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Fluorine in PDB 4z53: Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae

Enzymatic activity of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae

All present enzymatic activity of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae:
5.99.1.3;

Protein crystallography data

The structure of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae, PDB code: 4z53 was solved by I.Laponogov, D.A.Veselkov, X.-S.Pan, J.Selvarajah, I.M.-T.Crevel, L.M.Fisher, M.R.Sanderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.90 / 3.26
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.830, 157.830, 210.580, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 20.7

Other elements in 4z53:

The structure of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae (pdb code 4z53). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae, PDB code: 4z53:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4z53

Go back to Fluorine Binding Sites List in 4z53
Fluorine binding site 1 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:90.5
occ:1.00
 F04 F:TR6101 0.0 90.5 1.0
C03 F:TR6101 1.3 0.6 1.0
C02 F:TR6101 2.3 94.2 1.0
C05 F:TR6101 2.3 0.1 1.0
H021 F:TR6101 2.5 1.0 1.0
H051 F:TR6101 2.5 0.9 1.0
CA A:ARG456 3.3 73.2 1.0
C01 F:TR6101 3.6 89.2 1.0
C06 F:TR6101 3.6 0.6 1.0
CB A:ARG456 3.7 69.7 1.0
O5' H:DG1 3.7 0.5 1.0
N A:GLY457 3.7 86.8 1.0
OP1 H:DG1 3.8 0.1 1.0
CA A:GLY434 3.8 86.6 1.0
C A:ARG456 3.8 83.6 1.0
OD2 A:ASP435 4.0 0.5 1.0
N A:ASP435 4.0 90.9 1.0
O A:LEU455 4.0 81.8 1.0
C08 F:TR6101 4.1 97.2 1.0
P H:DG1 4.3 0.6 1.0
N A:ARG456 4.4 71.5 1.0
H011 F:TR6101 4.4 0.1 1.0
C A:GLY434 4.4 90.0 1.0
C A:LEU455 4.6 74.8 1.0
N A:GLY434 4.7 90.5 1.0
F07 F:TR6101 4.7 0.7 1.0
H142 F:TR6101 4.7 0.9 1.0
O A:ARG456 4.7 85.1 1.0
CG A:ASP435 4.8 0.7 1.0
C4' H:DG1 4.8 0.8 1.0
CA A:GLY457 4.8 81.3 1.0
O4' H:DG1 4.8 0.9 1.0
C5' H:DG1 4.9 0.7 1.0
CB A:ASP435 5.0 0.5 1.0

Fluorine binding site 2 out of 6 in 4z53

Go back to Fluorine Binding Sites List in 4z53
Fluorine binding site 2 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:0.7
occ:1.00
 F07 F:TR6101 0.0 0.7 1.0
C06 F:TR6101 1.4 0.6 1.0
C05 F:TR6101 2.4 0.1 1.0
C08 F:TR6101 2.4 97.2 1.0
H051 F:TR6101 2.6 0.9 1.0
H251 F:TR6101 2.8 0.0 1.0
N09 F:TR6101 2.8 99.8 1.0
N1 E:DT15 2.9 82.8 1.0
C2 E:DT15 3.0 93.9 1.0
C25 F:TR6101 3.0 0.0 1.0
C6 E:DT15 3.0 80.0 1.0
N3 E:DT15 3.2 80.1 1.0
C2' E:DT15 3.3 82.6 1.0
C5 E:DT15 3.3 78.4 1.0
C4 E:DT15 3.4 0.7 1.0
C1' E:DT15 3.5 80.0 1.0
O2 E:DT15 3.6 96.6 1.0
C01 F:TR6101 3.6 89.2 1.0
C03 F:TR6101 3.6 0.6 1.0
C10 F:TR6101 3.8 0.1 1.0
C24 F:TR6101 4.1 0.3 1.0
C02 F:TR6101 4.1 94.2 1.0
O4 E:DT15 4.2 0.3 1.0
N11 F:TR6101 4.3 86.7 1.0
C7 E:DT15 4.3 0.4 1.0
H011 F:TR6101 4.4 0.1 1.0
F04 F:TR6101 4.7 90.5 1.0
CA A:GLY457 4.7 81.3 1.0
C22 F:TR6101 4.7 99.5 1.0
O28 F:TR6101 4.7 0.7 1.0
O4' E:DT15 4.8 81.3 1.0
C3' E:DT15 4.8 95.1 1.0
C23 F:TR6101 4.9 0.6 1.0
C26 F:TR6101 4.9 0.3 1.0
N1 F:DA5 5.0 0.6 1.0

