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Iodine in PDB 3men: Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak

Protein crystallography data

The structure of Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak, PDB code: 3men was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.700, 162.120, 173.070, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 23.7

Other elements in 3men:

The structure of Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak also contains other interesting chemical elements:

Potassium (K) 4 atoms
Zinc (Zn) 4 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 35;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak (pdb code 3men). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 35 binding sites of Iodine where determined in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak, PDB code: 3men:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 35 in 3men

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Iodine binding site 1 out of 35 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I342

b:23.5
occ:1.00
 O A:HOH485 3.5 13.0 1.0
N A:PRO247 3.8 16.0 1.0
C A:MET246 3.9 15.4 1.0
CD A:PRO247 3.9 17.1 1.0
CB A:ASP217 4.1 17.1 1.0
O A:PRO245 4.1 13.3 1.0
CG A:PRO245 4.2 16.4 1.0
CB A:PRO245 4.2 15.2 1.0
CG A:PRO247 4.2 17.1 1.0
C A:PRO245 4.2 14.8 1.0
N A:MET246 4.2 14.8 1.0
CA A:PRO247 4.3 15.9 1.0
O A:MET246 4.3 13.6 1.0
CA A:MET246 4.3 15.6 1.0
CG A:ASP217 4.3 18.1 1.0
OD2 A:ASP217 4.6 17.3 1.0
CA A:ASP217 4.8 16.4 1.0
OD1 A:ASP217 4.8 16.9 1.0
O A:HOH467 4.8 27.3 1.0
CA A:PRO245 4.9 14.3 1.0
CB A:PRO247 4.9 16.7 1.0

Iodine binding site 2 out of 35 in 3men

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Iodine binding site 2 out of 35 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I343

b:34.2
occ:1.00
 N A:HIS13 3.7 22.8 1.0
N A:GLU120 3.7 20.9 1.0
CA A:GLY119 3.8 19.6 1.0
N A:HIS121 3.8 21.0 1.0
O A:HOH371 3.9 24.6 1.0
C A:GLY119 4.0 20.5 1.0
O A:LEU11 4.2 23.0 1.0
OG1 A:THR122 4.2 11.9 1.0
C A:HIS13 4.2 24.4 1.0
N A:PRO14 4.3 25.6 1.0
CA A:HIS12 4.3 21.5 1.0
CB A:HIS121 4.4 21.4 1.0
O A:HIS13 4.4 25.1 1.0
ND1 A:HIS13 4.5 30.8 0.5
C A:HIS12 4.5 21.7 1.0
CA A:HIS13 4.5 23.5 0.5
CA A:HIS13 4.5 23.9 0.5
N A:THR122 4.6 18.0 1.0
CA A:HIS121 4.6 20.6 1.0
CA A:PRO14 4.6 27.5 1.0
N A:GLY119 4.6 18.7 1.0
CA A:GLU120 4.6 22.1 1.0
CD2 A:HIS121 4.7 27.5 1.0
C A:GLU120 4.7 21.5 1.0
ND1 A:HIS12 4.8 19.3 1.0
C A:HIS121 4.8 18.8 1.0
CB A:PRO14 4.8 27.9 1.0
O A:GLY119 4.9 19.7 1.0
CG A:HIS121 4.9 25.1 1.0
CG A:PRO14 4.9 27.3 1.0
CB A:GLU120 4.9 23.2 1.0
CE1 A:HIS13 5.0 31.7 0.5

Iodine binding site 3 out of 35 in 3men

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Iodine binding site 3 out of 35 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I344

b:36.0
occ:0.97
 O A:HOH428 3.5 18.4 1.0
O A:HOH547 3.8 19.8 1.0
O A:LEU266 4.0 17.1 1.0
O A:HOH505 4.1 28.0 1.0
C A:LEU266 4.1 15.7 1.0
CA A:ARG267 4.1 16.8 1.0
CD A:PRO271 4.2 15.0 1.0
CD1 A:LEU310 4.2 21.4 1.0
N A:ARG267 4.2 16.4 1.0
CB A:LEU266 4.5 15.3 1.0
CG A:ARG267 4.5 18.3 1.0
CG A:PRO271 4.6 15.9 1.0
CD2 A:LEU308 4.8 20.3 1.0
CG A:LEU310 4.8 21.7 1.0
CD2 A:LEU310 4.9 20.6 1.0
CA A:LEU266 5.0 15.0 1.0
CB A:ARG267 5.0 17.4 1.0

