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Iodine in PDB 4gs5: The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053

Protein crystallography data

The structure of The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053, PDB code: 4gs5 was solved by K.Tan, J.Holowicki, S.Clancy, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.98 / 2.02
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 67.148, 67.148, 176.257, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 25.5

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053 (pdb code 4gs5). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053, PDB code: 4gs5:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 4gs5

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Iodine binding site 1 out of 12 in the The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:54.5
occ:0.44
N A:ALA160 3.9 38.7 1.0
CG A:ASN158 4.0 45.6 1.0
CB A:ASN158 4.0 40.8 1.0
N A:HIS159 4.0 30.9 1.0
OD1 A:ASN158 4.0 45.4 1.0
CB A:ALA160 4.2 42.0 1.0
CB A:HIS159 4.4 48.0 1.0
CA A:HIS159 4.6 40.9 1.0
ND2 A:ASN158 4.6 48.2 1.0
CA A:ALA160 4.7 37.5 1.0
C A:HIS159 4.7 38.5 1.0
C A:ASN158 4.7 34.5 1.0
CA A:ASN158 5.0 33.4 1.0

Iodine binding site 2 out of 12 in 4gs5

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Iodine binding site 2 out of 12 in the The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:91.5
occ:0.78
OG A:SER45 3.4 48.9 1.0
N A:SER45 3.7 39.5 1.0
CB A:SER45 4.1 43.1 1.0
NZ A:LYS50 4.1 52.8 1.0
CD A:LYS50 4.4 51.4 1.0
CA A:GLY44 4.4 35.4 1.0
CA A:SER45 4.5 42.4 1.0
C A:GLY44 4.5 33.3 1.0
O2 A:EDO416 4.6 69.8 1.0
CE A:LYS50 4.6 52.3 1.0
O A:HOH614 4.8 38.3 1.0

Iodine binding site 3 out of 12 in 4gs5

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Iodine binding site 3 out of 12 in the The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:33.9
occ:0.70
OE1 A:GLN132 2.6 40.6 0.4
CD A:GLN132 3.3 38.3 0.4
O1 A:EDO422 3.5 62.4 1.0
O A:HOH592 3.6 29.0 1.0
ND2 A:ASN158 3.8 48.2 1.0
NE2 A:GLN132 3.9 42.9 0.4
CB A:GLN132 4.0 29.9 0.6
CA A:MSE129 4.0 29.7 1.0
CB A:GLN132 4.0 30.5 0.4
CG A:GLN132 4.1 34.3 0.6
N A:MSE129 4.3 24.6 1.0
CG A:GLN132 4.3 34.5 0.4
CG A:MSE129 4.4 36.3 1.0
CB A:MSE129 4.4 30.2 1.0
CE A:MSE129 4.5 45.9 1.0
O A:PRO128 4.5 27.9 1.0
C A:PRO128 4.5 29.2 1.0
CD2 A:LEU161 4.7 26.0 1.0
CG A:ASN158 4.7 45.6 1.0
CD A:GLN132 4.8 39.3 0.6
C1 A:EDO422 4.9 57.6 1.0
OD1 A:ASN158 4.9 45.4 1.0
OE1 A:GLN132 5.0 36.3 0.6
CB A:PRO128 5.0 30.9 1.0

Iodine binding site 4 out of 12 in 4gs5

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Iodine binding site 4 out of 12 in the The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:40.0
occ:0.43
O1 A:EDO414 3.7 40.4 1.0
N A:HIS184 3.8 35.2 1.0
C A:SER183 3.8 36.8 1.0
CA A:GLY177 3.9 28.5 1.0
CB A:SER175 3.9 27.7 1.0
N A:GLY177 4.0 25.9 1.0
CA A:HIS184 4.0 35.4 1.0
C1 A:EDO414 4.1 39.3 1.0
C A:GLY177 4.2 30.2 1.0
O A:SER183 4.2 34.1 1.0
CB A:HIS184 4.2 41.5 1.0
CA A:SER183 4.3 41.9 1.0
OG A:SER183 4.3 49.4 1.0
C A:TYR176 4.6 24.2 1.0
N A:MSE178 4.6 30.7 1.0
OG A:SER175 4.6 36.9 1.0
O A:GLY177 4.6 28.3 1.0
O A:HOH653 4.9 40.8 1.0
CB A:SER183 4.9 46.0 1.0
O A:TYR176 4.9 22.4 1.0
O A:HOH521 4.9 27.6 1.0

