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Iodine in PDB 4j3s: Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose

Enzymatic activity of Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose

All present enzymatic activity of Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose:
3.2.1.41;

Protein crystallography data

The structure of Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose, PDB code: 4j3s 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) 46.96 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.260, 81.240, 58.230, 90.00, 101.14, 90.00
R / Rfree (%) 13.6 / 18.2

Other elements in 4j3s:

The structure of Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose 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 Soaked with 300MM Maltotetraose (pdb code 4j3s). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose, PDB code: 4j3s:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 4j3s

Go back to Iodine Binding Sites List in 4j3s
Iodine binding site 1 out of 9 in the Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose


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 Soaked with 300MM Maltotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I912

b:40.9
occ:1.00
 O A:HOH1163 2.9 34.0 1.0
NE2 A:GLN850 3.4 20.0 1.0
CD1 A:ILE761 3.7 22.3 1.0
O A:HOH1107 3.7 23.6 1.0
CE1 A:HIS668 3.7 22.3 1.0
CG1 A:ILE761 3.9 20.8 1.0
NE2 A:HIS668 3.9 24.3 1.0
CG A:GLN850 4.2 18.7 1.0
O A:SER757 4.2 15.3 1.0
CB A:ASP760 4.2 18.1 1.0
CD A:GLN850 4.3 19.3 1.0
O A:HOH1261 4.3 29.2 1.0
CB A:SER757 4.5 21.2 1.0
OG A:SER853 4.6 20.7 1.0
CA A:SER757 4.7 18.7 1.0
CG1 A:VAL858 4.7 18.3 1.0
OD2 A:ASP760 4.8 26.7 1.0
ND1 A:HIS668 4.9 22.4 1.0
CG2 A:VAL858 4.9 20.2 1.0
C A:SER757 4.9 17.0 1.0
N A:ILE761 5.0 16.4 1.0
O A:VAL877 5.0 16.4 1.0

Iodine binding site 2 out of 9 in 4j3s

Go back to Iodine Binding Sites List in 4j3s
Iodine binding site 2 out of 9 in the Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose


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 Soaked with 300MM Maltotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I913

b:40.8
occ:1.00
 O A:HOH1272 3.0 31.4 1.0
NH2 A:ARG222 3.9 24.1 1.0
CA A:PRO162 4.0 18.8 1.0
O A:GLY161 4.1 19.2 1.0
N A:PRO162 4.4 20.0 1.0
C A:GLY161 4.4 22.1 1.0
O A:ALA160 4.6 31.1 1.0
CB A:PRO162 4.6 17.8 1.0

Iodine binding site 3 out of 9 in 4j3s

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Iodine binding site 3 out of 9 in the Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose


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 Soaked with 300MM Maltotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I914

b:49.5
occ:1.00
 O A:HOH1202 3.3 29.3 1.0
N A:THR495 3.6 23.4 1.0
OG1 A:THR495 3.9 35.6 1.0
OD1 A:ASP501 3.9 24.4 1.0
CG A:ASP501 3.9 25.5 1.0
CA A:THR494 3.9 23.0 1.0
CG2 A:THR495 4.0 26.0 1.0
CB A:THR494 4.0 24.6 1.0
CB A:ASP501 4.2 23.0 1.0
OD2 A:ASP501 4.3 30.7 1.0
C A:THR494 4.3 22.5 1.0
CA A:ASP501 4.3 20.6 1.0
CB A:THR495 4.4 28.3 1.0
CG2 A:THR494 4.4 26.5 1.0
CA A:THR495 4.6 27.0 1.0
O A:LEU493 4.9 18.8 1.0
O A:HOH1252 5.0 38.0 1.0

Iodine binding site 4 out of 9 in 4j3s

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Iodine binding site 4 out of 9 in the Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose


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 Soaked with 300MM Maltotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I915

b:34.7
occ:0.50
 I A:IOD915 0.0 34.7 0.5
I A:IOD915 2.8 74.4 0.5
O A:HOH1490 3.6 42.2 1.0
ND2 A:ASN852 3.8 32.6 1.0
CB A:ASN852 4.2 28.2 1.0
CA A:VAL849 4.2 19.6 1.0
O A:HOH1218 4.2 27.8 1.0
CG2 A:VAL849 4.3 18.6 1.0
CG A:ASN852 4.5 30.4 1.0
O A:PRO848 4.7 20.2 1.0
CB A:VAL849 4.7 18.5 1.0
N A:VAL849 4.7 19.4 1.0
CG1 A:VAL849 4.9 18.1 1.0
C A:PRO848 5.0 21.2 1.0

