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Iodine in PDB 4j3v: Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide

Enzymatic activity of Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide

All present enzymatic activity of Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide:
3.2.1.41;

Protein crystallography data

The structure of Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide, PDB code: 4j3v 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) 28.84 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 173.990, 85.820, 61.550, 90.00, 95.98, 90.00
R / Rfree (%) 13.4 / 16.9

Other elements in 4j3v:

The structure of Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide (pdb code 4j3v). 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 in Complex with A Branched Thio-Linked Hexasaccharide, PDB code: 4j3v:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 4j3v

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Iodine binding site 1 out of 10 in the Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide


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 in Complex with A Branched Thio-Linked Hexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I911

b:19.7
occ:1.00
 O A:HOH1986 3.0 30.2 1.0
O A:HOH1106 3.4 13.9 1.0
CA A:GLY423 3.7 9.7 1.0
NE A:ARG428 3.8 13.4 1.0
CZ A:ARG428 3.9 13.0 1.0
N A:GLY423 4.0 10.4 1.0
NH2 A:ARG428 4.0 14.5 1.0
CG A:PRO198 4.1 15.1 1.0
CB A:PRO198 4.2 16.4 1.0
CD A:ARG428 4.3 11.9 1.0
CG2 A:THR199 4.3 17.9 1.0
O A:HOH2003 4.4 45.7 1.0
NH1 A:ARG428 4.4 15.1 1.0
CD A:PRO198 4.4 14.7 1.0
O A:GLY432 4.5 13.8 1.0
O A:HOH1176 4.6 15.4 1.0
CD1 A:ILE434 4.7 14.3 1.0
CG1 A:ILE434 4.7 13.3 1.0
O A:HOH1271 4.7 23.4 1.0
C A:PRO422 4.8 10.8 1.0
CG A:ARG428 5.0 12.1 1.0

Iodine binding site 2 out of 10 in 4j3v

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Iodine binding site 2 out of 10 in the Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide


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 in Complex with A Branched Thio-Linked Hexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I912

b:17.1
occ:1.00
 O A:HOH1059 3.5 11.8 1.0
O A:HOH1069 3.6 13.9 1.0
CD A:ARG452 3.8 9.3 1.0
CG A:ARG452 3.9 9.9 1.0
CG2 A:THR127 3.9 11.8 1.0
CB A:THR127 4.0 11.1 1.0
NE A:ARG452 4.0 10.0 1.0
CA A:THR127 4.1 9.8 1.0
O A:THR127 4.5 12.4 1.0
CZ A:ARG452 4.5 9.9 1.0
NH1 A:ARG452 4.7 10.0 1.0
CB A:ARG452 4.8 9.3 1.0
C A:THR127 4.8 10.6 1.0
NH1 A:ARG485 4.8 10.9 1.0
O A:TYR126 4.8 9.4 1.0
NH2 A:ARG485 4.9 9.4 1.0

Iodine binding site 3 out of 10 in 4j3v

Go back to Iodine Binding Sites List in 4j3v
Iodine binding site 3 out of 10 in the Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide


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 in Complex with A Branched Thio-Linked Hexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I913

b:18.8
occ:1.00
 O A:HOH1582 3.3 26.6 1.0
NE2 A:GLN850 3.6 12.7 1.0
NE2 A:HIS668 3.7 15.5 1.0
CE1 A:HIS668 3.7 12.3 1.0
CB A:ASP760 4.2 10.4 1.0
CG A:GLN850 4.2 11.9 1.0
O A:HOH1122 4.2 15.0 1.0
O A:HOH1092 4.2 18.4 1.0
O A:SER757 4.3 9.1 0.4
O A:SER757 4.3 11.0 0.6
CD1 A:ILE761 4.4 14.1 1.0
CD A:GLN850 4.4 11.5 1.0
CD1 A:ILE764 4.5 13.4 1.0
N A:ILE761 4.6 10.7 1.0
C A:ASP760 4.8 9.8 1.0
CB A:ILE761 4.9 11.0 1.0
CB A:SER757 4.9 16.2 0.6
CA A:ILE761 4.9 10.0 1.0
CA A:SER757 4.9 12.2 0.6
ND1 A:HIS668 4.9 14.7 1.0
CD2 A:HIS668 4.9 12.3 1.0

