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Iodine in PDB 7f9v: Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone

Protein crystallography data

The structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone, PDB code: 7f9v was solved by Y.Manickam, N.Malhotra, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.07 / 1.82
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.067, 82.981, 105.521, 90, 103.08, 90
R / Rfree (%) 17.2 / 19.7

Other elements in 7f9v:

The structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone also contains other interesting chemical elements:

Fluorine (F) 5 atoms
Bromine (Br) 8 atoms
Chlorine (Cl) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone (pdb code 7f9v). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone, PDB code: 7f9v:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 7f9v

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Iodine binding site 1 out of 10 in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I906

b:57.2
occ:0.65
 O A:HOH1134 3.1 47.2 1.0
CG A:PRO801 4.0 40.4 1.0
CD1 A:ILE524 4.0 36.2 1.0
CG2 A:ILE524 4.3 32.6 1.0
CD1 A:LEU756 4.3 35.0 1.0
CB A:PRO801 4.4 36.9 1.0
CD1 A:ILE736 4.4 34.0 1.0
CD2 A:LEU756 4.5 43.0 1.0
CD1 A:LEU825 4.5 36.9 1.0
CG1 A:ILE524 4.7 36.2 1.0
CD2 A:LEU825 4.8 37.3 1.0
CG A:LEU756 5.0 34.5 1.0

Iodine binding site 2 out of 10 in 7f9v

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Iodine binding site 2 out of 10 in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I907

b:56.6
occ:0.33
 O A:HOH1071 3.1 37.9 1.0
O B:TYR358 3.9 43.4 1.0
CB A:ALA447 4.0 35.2 1.0
CA A:ALA447 4.0 36.1 1.0
N A:ALA447 4.0 35.6 1.0
CG B:GLU357 4.2 39.5 1.0
CD1 B:ILE366 4.2 35.4 1.0
C A:PRO446 4.5 36.8 1.0
NZ A:LYS404 4.5 56.4 1.0
OE2 B:GLU357 4.6 55.6 1.0
CB A:PRO446 4.7 35.5 1.0
CD B:GLU357 4.8 49.4 1.0
CD1 B:TYR359 4.8 40.2 1.0
O A:PRO446 4.8 35.1 1.0

Iodine binding site 3 out of 10 in 7f9v

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Iodine binding site 3 out of 10 in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I909

b:78.3
occ:0.65
 CD A:ARG552 3.4 54.3 1.0
NE A:ARG552 3.5 55.6 1.0
NH2 A:ARG481 3.8 41.7 1.0
CB A:MET791 3.9 74.9 1.0
CZ A:ARG552 3.9 51.0 1.0
CE1 A:TYR830 4.0 43.7 1.0
CD1 A:TYR830 4.2 37.1 1.0
NH1 A:ARG552 4.3 49.8 1.0
CZ A:TYR830 4.4 38.7 1.0
CA A:MET791 4.6 71.3 1.0
NH2 A:ARG552 4.6 53.1 1.0
CZ A:ARG481 4.7 45.0 1.0
CG A:TYR830 4.8 34.5 1.0
OH A:TYR830 4.8 41.7 1.0
CG A:ARG552 4.8 49.4 1.0
NH1 A:ARG481 4.8 46.4 1.0
O A:HOH1084 4.9 51.9 1.0
CE2 A:TYR830 4.9 34.5 1.0
O A:SER829 4.9 39.3 1.0

Iodine binding site 4 out of 10 in 7f9v

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Iodine binding site 4 out of 10 in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I910

b:67.2
occ:0.65
 OH A:TYR830 3.4 41.7 1.0
BR A:BR908 3.8 72.9 0.5
CE A:MET601 4.1 37.0 1.0
CG2 A:THR477 4.2 40.9 1.0
CZ A:TYR830 4.5 38.7 1.0
CB A:SER343 4.5 53.0 1.0
CE2 A:PHE342 4.6 33.8 1.0
CE1 A:TYR830 4.6 43.7 1.0
ND2 A:ASN550 4.6 41.3 1.0
OG1 A:THR477 4.6 45.3 1.0
CA A:SER343 4.7 46.2 1.0
CD2 A:PHE342 4.7 38.1 1.0

Iodine binding site 5 out of 10 in 7f9v

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Iodine binding site 5 out of 10 in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I901

b:44.8
occ:0.49
 O B:HOH1178 3.7 46.5 1.0
CB B:SER343 4.2 38.2 1.0
CG2 B:THR347 4.2 45.9 0.5
CG2 B:THR477 4.2 48.3 1.0
O B:HOH1171 4.2 45.3 1.0
OG1 B:THR347 4.3 45.9 0.5
OG1 B:THR477 4.3 51.3 1.0
CD B:PRO478 4.5 42.6 1.0
O B:PRO476 4.6 41.9 1.0
CA B:THR477 4.6 47.9 1.0
CB B:THR477 4.6 52.9 1.0
O B:SER343 4.7 40.3 1.0
CD2 B:TYR346 4.8 34.0 1.0
CA B:SER343 4.9 41.5 1.0

