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Iodine in PDB 4j3w: Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide

Enzymatic activity of Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide

All present enzymatic activity of Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide:
3.2.1.41;

Protein crystallography data

The structure of Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide, PDB code: 4j3w was solved by L.Sim, M.S.Windahl, M.S.Moeller, A.Henriksen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.83 / 1.67
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.850, 80.940, 58.290, 90.00, 100.82, 90.00
R / Rfree (%) 15.3 / 18.1

Other elements in 4j3w:

The structure of Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide (pdb code 4j3w). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide, PDB code: 4j3w:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 4j3w

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Iodine binding site 1 out of 10 in the Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I908

b:34.9
occ:1.00
 NZ A:LYS487 3.7 21.3 1.0
CE A:LYS487 4.1 19.9 1.0
CD1 A:ILE632 4.1 13.8 1.0
CA A:GLY535 4.3 12.6 1.0
CE2 A:PHE251 4.7 17.4 1.0
O A:GLY535 4.8 13.3 1.0
CD2 A:PHE251 4.9 15.8 1.0
NE2 A:GLN491 4.9 20.6 1.0

Iodine binding site 2 out of 10 in 4j3w

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Iodine binding site 2 out of 10 in the Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I909

b:46.2
occ:1.00
 N A:THR495 3.5 16.7 1.0
OG1 A:THR495 3.8 26.9 1.0
CA A:THR494 3.9 16.7 1.0
CB A:THR494 3.9 17.7 1.0
OD1 A:ASP501 4.0 19.1 1.0
CG2 A:THR495 4.0 19.6 1.0
CG A:ASP501 4.1 20.9 1.0
CG2 A:THR494 4.2 19.2 1.0
C A:THR494 4.3 15.7 1.0
CA A:ASP501 4.3 16.5 1.0
CB A:ASP501 4.3 19.2 1.0
CB A:THR495 4.3 21.0 1.0
CA A:THR495 4.5 19.4 1.0
OD2 A:ASP501 4.6 26.2 1.0
O A:HOH1224 4.7 25.0 1.0
O A:LEU493 4.8 14.0 1.0
O A:VAL500 5.0 16.5 1.0

Iodine binding site 3 out of 10 in 4j3w

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Iodine binding site 3 out of 10 in the Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I910

b:40.7
occ:1.00
 O A:HOH1270 3.1 21.8 1.0
O A:HOH1257 3.3 25.2 1.0
CD1 A:LEU722 3.9 11.4 1.0
CE3 A:TRP732 4.2 12.2 1.0
O A:HOH1297 4.3 26.6 1.0
CD A:LYS736 4.5 18.4 1.0
CZ3 A:TRP732 4.7 12.7 1.0
O A:HOH1132 4.7 14.0 1.0
OD2 A:ASP338 4.9 23.9 1.0

Iodine binding site 4 out of 10 in 4j3w

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Iodine binding site 4 out of 10 in the Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I911

b:56.0
occ:1.00
 CE1 A:HIS847 4.0 13.8 1.0
CB A:SER767 4.1 12.8 1.0
CG2 A:VAL849 4.2 14.2 1.0
CG A:PRO848 4.7 18.9 1.0
NE2 A:HIS847 4.8 13.2 1.0
CB A:PRO848 4.8 17.0 1.0
ND1 A:HIS847 4.9 14.7 1.0
OG A:SER767 4.9 13.0 1.0

Iodine binding site 5 out of 10 in 4j3w

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Iodine binding site 5 out of 10 in the Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I912

b:28.4
occ:1.00
 O A:HOH1213 3.5 15.1 1.0
NE2 A:GLN850 3.6 14.5 1.0
CE1 A:HIS668 3.6 16.5 1.0
NE2 A:HIS668 3.9 15.9 1.0
CG1 A:ILE761 4.0 17.5 1.0
CD1 A:ILE761 4.1 18.1 1.0
CG A:GLN850 4.1 13.9 1.0
O A:HOH1142 4.1 17.0 1.0
O A:SER757 4.3 5.4 0.6
CD A:GLN850 4.3 14.0 1.0
CB A:SER757 4.4 7.7 0.6
CB A:ASP760 4.4 12.9 1.0
OG A:SER853 4.5 15.9 1.0
CG1 A:VAL858 4.6 14.6 1.0
CA A:SER757 4.7 7.5 0.6
ND1 A:HIS668 4.8 17.1 1.0
CG2 A:VAL858 4.8 16.4 1.0
C A:SER757 4.9 7.2 0.6