Fluorine binding site 3 out of 6 in 4z53

Go back to Fluorine Binding Sites List in 4z53
Fluorine binding site 3 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:84.9
occ:1.00
 F30 F:TR6101 0.0 84.9 1.0
C20 F:TR6101 1.3 1.0 1.0
C21 F:TR6101 2.4 96.3 1.0
C12 F:TR6101 2.4 99.8 1.0
H211 F:TR6101 2.6 0.5 1.0
H191 F:TR6101 2.6 0.2 1.0
H192 F:TR6101 2.7 0.2 1.0
C19 F:TR6101 2.8 97.7 1.0
C2 F:DC4 2.9 0.2 1.0
N13 F:TR6101 2.9 96.0 1.0
N1 F:DC4 3.0 0.5 1.0
N3 F:DC4 3.0 0.9 1.0
C6 F:DC4 3.2 0.5 1.0
N7 F:DA5 3.2 0.7 1.0
C4 F:DC4 3.2 98.1 1.0
C5 F:DC4 3.3 97.9 1.0
C5 F:DA5 3.4 99.2 1.0
O2 F:DC4 3.5 0.1 1.0
N11 F:TR6101 3.6 86.7 1.0
C22 F:TR6101 3.6 99.5 1.0
C8 F:DA5 3.7 0.4 1.0
C1' F:DC4 3.8 0.9 1.0
C6 F:DA5 3.8 0.8 1.0
C2' F:DC4 3.9 0.4 1.0
C4 F:DA5 4.0 94.5 1.0
N4 F:DC4 4.1 0.9 1.0
N6 F:DA5 4.1 0.1 1.0
C10 F:TR6101 4.1 0.1 1.0
N9 F:DA5 4.1 0.3 1.0
C14 F:TR6101 4.3 93.3 1.0
C18 F:TR6101 4.3 0.7 1.0
H141 F:TR6101 4.6 0.9 1.0
N2 H:DG1 4.6 0.2 1.0
N1 H:DG1 4.6 0.4 1.0
N1 F:DA5 4.7 0.6 1.0
C23 F:TR6101 4.8 0.6 1.0
H142 F:TR6101 4.8 0.9 1.0
N3 F:DA5 4.9 94.6 1.0
H161 F:TR6101 4.9 0.9 1.0
O29 F:TR6101 4.9 0.6 1.0
H181 F:TR6101 4.9 0.6 1.0
C2 H:DG1 4.9 0.5 1.0
O4' F:DA5 5.0 0.4 1.0

Fluorine binding site 4 out of 6 in 4z53

Go back to Fluorine Binding Sites List in 4z53
Fluorine binding site 4 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:0.1
occ:1.00
 F04 H:TR6101 0.0 0.1 1.0
C03 H:TR6101 1.3 0.8 1.0
C02 H:TR6101 2.3 1.0 1.0
C05 H:TR6101 2.3 0.1 1.0
H021 H:TR6101 2.5 0.2 1.0
H051 H:TR6101 2.5 0.8 1.0
CA B:ARG456 3.3 91.2 1.0
CA B:GLY434 3.4 85.7 1.0
OP1 F:DA1 3.5 0.7 1.0
C01 H:TR6101 3.6 0.1 1.0
C06 H:TR6101 3.6 0.8 1.0
N B:GLY457 3.6 96.0 1.0
CB B:ARG456 3.8 89.7 1.0
OD2 B:ASP435 3.8 0.0 1.0
N B:ASP435 3.8 86.9 1.0
C B:ARG456 3.8 93.8 1.0
O5' F:DA1 3.8 1.0 1.0
O B:LEU455 4.0 96.0 1.0
C08 H:TR6101 4.1 0.3 1.0
C B:GLY434 4.1 80.5 1.0
P F:DA1 4.3 0.5 1.0
N B:GLY434 4.3 86.7 1.0
N B:ARG456 4.3 93.4 1.0
H011 H:TR6101 4.4 0.1 1.0
C B:LEU455 4.6 91.0 1.0
CA B:GLY457 4.7 93.4 1.0
F07 H:TR6101 4.7 0.5 1.0
CG B:ASP435 4.8 0.5 1.0
O B:ARG456 4.9 94.0 1.0
O4' F:DA1 5.0 0.4 1.0
H142 H:TR6101 5.0 0.2 1.0

