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Iodine in PDB 4kqv: Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor

Enzymatic activity of Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor

All present enzymatic activity of Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor:
5.99.1.3;

Protein crystallography data

The structure of Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor, PDB code: 4kqv was solved by D.C Bensen, S.Akers-Rodriguez, T.Lam, L.W.Tari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.06 / 2.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.200, 163.160, 72.280, 90.00, 91.81, 90.00
R / Rfree (%) 25.5 / 29.9

Other elements in 4kqv:

The structure of Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor (pdb code 4kqv). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor, PDB code: 4kqv:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 4kqv

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Iodine binding site 1 out of 8 in the Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:51.0
occ:1.00
 O A:HOH574 3.0 42.8 1.0
ND2 A:ASN32 3.4 41.6 1.0
NE2 A:GLN36 3.5 47.1 1.0
O A:ALA182 3.8 44.5 1.0
C A:ALA182 3.9 42.3 1.0
N A:LEU183 4.0 37.8 1.0
CB A:ASN32 4.0 39.5 1.0
CA A:LEU183 4.0 39.1 1.0
O A:HOH521 4.2 62.0 1.0
CG A:ASN32 4.2 43.8 1.0
CB A:LEU186 4.2 40.9 1.0
CB A:ALA182 4.3 38.9 1.0
CG A:GLN36 4.4 43.2 1.0
CD A:GLN36 4.4 49.0 1.0
CD2 A:LEU186 4.6 37.0 1.0
CD1 A:LEU186 4.7 38.9 1.0
CG A:LEU186 4.7 42.5 1.0
CA A:ALA182 4.8 39.8 1.0
CB A:LEU183 4.8 38.2 1.0
CD1 A:LEU183 4.8 36.8 1.0
O A:ASN32 4.9 34.8 1.0

Iodine binding site 2 out of 8 in 4kqv

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Iodine binding site 2 out of 8 in the Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:59.7
occ:1.00
 N A:GLY23 3.7 38.4 1.0
CA A:GLY23 3.9 39.2 1.0
CA A:ARG21 4.0 49.5 1.0
C A:ARG21 4.0 49.7 1.0
CB A:ARG21 4.1 52.0 1.0
CD A:PRO22 4.3 45.1 1.0
N A:PRO22 4.3 45.1 1.0
O A:ARG21 4.4 51.2 1.0
C A:GLY23 4.5 41.0 1.0
CG A:ARG21 4.6 54.6 1.0
N A:MET24 4.6 43.5 1.0
C A:PRO22 4.8 40.5 1.0
CD A:ARG21 5.0 63.4 1.0
CG A:MET24 5.0 60.1 1.0

Iodine binding site 3 out of 8 in 4kqv

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Iodine binding site 3 out of 8 in the Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:0.1
occ:1.00
 O A:LEU12 3.6 42.8 1.0
NZ A:LYS92 3.8 54.4 1.0
CD A:LYS92 4.1 50.5 1.0
CE A:LYS92 4.1 52.2 1.0
C A:LEU12 4.2 41.1 1.0
CA A:THR13 4.3 38.5 1.0
C A:THR13 4.4 38.0 1.0
N A:THR13 4.6 39.9 1.0
N A:GLY14 4.6 37.3 1.0
O A:THR13 4.7 37.1 1.0
CB A:LEU12 4.8 41.9 1.0
CG A:LYS92 4.8 43.9 1.0

Iodine binding site 4 out of 8 in 4kqv

Go back to Iodine Binding Sites List in 4kqv
Iodine binding site 4 out of 8 in the Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I405

b:0.8
occ:1.00
 O A:HOH524 3.5 39.5 1.0
O A:ASP68 3.8 37.0 1.0
C A:ASP68 3.9 38.2 1.0
N A:ASP69 4.1 36.9 1.0
CB A:ASP69 4.2 38.9 1.0
CA A:ASP69 4.4 38.5 1.0
CA A:ASP68 4.4 38.6 1.0
ND2 A:ASN55 4.5 48.1 1.0
CB A:LYS53 4.6 42.8 1.0
O A:HOH541 4.6 39.9 1.0
CD A:LYS53 4.6 46.2 1.0
O A:ALA67 4.6 38.6 1.0
N A:ASP68 4.6 37.7 1.0
CB A:ALA67 4.7 38.8 1.0
C A:ALA67 4.7 37.9 1.0
CG A:ASN55 4.7 47.8 1.0
OD1 A:ASN55 4.9 47.2 1.0
O A:LYS53 5.0 39.5 1.0