Iodine binding site 4 out of 10 in 4j3v

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Iodine binding site 4 out of 10 in the Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide


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 in Complex with A Branched Thio-Linked Hexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I914

b:27.1
occ:1.00
 OG A:SER414 3.1 25.0 1.0
O A:HOH1148 3.5 14.2 1.0
O A:HOH1641 3.6 39.0 1.0
O A:HOH1655 3.6 22.8 1.0
O A:HOH1292 3.8 18.2 1.0
O A:ASN219 3.9 11.6 1.0
CB A:SER414 4.0 17.0 1.0
CB A:ALA313 4.1 9.3 1.0
CE1 A:HIS311 4.1 10.4 1.0
NE2 A:HIS311 4.2 10.6 1.0
CG2 A:ILE413 4.2 21.0 1.0
CA A:SER414 4.2 15.5 1.0
CA A:ALA313 4.3 9.2 1.0
CG2 A:VAL360 4.4 9.1 1.0
N A:SER414 4.5 15.6 1.0
CG1 A:ILE413 4.7 19.0 1.0
C A:ILE413 4.7 17.4 1.0
C A:ASN219 4.7 11.1 1.0
O A:ILE413 4.7 18.0 1.0
CB A:ASN219 4.8 11.3 1.0
O A:HOH1863 4.8 32.2 1.0
N A:ALA313 4.9 9.6 1.0
CA A:ASN219 4.9 11.0 1.0
O A:PHE312 5.0 9.1 1.0
CB A:ILE413 5.0 20.3 1.0

Iodine binding site 5 out of 10 in 4j3v

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Iodine binding site 5 out of 10 in the Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide


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 in Complex with A Branched Thio-Linked Hexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I915

b:45.8
occ:1.00
 O A:HOH1332 3.3 27.3 1.0
O A:HOH1504 3.4 28.0 1.0
O A:HOH2006 3.5 63.0 1.0
OG A:SER53 3.8 23.9 1.0
CB A:SER53 3.9 22.2 1.0
CG2 A:VAL87 4.0 26.6 1.0
CB A:VAL55 4.2 23.0 1.0
CG1 A:VAL55 4.2 22.8 1.0
CG1 A:VAL87 4.4 24.2 1.0
CD1 A:LEU92 4.5 24.5 1.0
CB A:VAL87 4.6 25.3 1.0
CA A:VAL87 4.6 23.7 1.0
CD2 A:LEU92 4.7 28.7 1.0
CG A:LEU92 4.9 27.1 1.0
CG2 A:VAL55 4.9 24.6 1.0
O A:LYS54 5.0 27.3 1.0
C A:LYS54 5.0 23.3 1.0

Iodine binding site 6 out of 10 in 4j3v

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Iodine binding site 6 out of 10 in the Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide


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 in Complex with A Branched Thio-Linked Hexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I916

b:49.2
occ:1.00
 O A:HOH1952 3.1 41.6 1.0
NH1 A:ARG581 3.8 14.2 1.0
O A:HOH1479 3.9 27.8 1.0
CD A:ARG581 3.9 16.8 1.0
CE1 A:PHE566 4.0 14.3 1.0
CZ A:PHE566 4.2 14.3 1.0
CB A:GLU577 4.4 27.1 1.0
O A:GLU577 4.4 20.5 1.0
C A:GLU577 4.5 17.7 1.0
OE1 A:GLU577 4.5 45.6 1.0
N A:ALA578 4.6 18.8 1.0
CZ A:ARG581 4.6 14.8 1.0
CB A:ARG581 4.6 13.8 1.0
NE A:ARG581 4.7 14.5 1.0
CA A:ALA578 4.7 18.4 1.0
CG A:ARG581 4.8 14.2 1.0

Iodine binding site 7 out of 10 in 4j3v

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Iodine binding site 7 out of 10 in the Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide


