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Fluorine in PDB 4z2e: Quinolone(Trovafloxacin)-Dna Cleavage Complex of Gyrase From S. Pneumoniae

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

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

Protein crystallography data

The structure of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Gyrase From S. Pneumoniae, PDB code: 4z2e 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) 56.05 / 3.46
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.190, 96.620, 275.210, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 29.2

Other elements in 4z2e:

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

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Gyrase From S. Pneumoniae (pdb code 4z2e). 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 Gyrase From S. Pneumoniae, PDB code: 4z2e:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4z2e

Go back to Fluorine Binding Sites List in 4z2e
Fluorine binding site 1 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Gyrase 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 Gyrase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:0.4
occ:1.00
 F04 F:TR6101 0.0 0.4 1.0
C03 F:TR6101 1.3 0.3 1.0
C02 F:TR6101 2.3 0.2 1.0
C05 F:TR6101 2.3 0.7 1.0
H051 F:TR6101 2.5 0.0 1.0
H021 F:TR6101 2.5 0.8 1.0
CA C:GLY434 3.5 0.7 1.0
C01 F:TR6101 3.6 0.4 1.0
C06 F:TR6101 3.6 0.1 1.0
CG C:ARG456 3.6 0.2 1.0
N C:GLY457 3.7 0.4 1.0
CA C:ARG456 3.8 0.2 1.0
CB C:ARG456 4.0 0.2 1.0
OP1 F:DA2 4.0 0.4 1.0
C08 F:TR6101 4.1 0.1 1.0
C C:ARG456 4.2 0.0 1.0
N C:GLY434 4.2 0.7 1.0
O3' F:DG1 4.4 0.3 1.0
H011 F:TR6101 4.4 0.1 1.0
O C:ILE455 4.6 0.2 1.0
CA C:GLY457 4.6 0.0 1.0
F07 F:TR6101 4.7 0.4 1.0
P F:DA2 4.7 0.9 1.0
C C:GLY434 4.8 0.4 1.0
H142 F:TR6101 4.9 0.6 1.0
N C:ASP435 4.9 0.1 1.0
O5' F:DA2 4.9 0.3 1.0
N C:ARG456 4.9 0.6 1.0

Fluorine binding site 2 out of 6 in 4z2e

Go back to Fluorine Binding Sites List in 4z2e
Fluorine binding site 2 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Gyrase 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 Gyrase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:0.4
occ:1.00
 F07 F:TR6101 0.0 0.4 1.0
C06 F:TR6101 1.4 0.1 1.0
C05 F:TR6101 2.4 0.7 1.0
C08 F:TR6101 2.4 0.1 1.0
H051 F:TR6101 2.6 0.0 1.0
N09 F:TR6101 2.8 0.4 1.0
N1 G:DT15 2.8 0.1 1.0
H251 F:TR6101 2.8 0.2 1.0
C6 G:DT15 3.0 0.9 1.0
C25 F:TR6101 3.0 0.9 1.0
C2 G:DT15 3.0 0.7 1.0
C2' G:DT15 3.0 0.3 1.0
N3 G:DT15 3.3 0.1 1.0
C5 G:DT15 3.3 0.3 1.0
C1' G:DT15 3.4 0.5 1.0
C4 G:DT15 3.5 0.3 1.0
O2 G:DT15 3.6 0.2 1.0
C01 F:TR6101 3.6 0.4 1.0
C03 F:TR6101 3.6 0.3 1.0
C10 F:TR6101 3.7 0.7 1.0
C24 F:TR6101 4.1 0.1 1.0
C02 F:TR6101 4.1 0.2 1.0
N11 F:TR6101 4.2 0.2 1.0
C7 G:DT15 4.4 0.1 1.0
H011 F:TR6101 4.4 0.1 1.0
O4 G:DT15 4.4 0.3 1.0
O4' F:DG1 4.4 0.8 1.0
C3' G:DT15 4.5 0.8 1.0
O4' G:DT15 4.6 0.8 1.0
C22 F:TR6101 4.6 0.0 1.0
F04 F:TR6101 4.7 0.4 1.0
O27 F:TR6101 4.8 0.1 1.0
C23 F:TR6101 4.8 0.0 1.0
O5' G:DT15 4.9 0.0 1.0
C26 F:TR6101 4.9 0.9 1.0
CA C:GLY457 5.0 0.0 1.0