Iodine binding site 5 out of 12 in 4gs5

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Iodine binding site 5 out of 12 in the The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I405

b:44.3
occ:0.45
O A:HOH528 3.2 36.9 1.0
O A:HOH534 3.5 52.3 1.0
CE A:LYS256 3.9 50.5 1.0
O A:VAL249 4.0 31.6 1.0
CG1 A:VAL249 4.2 28.0 1.0
CD2 A:LEU232 4.2 43.3 1.0
CB A:ASN251 4.2 33.9 1.0
CG A:LYS256 4.3 42.0 1.0
NZ A:LYS256 4.3 50.8 1.0
C A:ILE250 4.3 30.9 1.0
N A:ASN251 4.4 26.6 1.0
C A:VAL249 4.4 31.6 1.0
O A:ILE250 4.5 27.2 1.0
CB A:VAL249 4.5 27.1 1.0
CA A:ILE250 4.6 25.4 1.0
O A:HOH615 4.7 50.6 1.0
CD A:LYS256 4.7 47.5 1.0
N A:ILE250 4.8 24.6 1.0
CA A:ASN251 4.8 31.3 1.0
CG A:LEU232 4.9 42.6 1.0

Iodine binding site 6 out of 12 in 4gs5

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Iodine binding site 6 out of 12 in the The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:0.3
occ:0.57
O A:HOH645 3.1 66.3 1.0
NZ A:LYS339 3.4 51.8 1.0
OG1 A:THR337 3.5 78.3 1.0
CG2 A:THR337 3.6 77.0 1.0
CE A:LYS339 4.0 51.2 1.0
CB A:THR337 4.1 73.4 1.0
CD A:LYS339 4.2 50.0 1.0

Iodine binding site 7 out of 12 in 4gs5

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Iodine binding site 7 out of 12 in the The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:35.2
occ:0.48
I A:IOD408 2.5 38.9 0.5
CD2 A:HIS41 3.7 50.4 1.0
NE2 A:HIS41 3.7 59.3 1.0
CD A:PRO51 3.7 40.0 1.0
O A:PRO49 3.9 30.1 1.0
C A:PRO49 4.2 32.1 1.0
CB A:PRO49 4.2 34.9 1.0
CA A:LYS50 4.3 43.7 1.0
N A:PRO51 4.4 36.5 1.0
N A:LYS50 4.5 35.9 1.0
CG A:PRO51 4.5 44.9 1.0
C A:LYS50 4.6 36.9 1.0
CA A:PRO49 4.9 28.3 1.0
CE1 A:HIS41 4.9 61.3 1.0
CG A:HIS41 5.0 50.3 1.0

Iodine binding site 8 out of 12 in 4gs5

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Iodine binding site 8 out of 12 in the The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I408

b:38.9
occ:0.46
I A:IOD407 2.5 35.2 0.5
CD A:PRO51 4.4 40.0 1.0
CG A:PRO51 4.7 44.9 1.0

Iodine binding site 9 out of 12 in 4gs5

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Iodine binding site 9 out of 12 in the The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I409

b:60.2
occ:0.52
CB A:LEU116 3.8 78.3 1.0
CG A:LEU116 3.9 73.9 1.0
CD1 A:ILE2 4.1 70.5 1.0
CZ A:PHE121 4.2 44.2 1.0
O A:ASP117 4.3 87.1 1.0
CA A:ALA119 4.4 47.7 1.0
CD1 A:LEU116 4.4 74.4 1.0
O A:HIS118 4.5 57.2 1.0
N A:ALA119 4.5 52.4 1.0
C A:HIS118 4.7 63.2 1.0
CG2 A:THR104 4.8 36.7 1.0
CE1 A:PHE121 4.9 41.3 1.0
CE2 A:PHE121 4.9 40.2 1.0

Iodine binding site 10 out of 12 in 4gs5

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Iodine binding site 10 out of 12 in the The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I410

b:57.1
occ:0.46
N A:ALA300 3.3 66.5 1.0
CB A:ALA300 3.7 75.4 1.0
CA A:ALA300 3.9 68.9 1.0
N A:LYS330 3.9 62.1 1.0
C A:ASN299 4.0 58.7 1.0
CA A:LYS330 4.0 63.5 1.0
C A:ALA329 4.0 57.7 1.0
O A:ALA329 4.1 59.4 1.0
CA A:ASN299 4.2 57.7 1.0
CB A:PHE328 4.2 51.1 1.0
O A:PHE328 4.5 51.2 1.0
C A:PHE328 4.5 48.8 1.0
CB A:LYS330 4.5 69.2 1.0
N A:ALA329 4.6 48.7 1.0
N A:ASN299 4.7 47.9 1.0
CA A:ALA329 4.7 53.5 1.0
O A:ASN299 4.8 51.4 1.0

Reference:

K.Tan, J.Holowicki, S.Clancy, A.Joachimiak. The Crystal Structure of Acyl-Coa Synthetase (Amp-Forming)/Amp-Acid Ligase II-Like Protein From Dyadobacter Fermentans Dsm 18053 To Be Published.
Page generated: Sun Dec 13 19:32:53 2020

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