Iodine binding site 5 out of 9 in 4j3s

Go back to Iodine Binding Sites List in 4j3s
Iodine binding site 5 out of 9 in the Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose


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 Soaked with 300MM Maltotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I915

b:74.4
occ:0.50
 I A:IOD915 0.0 74.4 0.5
I A:IOD915 2.8 34.7 0.5
O A:HOH1521 3.6 23.8 1.0
CB A:PRO848 4.1 21.2 1.0
ND2 A:ASN852 4.1 32.6 1.0
CG2 A:VAL849 4.3 18.6 1.0
N A:VAL849 4.4 19.4 1.0
C A:PRO848 4.5 21.2 1.0
O A:PRO848 4.7 20.2 1.0
CA A:VAL849 4.7 19.6 1.0
CA A:PRO848 5.0 20.6 1.0

Iodine binding site 6 out of 9 in 4j3s

Go back to Iodine Binding Sites List in 4j3s
Iodine binding site 6 out of 9 in the Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose


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 Soaked with 300MM Maltotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I916

b:35.0
occ:0.50
 I A:IOD916 0.0 35.0 0.5
I A:IOD916 2.4 40.6 0.5
O A:HOH1143 3.6 19.0 1.0
N A:ARG481 4.1 15.4 1.0
CG A:LYS480 4.2 16.8 1.0
CB A:LYS480 4.2 15.7 1.0
CD A:LYS480 4.3 18.0 1.0
CB A:ILE524 4.3 18.8 1.0
CB A:ARG481 4.3 20.0 1.0
CA A:ARG481 4.4 17.5 1.0
O A:HOH1379 4.5 37.8 1.0
CG2 A:ILE524 4.5 17.6 1.0
C A:LYS480 4.6 14.9 1.0
CG1 A:ILE524 4.8 21.3 1.0
CE A:LYS480 4.8 19.8 1.0
CA A:LYS480 5.0 15.7 1.0

Iodine binding site 7 out of 9 in 4j3s

Go back to Iodine Binding Sites List in 4j3s
Iodine binding site 7 out of 9 in the Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose


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 Soaked with 300MM Maltotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I916

b:40.6
occ:0.50
 I A:IOD916 0.0 40.6 0.5
I A:IOD916 2.4 35.0 0.5
CA A:ARG481 3.9 17.5 1.0
CG A:MET484 4.0 18.0 1.0
N A:ARG481 4.2 15.4 1.0
CG A:LYS480 4.2 16.8 1.0
CB A:ARG481 4.3 20.0 1.0
CB A:MET484 4.4 16.7 1.0
C A:LYS480 4.4 14.9 1.0
CE A:LYS480 4.5 19.8 1.0
O A:LYS480 4.5 13.7 1.0
O A:HOH1237 4.5 29.4 1.0
CD A:LYS480 4.5 18.0 1.0
CB A:LYS480 4.8 15.7 1.0

Iodine binding site 8 out of 9 in 4j3s

Go back to Iodine Binding Sites List in 4j3s
Iodine binding site 8 out of 9 in the Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose


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 Soaked with 300MM Maltotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I917

b:0.1
occ:0.50
 I A:IOD917 0.0 0.1 0.5
I A:IOD917 3.4 46.4 0.5
NZ A:LYS748 4.4 31.4 1.0
CE A:LYS748 4.5 27.8 1.0
CD A:LYS748 4.7 25.0 1.0
CD1 A:LEU752 4.8 24.4 1.0

Iodine binding site 9 out of 9 in 4j3s

Go back to Iodine Binding Sites List in 4j3s
Iodine binding site 9 out of 9 in the Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose


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 Soaked with 300MM Maltotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I917

b:46.4
occ:0.50
 I A:IOD917 0.0 46.4 0.5
I A:IOD917 3.4 0.1 0.5
O A:HOH1135 3.8 28.7 1.0
N A:GLY749 4.0 18.0 1.0
CA A:GLY749 4.0 17.7 1.0
CG A:LYS748 4.4 21.4 1.0
CD1 A:LEU752 4.5 24.4 1.0
CB A:LYS748 4.5 19.1 1.0
CD A:LYS748 4.5 25.0 1.0
C A:LYS748 4.6 17.0 1.0

Reference:

L.Sim, M.S.Windahl, M.S.Moeller, A.Henriksen. Crystal Structure of Barley Limit Dextrinase Soaked with 300MM Maltotetraose To Be Published.
Page generated: Sun Aug 11 18:13:31 2024

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