2 1.0
CZ A:ARG428 4.0 48.7 1.0
CB A:PRO198 4.1 49.6 1.0
N A:GLY423 4.1 33.5 1.0
NH2 A:ARG428 4.3 52.4 1.0
CG2 A:THR199 4.3 53.0 1.0
CD A:ARG428 4.4 44.8 1.0
O A:GLY432 4.4 39.2 1.0
NH1 A:ARG428 4.5 46.1 1.0
CD A:PRO198 4.5 49.4 1.0
CG1 A:ILE434 4.6 42.6 1.0
CD1 A:ILE434 4.7 42.2 1.0
C A:PRO422 4.9 34.4 1.0
O A:HOH2125 5.0 37.4 1.0

Iodine binding site 2 out of 9 in 2y5e

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Iodine binding site 2 out of 9 in the Barley Limit Dextrinase in Complex with Alpha-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 Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1891

b:84.0
occ:1.00
 NE2 A:GLN850 3.7 28.7 1.0
CD1 A:ILE761 3.7 42.9 1.0
CE1 A:HIS668 3.8 37.0 1.0
CG A:GLN850 4.0 33.5 1.0
CG1 A:ILE761 4.1 41.3 1.0
O A:SER757 4.2 34.0 1.0
NE2 A:HIS668 4.2 36.7 1.0
CB A:ASP760 4.3 38.8 1.0
CD A:GLN850 4.4 32.4 1.0
CB A:SER757 4.6 38.2 1.0
OG A:SER853 4.6 50.3 1.0
CA A:SER757 4.7 38.1 1.0
OD2 A:ASP760 4.9 48.5 1.0
CG1 A:VAL858 4.9 36.7 1.0
C A:SER757 4.9 36.1 1.0
ND1 A:HIS668 4.9 37.1 1.0
N A:ILE761 5.0 29.1 1.0

Iodine binding site 3 out of 9 in 2y5e

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Iodine binding site 3 out of 9 in the Barley Limit Dextrinase in Complex with Alpha-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 Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1892

b:79.9
occ:0.50
 O A:HOH2136 3.4 27.6 1.0
CG A:ARG452 3.8 27.2 1.0
CD A:ARG452 3.9 26.9 1.0
NE A:ARG452 3.9 27.6 1.0
O A:HOH2137 4.0 49.6 1.0
CB A:THR127 4.1 29.5 1.0
CG2 A:THR127 4.1 32.8 1.0
CA A:THR127 4.2 24.1 1.0
CZ A:ARG452 4.4 30.2 1.0
O A:THR127 4.4 31.8 1.0
CB A:ARG452 4.7 21.4 1.0
NH1 A:ARG452 4.8 33.8 1.0
C A:THR127 4.8 27.0 1.0
NH1 A:ARG485 4.9 23.3 1.0
OD1 A:ASP456 4.9 48.8 1.0
NH2 A:ARG452 4.9 33.6 1.0
NH2 A:ARG485 5.0 22.2 1.0

Iodine binding site 4 out of 9 in 2y5e

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Iodine binding site 4 out of 9 in the Barley Limit Dextrinase in Complex with Alpha-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 Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1893

b:100.0
occ:0.50
 NZ A:LYS736 3.5 64.1 1.0
CA A:SER337 3.8 34.9 1.0
CB A:PRO334 3.9 44.6 1.0
CB A:SER337 4.0 37.9 1.0
OE2 A:GLU740 4.1 71.2 1.0
CG A:PRO334 4.1 41.9 1.0
N A:SER337 4.1 34.2 1.0
O A:GLY336 4.2 39.8 1.0
C A:GLY336 4.3 37.0 1.0
OG A:SER337 4.5 42.9 1.0
CE A:LYS736 4.9 63.0 1.0