Fluorine binding site 3 out of 6 in 4z2e

Go back to Fluorine Binding Sites List in 4z2e
Fluorine binding site 3 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Gyrase 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 Gyrase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:0.1
occ:1.00
 F30 F:TR6101 0.0 0.1 1.0
C20 F:TR6101 1.3 0.8 1.0
C21 F:TR6101 2.3 0.1 1.0
C12 F:TR6101 2.4 0.8 1.0
H211 F:TR6101 2.5 0.7 1.0
H192 F:TR6101 2.6 0.7 1.0
N7 H:DA5 2.8 0.7 1.0
H191 F:TR6101 2.8 0.7 1.0
C19 F:TR6101 2.9 0.9 1.0
N13 F:TR6101 3.0 0.9 1.0
N3 H:DC4 3.1 0.7 1.0
C5 H:DA5 3.2 0.6 1.0
C4 H:DC4 3.3 0.3 1.0
C2 H:DC4 3.4 0.1 1.0
N6 H:DA5 3.5 0.4 1.0
C6 H:DA5 3.5 0.5 1.0
C8 H:DA5 3.5 0.4 1.0
N11 F:TR6101 3.6 0.2 1.0
C22 F:TR6101 3.6 0.0 1.0
C5 H:DC4 3.7 0.9 1.0
N4 H:DC4 3.7 0.1 1.0
N1 H:DC4 3.8 0.8 1.0
N2 F:DG1 3.8 0.0 1.0
C6 H:DC4 3.9 0.7 1.0
O2 H:DC4 4.0 0.7 1.0
C4 H:DA5 4.1 0.6 1.0
C10 F:TR6101 4.1 0.7 1.0
N9 H:DA5 4.3 0.1 1.0
N1 F:DG1 4.3 0.7 1.0
C2 F:DG1 4.3 0.6 1.0
C18 F:TR6101 4.4 0.8 1.0
C14 F:TR6101 4.4 0.0 1.0
N1 H:DA5 4.6 0.1 1.0
C2' H:DC4 4.7 0.3 1.0
H141 F:TR6101 4.7 0.6 1.0
C23 F:TR6101 4.8 0.0 1.0
C1' H:DC4 4.8 0.4 1.0
H142 F:TR6101 4.8 0.6 1.0
O29 F:TR6101 4.9 0.4 1.0
H181 F:TR6101 4.9 0.1 1.0

Fluorine binding site 4 out of 6 in 4z2e

Go back to Fluorine Binding Sites List in 4z2e
Fluorine binding site 4 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Gyrase 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 Gyrase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:0.9
occ:1.00
 F04 H:TR6101 0.0 0.9 1.0
C03 H:TR6101 1.3 0.7 1.0
C02 H:TR6101 2.3 0.4 1.0
C05 H:TR6101 2.3 0.3 1.0
H021 H:TR6101 2.5 0.9 1.0
H051 H:TR6101 2.5 0.6 1.0
N D:GLY457 2.8 0.2 1.0
CA D:ARG456 3.4 0.4 1.0
C D:ARG456 3.5 0.9 1.0
C01 H:TR6101 3.6 0.1 1.0
C06 H:TR6101 3.6 0.8 1.0
CA D:GLY457 3.7 0.1 1.0
CA D:GLY434 4.0 0.9 1.0
CB D:ARG456 4.0 90.4 1.0
C08 H:TR6101 4.1 0.3 1.0
H011 H:TR6101 4.4 0.4 1.0
N D:GLY434 4.4 0.1 1.0
O D:ILE455 4.4 0.9 1.0
O3' H:DG1 4.6 0.4 1.0
N D:ARG456 4.6 0.3 1.0
OP1 H:DA2 4.7 0.8 1.0
O D:ARG456 4.7 0.0 1.0
F07 H:TR6101 4.7 0.1 1.0
C D:GLY457 4.9 0.3 1.0
C D:ILE455 4.9 0.2 1.0