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 in Complex with A Branched Thio-Linked Hexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I917

b:49.3
occ:1.00
 CE1 A:HIS847 3.7 12.1 1.0
O A:HOH1752 4.1 30.2 1.0
CB A:SER767 4.2 10.8 1.0
NE2 A:HIS847 4.4 12.7 1.0
CG A:PRO848 4.4 18.1 1.0
CB A:PRO848 4.5 16.0 1.0
ND1 A:HIS847 4.6 11.9 1.0
CZ A:PHE818 4.6 19.0 1.0
CD A:PRO848 4.7 13.6 1.0
CG2 A:VAL849 4.7 14.0 1.0
OG A:SER767 5.0 10.7 1.0

Iodine binding site 8 out of 10 in 4j3v

Go back to Iodine Binding Sites List in 4j3v
Iodine binding site 8 out of 10 in the Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide


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 in Complex with A Branched Thio-Linked Hexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I918

b:36.5
occ:0.50
 I A:IOD918 0.0 36.5 0.5
I A:IOD918 2.4 23.3 0.5
O A:HOH1453 3.5 24.6 1.0
CA A:ARG481 4.0 10.0 1.0
CG A:MET484 4.0 12.0 1.0
O A:HOH1088 4.0 13.8 1.0
CB A:MET484 4.2 10.7 1.0
O A:HOH1829 4.3 39.3 1.0
CB A:ARG481 4.3 12.5 1.0
O A:HOH1867 4.4 42.2 1.0
N A:ARG481 4.4 10.2 1.0
CG A:LYS480 4.4 9.4 1.0
O A:LYS480 4.5 10.0 1.0
C A:LYS480 4.6 8.8 1.0
CE A:LYS480 4.7 11.9 1.0
O A:HOH1963 4.8 37.4 1.0
CD A:LYS480 4.8 10.3 1.0

Iodine binding site 9 out of 10 in 4j3v

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Iodine binding site 9 out of 10 in the Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide


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 in Complex with A Branched Thio-Linked Hexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I918

b:23.3
occ:0.50
 I A:IOD918 0.0 23.3 0.5
I A:IOD918 2.4 36.5 0.5
O A:HOH1963 2.6 37.4 1.0
O A:HOH1115 3.8 12.7 1.0
CG A:LYS480 3.9 9.4 1.0
N A:ARG481 4.0 10.2 1.0
O A:HOH1639 4.0 38.6 1.0
CD A:LYS480 4.0 10.3 1.0
CB A:LYS480 4.1 8.9 1.0
CA A:ARG481 4.2 10.0 1.0
CB A:ARG481 4.2 12.5 1.0
O A:HOH1254 4.3 27.0 1.0
C A:LYS480 4.4 8.8 1.0
CE A:LYS480 4.5 11.9 1.0
CB A:ILE524 4.7 11.7 0.5
O A:HOH1867 4.7 42.2 1.0
CD1 A:ILE524 4.7 13.6 0.5
CB A:ILE524 4.8 11.7 0.5
CG2 A:ILE524 4.8 11.9 0.5
CG2 A:ILE524 4.9 11.6 0.5
CA A:LYS480 4.9 8.9 1.0
O A:LYS480 5.0 10.0 1.0

Iodine binding site 10 out of 10 in 4j3v

Go back to Iodine Binding Sites List in 4j3v
Iodine binding site 10 out of 10 in the Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide


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 in Complex with A Branched Thio-Linked Hexasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I919

b:57.1
occ:0.50
 O A:HOH1369 2.9 25.5 1.0
O A:PRO829 3.7 16.4 1.0
CD2 A:HIS830 4.0 10.9 1.0
CB A:HIS830 4.1 10.8 1.0
O A:HOH1819 4.3 33.2 1.0
CG A:HIS830 4.3 11.3 1.0
O A:HOH1878 4.4 35.0 1.0
CG A:PRO829 4.4 12.5 1.0
C A:PRO829 4.5 12.3 1.0
O A:HOH1787 4.7 33.4 1.0
CB A:PRO829 4.9 11.8 1.0
O A:HOH1282 5.0 18.9 1.0

Reference:

L.Sim, M.S.Windahl, M.S.Moeller, A.Henriksen. Crystal Structure of Barley Limit Dextrinase in Complex with A Branched Thio-Linked Hexasaccharide To Be Published.
Page generated: Sun Aug 11 18:17:10 2024

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