Iodine binding site 5 out of 9 in 2y5e

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Iodine binding site 5 out of 9 in the Barley Limit Dextrinase in Complex with Alpha-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 Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1894

b:96.9
occ:0.50
 NH2 A:ARG262 3.8 31.1 1.0
O A:ARG276 3.9 31.3 1.0
NH1 A:ARG262 3.9 28.8 1.0
CZ A:ARG262 4.4 30.7 1.0
CZ3 A:TRP322 4.5 33.1 1.0
O A:SER273 4.5 52.8 1.0
CZ A:PHE324 4.6 29.4 1.0
C A:ARG276 4.8 26.8 1.0
CE1 A:PHE324 4.8 31.8 1.0
CE3 A:TRP322 4.9 32.4 1.0
CB A:ARG276 5.0 34.8 1.0

Iodine binding site 6 out of 9 in 2y5e

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Iodine binding site 6 out of 9 in the Barley Limit Dextrinase in Complex with Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Barley Limit Dextrinase in Complex with Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1895

b:48.7
occ:0.50
 I A:IOD1895 0.0 48.7 0.5
I A:IOD1895 2.7 53.4 0.5
O A:HOH2158 3.4 33.3 1.0
CD A:LYS480 4.0 19.7 1.0
CG A:LYS480 4.1 17.1 1.0
CB A:LYS480 4.2 17.8 1.0
N A:ARG481 4.2 29.0 1.0
CD1 A:ILE524 4.4 33.3 1.0
CB A:ARG481 4.5 37.3 1.0
CB A:ILE524 4.5 26.5 1.0
CE A:LYS480 4.5 21.7 1.0
CA A:ARG481 4.6 33.8 1.0
CG2 A:ILE524 4.6 23.2 1.0
C A:LYS480 4.8 28.8 1.0
CG1 A:ILE524 4.9 29.9 1.0

Iodine binding site 7 out of 9 in 2y5e

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Iodine binding site 7 out of 9 in the Barley Limit Dextrinase in Complex with Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Barley Limit Dextrinase in Complex with Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1895

b:53.4
occ:0.50
 I A:IOD1895 0.0 53.4 0.5
I A:IOD1895 2.7 48.7 0.5
CG A:MET484 3.8 29.8 1.0
CA A:ARG481 3.9 33.8 1.0
O A:HOH2144 4.2 36.8 1.0
CB A:MET484 4.2 31.6 1.0
N A:ARG481 4.2 29.0 1.0
CG A:LYS480 4.3 17.1 1.0
CB A:ARG481 4.3 37.3 1.0
CE A:LYS480 4.4 21.7 1.0
C A:LYS480 4.5 28.8 1.0
CD A:LYS480 4.6 19.7 1.0
O A:LYS480 4.6 32.9 1.0
CB A:LYS480 4.9 17.8 1.0

Iodine binding site 8 out of 9 in 2y5e

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Iodine binding site 8 out of 9 in the Barley Limit Dextrinase in Complex with Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Barley Limit Dextrinase in Complex with Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1896

b:0.1
occ:1.00
 CE1 A:HIS847 3.7 46.2 1.0
CB A:SER767 4.0 26.2 1.0
NE2 A:HIS847 4.3 46.4 1.0
CG A:PRO848 4.4 37.0 1.0
CZ A:PHE818 4.5 43.1 1.0
CB A:PRO848 4.5 36.6 1.0
OG A:SER767 4.5 29.3 1.0
ND1 A:HIS847 4.7 47.6 1.0
CG2 A:VAL849 4.8 37.6 1.0
CD A:PRO848 4.9 38.6 1.0

Iodine binding site 9 out of 9 in 2y5e

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Iodine binding site 9 out of 9 in the Barley Limit Dextrinase in Complex with Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Barley Limit Dextrinase in Complex with Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1897

b:95.1
occ:0.75
 O A:HOH2163 3.3 31.4 1.0
NZ A:LYS487 3.5 41.0 1.0
CE A:LYS487 4.1 37.3 1.0
CA A:GLY535 4.3 27.1 1.0
CD1 A:ILE632 4.3 29.4 1.0
O A:GLY535 4.8 25.4 1.0
NE2 A:GLN491 4.9 58.3 1.0
C A:GLY535 5.0 28.1 1.0
CE2 A:PHE251 5.0 35.3 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 14:33:47 2024

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