Iodine binding site 5 out of 8 in 4kqv

Go back to Iodine Binding Sites List in 4kqv
Iodine binding site 5 out of 8 in the Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:0.8
occ:1.00
 OG A:SER202 3.2 43.3 1.0
O A:ASN203 3.6 38.3 1.0
N A:GLU208 3.8 47.1 1.0
CG A:GLU204 3.9 46.8 1.0
C A:ASN203 3.9 40.7 1.0
CA A:GLU204 4.0 43.9 1.0
CA A:LYS207 4.0 47.3 1.0
CE A:LYS209 4.0 40.2 1.0
O A:GLU208 4.1 39.3 1.0
CG A:LYS209 4.1 38.9 1.0
N A:GLU204 4.1 42.5 1.0
C A:LYS207 4.2 47.8 1.0
CB A:SER202 4.3 41.1 1.0
O A:HOH552 4.3 44.9 1.0
N A:ASN203 4.3 35.0 1.0
C A:GLU208 4.5 42.3 1.0
CB A:GLU204 4.5 46.8 1.0
CD A:LYS209 4.7 39.4 1.0
C A:SER202 4.7 37.6 1.0
CA A:SER202 4.7 38.3 1.0
N A:LYS207 4.8 46.1 1.0
CA A:GLU208 4.8 44.7 1.0
CA A:ASN203 4.8 36.8 1.0
CB A:LYS207 4.8 49.3 1.0

Iodine binding site 6 out of 8 in 4kqv

Go back to Iodine Binding Sites List in 4kqv
Iodine binding site 6 out of 8 in the Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:0.3
occ:1.00
 C26 A:DOO403 3.8 36.7 1.0
CG A:PRO74 3.8 42.5 1.0
C25 A:DOO403 4.0 38.9 1.0
CD A:PRO74 4.0 40.9 1.0
CE A:MET73 4.1 35.0 0.5
C27 A:DOO403 4.3 41.8 1.0
CB A:PRO74 4.6 39.1 1.0
SD A:MET73 4.7 36.8 0.5
O A:HOH565 4.9 48.8 1.0

Iodine binding site 7 out of 8 in 4kqv

Go back to Iodine Binding Sites List in 4kqv
Iodine binding site 7 out of 8 in the Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I401

b:82.7
occ:1.00
 ND2 B:ASN32 3.6 54.5 1.0
CD2 B:LEU186 3.8 66.9 1.0
N B:LEU183 4.0 68.9 1.0
CB B:LEU186 4.0 70.0 1.0
CA B:LEU183 4.0 70.4 1.0
C B:ALA182 4.0 70.8 1.0
CB B:ALA182 4.1 65.0 1.0
O B:ALA182 4.1 75.0 1.0
CB B:ASN32 4.1 57.2 1.0
CG B:LEU186 4.3 69.7 1.0
CG B:ASN32 4.4 59.6 1.0
O B:ASN32 4.6 62.8 1.0
CD1 B:LEU186 4.7 68.8 1.0
CA B:ALA182 4.7 68.7 1.0
CB B:LEU183 4.7 66.7 1.0
NE2 B:GLN36 4.8 73.1 1.0
CD1 B:LEU183 4.8 60.6 1.0
C B:ASN32 4.9 61.3 1.0
CD B:GLN36 5.0 76.3 1.0

Iodine binding site 8 out of 8 in 4kqv

Go back to Iodine Binding Sites List in 4kqv
Iodine binding site 8 out of 8 in the Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Topoisomerase IV Atp Binding Domain of Francisella Tularensis in Complex with A Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I402

b:0.1
occ:1.00
 C25 B:DOO403 3.7 53.9 1.0
C26 B:DOO403 3.8 52.6 1.0
C27 B:DOO403 4.1 48.2 1.0
CG B:PRO74 4.4 51.1 1.0
CD B:PRO74 4.6 48.7 1.0

Reference:

L.W.Tari, D.C.Bensen, J.Finn. A New Class of Type Iia Topoisomerase Inhibitors with Broad-Spectrum Antibacterial Activity To Be Published.
Page generated: Sun Aug 11 18:29:27 2024

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