Iodine binding site 4 out of 35 in 3men

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Iodine binding site 4 out of 35 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I345

b:38.2
occ:0.96
 O A:HOH395 3.3 12.7 1.0
OG A:SER19 3.4 30.8 1.0
ND2 B:ASN91 3.5 20.0 1.0
NE A:ARG20 3.5 41.9 1.0
CB A:TYR222 3.9 14.6 1.0
CD A:ARG20 4.0 40.5 1.0
CD1 A:TYR222 4.1 13.5 1.0
CD1 B:ILE92 4.1 23.5 1.0
CG A:ARG20 4.3 37.9 1.0
CD2 B:LEU104 4.4 17.7 1.0
CG A:TYR222 4.5 14.1 1.0
CZ A:ARG20 4.5 44.6 1.0
N A:TYR222 4.5 14.4 1.0
CA A:TYR222 4.5 14.3 1.0
CG B:ASN91 4.5 24.1 1.0
NH2 A:ARG20 4.7 45.0 1.0
O A:HOH477 4.7 28.4 1.0
OD1 B:ASN91 4.8 27.4 1.0
CB A:SER19 4.8 32.7 1.0

Iodine binding site 5 out of 35 in 3men

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Iodine binding site 5 out of 35 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I346

b:44.1
occ:0.75
 O B:HOH356 3.2 18.4 1.0
ND2 A:ASN91 3.4 30.0 1.0
NE B:ARG20 3.9 43.0 1.0
CB B:TYR222 4.0 18.9 1.0
OG B:SER19 4.0 33.4 1.0
CD B:ARG20 4.2 41.6 1.0
CD1 B:TYR222 4.3 18.6 1.0
O B:HOH422 4.3 31.8 1.0
CB B:SER19 4.3 34.5 1.0
CG A:ASN91 4.4 26.6 1.0
CD2 A:LEU104 4.4 23.6 1.0
CG B:ARG20 4.4 39.2 1.0
N B:TYR222 4.5 18.3 1.0
OD1 A:ASN91 4.5 30.8 1.0
CA B:TYR222 4.6 18.0 1.0
CG B:TYR222 4.6 17.9 1.0
CD1 A:ILE92 4.6 28.1 1.0
CZ B:ARG20 4.8 46.6 1.0

Iodine binding site 6 out of 35 in 3men

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Iodine binding site 6 out of 35 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I347

b:36.2
occ:0.58
 OG A:SER115 3.3 15.2 1.0
CB A:SER19 3.6 32.7 1.0
CB A:TYR17 3.8 33.3 1.0
CE1 A:PHE166 3.9 16.1 1.0
CZ A:PHE166 4.0 20.1 1.0
OG A:SER19 4.0 30.8 1.0
CD1 A:TYR17 4.4 35.6 1.0
CB A:SER115 4.4 14.3 1.0
CG A:TYR17 4.5 35.1 1.0
O A:HOH477 4.8 28.4 1.0
CB A:ARG24 4.8 35.5 1.0
O A:PHE18 4.9 30.1 1.0
CA A:SER19 4.9 33.0 1.0
C A:TYR17 4.9 32.6 1.0
CA A:TYR17 4.9 33.1 1.0
C A:PHE18 4.9 32.2 1.0
CD A:ARG24 5.0 39.7 1.0
CA A:SER115 5.0 14.6 1.0
N A:SER19 5.0 32.7 1.0
NH2 A:ARG20 5.0 45.0 1.0

Iodine binding site 7 out of 35 in 3men

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Iodine binding site 7 out of 35 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I348