Fluorine binding site 5 out of 6 in 4z53

Go back to Fluorine Binding Sites List in 4z53
Fluorine binding site 5 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:0.5
occ:1.00
 F07 H:TR6101 0.0 0.5 1.0
C06 H:TR6101 1.4 0.8 1.0
C05 H:TR6101 2.4 0.1 1.0
C08 H:TR6101 2.4 0.3 1.0
H051 H:TR6101 2.6 0.8 1.0
N09 H:TR6101 2.8 0.7 1.0
N1 G:DT15 2.8 77.6 1.0
C2 G:DT15 2.8 78.7 1.0
H251 H:TR6101 2.9 0.8 1.0
C25 H:TR6101 3.0 0.9 1.0
N3 G:DT15 3.1 77.9 1.0
C6 G:DT15 3.1 73.4 1.0
C2' G:DT15 3.3 77.1 1.0
C5 G:DT15 3.3 80.5 1.0
C4 G:DT15 3.3 78.9 1.0
O2 G:DT15 3.4 85.8 1.0
C1' G:DT15 3.5 82.5 1.0
C01 H:TR6101 3.6 0.1 1.0
C03 H:TR6101 3.6 0.8 1.0
C10 H:TR6101 3.7 0.9 1.0
C02 H:TR6101 4.1 1.0 1.0
N11 H:TR6101 4.1 97.7 1.0
C24 H:TR6101 4.1 0.7 1.0
O4 G:DT15 4.2 79.7 1.0
C7 G:DT15 4.4 90.0 1.0
H011 H:TR6101 4.4 0.1 1.0
CA B:GLY457 4.5 93.4 1.0
C22 H:TR6101 4.6 0.0 1.0
F04 H:TR6101 4.7 0.1 1.0
C3' G:DT15 4.7 88.7 1.0
O4' G:DT15 4.8 72.2 1.0
C23 H:TR6101 4.8 1.0 1.0
N1 H:DA5 4.9 92.9 1.0
N B:GLY457 4.9 96.0 1.0
O27 H:TR6101 4.9 0.5 1.0
C26 H:TR6101 5.0 0.0 1.0

Fluorine binding site 6 out of 6 in 4z53

Go back to Fluorine Binding Sites List in 4z53
Fluorine binding site 6 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:95.5
occ:1.00
 F30 H:TR6101 0.0 95.5 1.0
C20 H:TR6101 1.3 96.2 1.0
H192 H:TR6101 2.2 0.5 1.0
C21 H:TR6101 2.3 0.1 1.0
C12 H:TR6101 2.4 0.8 1.0
H211 H:TR6101 2.5 0.4 1.0
C19 H:TR6101 2.7 0.9 1.0
H191 H:TR6101 2.8 0.5 1.0
C2 H:DT4 2.8 0.7 1.0
N13 H:TR6101 2.9 96.8 1.0
N3 H:DT4 2.9 0.9 1.0
N1 H:DT4 3.1 0.4 1.0
N7 H:DA5 3.1 91.8 1.0
O2 H:DT4 3.3 0.8 1.0
C5 H:DA5 3.3 90.6 1.0
C4 H:DT4 3.4 0.5 1.0
C6 H:DT4 3.4 0.9 1.0
C8 H:DA5 3.6 98.4 1.0
N11 H:TR6101 3.6 97.7 1.0
C5 H:DT4 3.6 0.3 1.0
C22 H:TR6101 3.6 0.0 1.0
C6 H:DA5 3.8 97.0 1.0
C1' H:DT4 3.8 0.2 1.0
C2' H:DT4 3.9 0.2 1.0
C4 H:DA5 3.9 87.3 1.0
N6 H:DA5 4.0 1.0 1.0
N9 H:DA5 4.0 96.7 1.0
C10 H:TR6101 4.1 0.9 1.0
O4 H:DT4 4.1 0.1 1.0
C18 H:TR6101 4.2 0.3 1.0
C14 H:TR6101 4.3 0.4 1.0
N1 H:DA5 4.6 92.9 1.0
N1 F:DA1 4.6 0.2 1.0
H181 H:TR6101 4.6 0.4 1.0
C7 H:DT4 4.7 0.3 1.0
H142 H:TR6101 4.7 0.2 1.0
N3 H:DA5 4.7 85.0 1.0
H141 H:TR6101 4.8 0.2 1.0
C23 H:TR6101 4.8 1.0 1.0
O29 H:TR6101 4.9 0.2 1.0
O4' H:DA5 4.9 97.5 1.0
C2 H:DA5 4.9 88.6 1.0
C15 H:TR6101 4.9 0.3 1.0

Reference:

I.Laponogov, D.A.Veselkov, X.-S.Pan, J.Selvarajah, I.M.-T.Crevel, L.M.Fisher, M.R.Sanderson. Structural Studies of the Drug-Stabilized Cleavage Complexes of Topoisomerase IV and Gyrase From Streptococcus Pneumoniae To Be Published.
Page generated: Tue Jul 15 01:50:43 2025

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