Iodine binding site 6 out of 10 in 7f9v

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Iodine binding site 6 out of 10 in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I906

b:42.4
occ:0.44
 O B:HOH1065 3.2 52.2 1.0
O B:HOH1266 3.5 69.4 1.0
CG B:PRO801 3.9 43.1 1.0
CD1 B:ILE524 4.1 39.1 1.0
CD1 B:ILE736 4.2 42.5 1.0
CD1 B:LEU756 4.3 38.3 1.0
CB B:PRO801 4.3 37.8 1.0
CG2 B:ILE524 4.4 33.8 1.0
CD2 B:LEU756 4.5 45.9 1.0
CD1 B:LEU825 4.6 36.9 1.0
CG1 B:ILE524 4.8 33.4 1.0
CD2 B:LEU825 4.8 38.2 1.0
CG B:LEU756 5.0 44.5 1.0

Iodine binding site 7 out of 10 in 7f9v

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Iodine binding site 7 out of 10 in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I907

b:63.9
occ:0.40
 N B:LYS628 3.4 92.9 1.0
O B:HOH1269 3.6 59.0 1.0
O B:TYR661 3.8 53.5 1.0
C B:TYR661 3.9 39.9 1.0
CB B:LYS628 4.0 101.6 1.0
CA B:PHE627 4.0 63.2 1.0
C B:PHE627 4.0 80.3 1.0
CA B:LYS628 4.1 100.9 1.0
N B:THR662 4.1 42.7 1.0
CA B:ASN660 4.1 58.1 1.0
C B:ASN660 4.2 59.2 1.0
N B:TYR661 4.2 45.2 1.0
CG2 B:THR662 4.2 43.1 1.0
CA B:THR662 4.3 41.0 1.0
CD1 B:PHE627 4.3 65.2 1.0
CB B:PHE627 4.5 63.7 1.0
N B:ASN660 4.6 47.8 1.0
CA B:TYR661 4.6 40.4 1.0
O B:ASN660 4.8 66.2 1.0
CG B:PHE627 4.8 64.9 1.0
CB B:THR662 4.9 42.0 1.0
O B:LEU626 4.9 65.4 1.0

Iodine binding site 8 out of 10 in 7f9v

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Iodine binding site 8 out of 10 in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I908

b:74.5
occ:0.45
 NE B:ARG658 3.8 47.7 1.0
CD B:ARG654 4.0 53.1 1.0
CZ2 B:TRP670 4.1 38.3 1.0
OD1 B:ASP656 4.2 45.5 1.0
CD B:ARG658 4.2 50.8 1.0
CG B:ASP656 4.3 42.4 1.0
CA B:ASP656 4.3 39.3 1.0
CG B:ARG654 4.3 39.5 1.0
CZ B:ARG658 4.4 48.1 1.0
O B:ILE655 4.4 36.1 1.0
CG B:ARG658 4.4 47.5 1.0
CB B:ASP656 4.6 37.4 1.0
CH2 B:TRP670 4.6 39.4 1.0
NH2 B:ARG658 4.6 42.3 1.0
OD2 B:ASP656 4.7 40.3 1.0

Iodine binding site 9 out of 10 in 7f9v

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Iodine binding site 9 out of 10 in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I909

b:66.0
occ:0.37
 O B:HOH1172 3.5 50.7 1.0
ND2 B:ASN550 3.5 45.4 1.0
O B:HOH1171 3.8 45.3 1.0
NH1 B:ARG552 4.1 49.9 1.0
CB B:ASN550 4.2 42.3 1.0
CB B:SER343 4.3 38.2 1.0
CG B:ASN550 4.4 43.2 1.0
CD2 B:PHE342 4.4 39.3 1.0
CZ B:ARG552 4.5 52.5 1.0
OG B:SER343 4.7 45.8 1.0
OH B:TYR830 4.7 45.9 1.0
N B:SER343 4.9 38.1 1.0
NH2 B:ARG552 4.9 55.4 1.0

Iodine binding site 10 out of 10 in 7f9v

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Iodine binding site 10 out of 10 in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I911

b:74.5
occ:0.40
 O B:HOH1204 3.1 59.4 1.0
N B:GLY633 3.2 58.9 1.0
N B:LEU636 3.4 41.2 1.0
CA B:GLY633 3.5 54.9 1.0
C B:GLY633 3.7 53.9 1.0
CB B:LEU636 3.7 48.1 1.0
N B:ILE635 3.8 44.3 1.0
CA B:ASN631 3.8 80.0 1.0
CG B:LEU636 3.8 54.7 1.0
CD2 B:LEU626 3.9 65.3 1.0
N B:THR632 4.0 80.5 1.0
N B:GLU634 4.0 46.1 1.0
CB B:ILE635 4.1 43.3 1.0
C B:ASN631 4.1 83.1 1.0
CD1 B:LEU636 4.2 58.7 1.0
CA B:LEU636 4.2 43.4 1.0
CA B:ILE635 4.2 40.2 1.0
O B:GLY633 4.3 57.1 1.0
C B:ILE635 4.3 38.9 1.0
CD1 B:LEU626 4.4 59.7 1.0
C B:THR632 4.4 70.3 1.0
CB B:ASN631 4.4 80.9 1.0
N B:ASN631 4.5 78.5 1.0
OG1 B:THR632 4.6 57.7 1.0
C B:GLU634 4.7 47.4 1.0
CA B:THR632 4.8 70.0 1.0
CG B:LEU626 4.8 58.9 1.0
CA B:GLU634 4.9 42.2 1.0
CG2 B:ILE635 4.9 43.4 1.0
BR B:BR912 4.9 74.7 0.5

Reference:

N.Malhotra, Y.Manickam, A.Sharma. Tgprs with Double Inhibitors To Be Published.
Page generated: Mon Aug 12 01:06:23 2024

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