b:39.6
occ:0.53
 OE1 A:GLN106 3.0 34.4 1.0
O A:HOH453 3.0 32.1 1.0
O A:HOH479 3.7 26.5 1.0
OG1 A:THR72 3.8 26.6 1.0
CG2 A:VAL103 3.9 23.3 1.0
CD1 A:PHE69 3.9 19.4 1.0
CG A:GLU76 3.9 29.8 1.0
CD A:GLN106 4.0 30.8 1.0
CB A:GLU76 4.2 27.5 1.0
CG A:GLN106 4.3 24.9 1.0
CA A:VAL73 4.4 21.5 1.0
CB A:VAL103 4.4 22.6 1.0
CA A:VAL103 4.4 22.6 1.0
CE1 A:PHE69 4.4 20.6 1.0
CB A:GLN106 4.4 20.9 1.0
CA A:PHE69 4.7 19.6 1.0
N A:VAL73 4.7 22.1 1.0
CB A:VAL73 4.7 21.1 1.0
O A:PHE69 4.7 18.3 1.0
C A:THR72 4.8 23.3 1.0
CG A:PHE69 4.9 18.3 1.0
CG2 A:VAL73 4.9 17.4 1.0
O A:THR72 4.9 24.4 1.0
CB A:THR72 5.0 25.1 1.0

Iodine binding site 8 out of 35 in 3men

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Iodine binding site 8 out of 35 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I349

b:37.0
occ:0.41
 O A:HOH480 2.7 41.2 1.0
O A:HOH525 3.3 45.3 1.0
NE2 A:GLN200 3.8 10.5 1.0
CA A:GLU201 4.1 13.9 1.0
O A:HOH382 4.1 37.1 1.0
CG B:PRO97 4.2 34.2 1.0
CB A:GLU201 4.2 14.5 1.0
CG A:GLU201 4.2 19.4 1.0
CG A:TYR204 4.3 13.8 1.0
CG A:GLN200 4.4 9.6 1.0
CD2 A:TYR204 4.4 12.9 1.0
CD1 A:TYR204 4.5 10.6 1.0
N A:GLU201 4.5 13.1 1.0
CD A:GLN200 4.6 10.3 1.0
CE2 A:TYR204 4.6 13.0 1.0
CE1 A:TYR204 4.7 12.2 1.0
O A:HOH502 4.7 28.4 1.0
CZ A:TYR204 4.8 10.7 1.0
CB A:TYR204 4.8 12.9 1.0
C A:GLN200 4.9 12.2 1.0

Iodine binding site 9 out of 35 in 3men

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Iodine binding site 9 out of 35 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I350

b:41.8
occ:0.37
 O A:HOH448 3.2 33.4 1.0
CB A:ARG182 3.9 24.2 1.0
CD A:ARG141 4.1 28.9 1.0
O A:ALA181 4.2 23.1 1.0
NE A:ARG141 4.3 32.2 1.0
C A:ALA181 4.3 21.9 1.0
CA A:ARG182 4.4 23.0 1.0
CG A:ARG141 4.4 25.8 1.0
CB A:ALA181 4.4 19.4 1.0
N A:ARG182 4.4 22.3 1.0
CG A:ARG182 5.0 29.7 1.0

Iodine binding site 10 out of 35 in 3men

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Iodine binding site 10 out of 35 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I342

b:42.2
occ:0.93
 CZ B:ARG340 3.9 35.5 1.0
NH2 B:ARG340 3.9 35.7 1.0
O B:HOH495 3.9 45.8 1.0
N B:GLY341 3.9 39.5 1.0
CG B:ARG309 3.9 34.7 1.0
CB B:ARG309 4.0 32.7 1.0
CA B:ARG309 4.0 31.3 1.0
NE B:ARG340 4.1 34.1 1.0
CB B:ARG340 4.1 34.6 1.0
NH1 B:ARG340 4.3 35.6 1.0
C B:ARG309 4.3 31.0 1.0
CG B:ARG340 4.4 33.5 1.0
CA B:ARG340 4.4 35.7 1.0
O B:ARG309 4.4 31.9 1.0
CD B:ARG309 4.4 39.7 1.0
C B:ARG340 4.7 37.2 1.0
CB B:PRO145 4.8 33.5 1.0
CD B:ARG340 4.8 33.4 1.0
CA B:GLY341 4.8 41.2 1.0

Reference:

J.Abendroth, A.S.Gardberg, J.I.Robinson, J.S.Christensen, B.L.Staker, P.J.Myler, L.J.Stewart, T.E.Edwards. Sad Phasing Using Iodide Ions in A High-Throughput Structural Genomics Environment. J Struct Funct Genomics V. 12 83 2011.
PubMed: 21359836
DOI: 10.1007/S10969-011-9101-7
Page generated: Sun Aug 11 15:45:53 2024

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