Iodine binding site 6 out of 10 in 4j3w

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Iodine binding site 6 out of 10 in the Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I913

b:36.2
occ:0.50
 CG2 A:VAL849 4.1 14.2 1.0
O A:HOH1336 4.1 24.7 1.0
CA A:VAL849 4.2 14.4 1.0
CB A:VAL849 4.5 14.4 1.0
CG1 A:VAL849 4.7 14.7 1.0
CB A:ASN852 4.7 31.0 1.0
N A:VAL849 4.8 15.2 1.0
O A:PRO848 4.9 16.7 1.0

Iodine binding site 7 out of 10 in 4j3w

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Iodine binding site 7 out of 10 in the Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I914

b:80.4
occ:0.50
 I A:IOD914 0.0 80.4 0.5
I A:IOD914 3.9 36.7 0.5
CA A:GLY749 4.0 11.6 1.0
O A:HOH1046 4.1 24.6 1.0
N A:GLY749 4.3 11.5 1.0
CD1 A:LEU752 4.4 14.4 1.0
CG A:LYS748 4.8 15.2 1.0
C A:LYS748 4.9 12.3 1.0

Iodine binding site 8 out of 10 in 4j3w

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Iodine binding site 8 out of 10 in the Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I914

b:36.7
occ:0.50
 I A:IOD914 0.0 36.7 0.5
I A:IOD914 3.9 80.4 0.5
NZ A:LYS748 3.9 25.3 1.0
CE A:LYS748 4.0 22.3 1.0
CD A:LYS748 4.3 18.8 1.0
CD1 A:LEU752 4.7 14.4 1.0

Iodine binding site 9 out of 10 in 4j3w

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Iodine binding site 9 out of 10 in the Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I915

b:34.8
occ:0.50
 I A:IOD915 0.0 34.8 0.5
I A:IOD915 2.4 36.2 0.5
CG A:MET484 3.9 12.6 1.0
CA A:ARG481 3.9 11.2 1.0
CB A:MET484 4.2 11.4 1.0
N A:ARG481 4.2 10.3 1.0
CG A:LYS480 4.2 10.2 1.0
CB A:ARG481 4.2 12.8 1.0
O A:HOH1211 4.3 19.3 1.0
O A:LYS480 4.4 10.0 1.0
C A:LYS480 4.4 9.8 1.0
CE A:LYS480 4.5 12.3 1.0
CD A:LYS480 4.6 11.1 1.0
O A:HOH1259 4.7 24.4 1.0
CB A:LYS480 4.9 10.2 1.0

Iodine binding site 10 out of 10 in 4j3w

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Iodine binding site 10 out of 10 in the Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I915

b:36.2
occ:0.50
 I A:IOD915 0.0 36.2 0.5
I A:IOD915 2.4 34.8 0.5
O A:HOH1259 2.8 24.4 1.0
O A:HOH1038 3.8 12.1 1.0
CD A:LYS480 4.0 11.1 1.0
CG A:LYS480 4.0 10.2 1.0
N A:ARG481 4.1 10.3 1.0
CB A:LYS480 4.2 10.2 1.0
CB A:ARG481 4.3 12.8 1.0
CA A:ARG481 4.4 11.2 1.0
CB A:ILE524 4.4 13.1 1.0
C A:LYS480 4.6 9.8 1.0
CG2 A:ILE524 4.6 14.0 1.0
CE A:LYS480 4.6 12.3 1.0
CG1 A:ILE524 4.9 14.9 1.0
CA A:LYS480 5.0 9.6 1.0

Reference:

L.Sim, M.S.Windahl, M.S.Moeller, A.Henriksen. Crystal Structure of Barley Limit Dextrinase (E510A Mutant) in Complex with A Branched Maltohexasaccharide To Be Published.
Page generated: Sun Aug 11 18:17:19 2024

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