Fluorine binding site 5 out of 6 in 4z2e

Go back to Fluorine Binding Sites List in 4z2e
Fluorine binding site 5 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Gyrase 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 Gyrase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:0.1
occ:1.00
 F07 H:TR6101 0.0 0.1 1.0
C06 H:TR6101 1.4 0.8 1.0
C05 H:TR6101 2.4 0.3 1.0
C08 H:TR6101 2.4 0.3 1.0
H051 H:TR6101 2.6 0.6 1.0
N09 H:TR6101 2.7 0.1 1.0
H251 H:TR6101 2.8 0.2 1.0
N1 E:DT15 2.8 0.7 1.0
C2 E:DT15 2.9 0.5 1.0
N3 E:DT15 2.9 0.3 1.0
C6 E:DT15 2.9 0.9 1.0
C25 H:TR6101 3.0 0.7 1.0
C5 E:DT15 3.1 0.1 1.0
C4 E:DT15 3.1 0.2 1.0
C2' E:DT15 3.5 0.2 1.0
O2 E:DT15 3.5 0.5 1.0
C01 H:TR6101 3.6 0.1 1.0
C03 H:TR6101 3.6 0.7 1.0
C10 H:TR6101 3.7 0.4 1.0
C1' E:DT15 3.7 0.1 1.0
O4 E:DT15 3.9 1.0 1.0
C24 H:TR6101 4.1 0.3 1.0
C7 E:DT15 4.1 0.3 1.0
C02 H:TR6101 4.1 0.4 1.0
N11 H:TR6101 4.2 0.3 1.0
H011 H:TR6101 4.4 0.4 1.0
C22 H:TR6101 4.6 0.2 1.0
O4' H:DG1 4.7 0.1 1.0
F04 H:TR6101 4.7 0.9 1.0
C23 H:TR6101 4.8 0.3 1.0
O28 H:TR6101 4.8 0.8 1.0
O4' E:DT15 4.8 0.7 1.0
C26 H:TR6101 4.9 0.9 1.0
CA D:GLY457 4.9 0.1 1.0
N1 F:DA5 4.9 0.5 1.0

Fluorine binding site 6 out of 6 in 4z2e

Go back to Fluorine Binding Sites List in 4z2e
Fluorine binding site 6 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Gyrase 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 Gyrase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:0.1
occ:1.00
 F30 H:TR6101 0.0 0.1 1.0
C20 H:TR6101 1.3 0.9 1.0
H192 H:TR6101 2.3 0.9 1.0
C21 H:TR6101 2.3 0.5 1.0
C12 H:TR6101 2.4 0.8 1.0
H211 H:TR6101 2.5 0.4 1.0
C19 H:TR6101 2.9 0.8 1.0
N13 H:TR6101 3.0 0.6 1.0
N7 F:DA5 3.0 0.6 1.0
C5 F:DC4 3.1 0.3 1.0
C4 F:DC4 3.1 0.1 1.0
C6 F:DC4 3.1 0.3 1.0
H191 H:TR6101 3.1 0.9 1.0
N3 F:DC4 3.3 0.1 1.0
N1 F:DC4 3.3 0.3 1.0
C2 F:DC4 3.3 0.5 1.0
C5 F:DA5 3.3 0.5 1.0
N6 F:DA5 3.5 0.5 1.0
C6 F:DA5 3.6 0.4 1.0
N11 H:TR6101 3.6 0.3 1.0
C22 H:TR6101 3.6 0.2 1.0
C8 F:DA5 3.8 1.0 1.0
N4 F:DC4 3.8 0.9 1.0
C10 H:TR6101 4.1 0.4 1.0
O2 F:DC4 4.1 0.4 1.0
C1' F:DC4 4.2 0.9 1.0
C2' F:DC4 4.2 0.4 1.0
C4 F:DA5 4.3 0.3 1.0
C18 H:TR6101 4.3 0.1 1.0
C14 H:TR6101 4.4 0.7 1.0
N2 H:DG1 4.5 0.8 1.0
N9 F:DA5 4.5 0.9 1.0
N1 H:DG1 4.5 0.6 1.0
N1 F:DA5 4.6 0.5 1.0
H142 H:TR6101 4.7 0.7 1.0
H181 H:TR6101 4.7 0.9 1.0
C2 H:DG1 4.7 0.3 1.0
C23 H:TR6101 4.8 0.3 1.0
O29 H:TR6101 4.9 0.5 1.0
H141 H:TR6101 5.0 0.7 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.
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