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Chlorine in PDB 8qmb: Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin

Enzymatic activity of Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin

All present enzymatic activity of Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin:
5.6.2.2;

Protein crystallography data

The structure of Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin, PDB code: 8qmb was solved by S.Najmudin, X.S.Pan, B.Wang, N.E.Chayen, 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) 83.63 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.215, 157.215, 211.948, 90, 90, 120
R / Rfree (%) 16.9 / 20.6

Other elements in 8qmb:

The structure of Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Fluorine (F) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin (pdb code 8qmb). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin, PDB code: 8qmb:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8qmb

Go back to Chlorine Binding Sites List in 8qmb
Chlorine binding site 1 out of 4 in the Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1504

b:58.6
occ:1.00
 O A:HOH1880 2.8 62.8 1.0
HH22 A:ARG1426 2.8 61.2 1.0
O A:HOH2034 2.9 35.4 1.0
HH12 A:ARG1371 2.9 29.5 1.0
O A:HOH1946 3.0 57.4 1.0
HH12 A:ARG1426 3.1 57.7 1.0
NH2 A:ARG1426 3.1 60.7 1.0
NH1 A:ARG1371 3.2 28.3 1.0
HH11 A:ARG1371 3.3 29.0 1.0
HH21 A:ARG1426 3.3 61.0 1.0
NH1 A:ARG1426 3.4 55.9 1.0
HH22 A:ARG1371 3.5 29.9 1.0
HD12 A:LEU1378 3.5 33.8 1.0
CZ A:ARG1426 3.7 62.1 1.0
HD13 A:LEU1378 3.7 34.2 1.0
HH11 A:ARG1426 3.8 57.5 1.0
CD1 A:LEU1378 4.1 33.9 1.0
NH2 A:ARG1371 4.1 29.1 1.0
CZ A:ARG1371 4.1 31.4 1.0
HD11 A:LEU1378 4.3 33.9 1.0
HD23 A:LEU1422 4.4 24.8 1.0
HD21 A:LEU1422 4.5 24.6 1.0
O A:HOH2062 4.6 29.0 1.0
O A:HOH1796 4.7 30.9 1.0
HG23 A:ILE1374 4.8 32.7 1.0
CD2 A:LEU1422 4.9 24.7 1.0
HG21 A:ILE1374 4.9 32.6 1.0
HH21 A:ARG1371 4.9 29.9 1.0
NE A:ARG1426 5.0 53.9 1.0
O A:HOH1606 5.0 30.3 1.0

Chlorine binding site 2 out of 4 in 8qmb

Go back to Chlorine Binding Sites List in 8qmb
Chlorine binding site 2 out of 4 in the Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1504

b:68.4
occ:1.00
 O B:HOH1966 2.5 55.2 1.0
O B:HOH2048 2.6 41.8 1.0
HH12 B:ARG1426 2.8 75.0 1.0
HH12 B:ARG1371 2.9 25.3 1.0
O B:HOH1895 3.0 50.9 1.0
NH1 B:ARG1371 3.2 25.2 1.0
HH11 B:ARG1371 3.2 25.1 1.0
HH11 B:ARG1426 3.3 75.0 1.0
HD12 B:LEU1378 3.3 27.8 1.0
NH1 B:ARG1426 3.4 82.6 1.0
H53 B:MPD1508 3.6 45.1 1.0
HH22 B:ARG1371 3.7 25.8 1.0
HD13 B:LEU1378 3.9 27.9 1.0
CD1 B:LEU1378 4.0 27.6 1.0
CZ B:ARG1371 4.1 25.0 1.0
NH2 B:ARG1371 4.1 26.1 1.0
HD23 B:LEU1422 4.2 24.4 1.0
HD11 B:LEU1378 4.3 27.7 1.0
H52 B:MPD1508 4.3 44.9 1.0
C5 B:MPD1508 4.3 45.6 1.0
HD21 B:LEU1422 4.5 24.5 1.0
H51 B:MPD1508 4.6 45.0 1.0
HG23 B:ILE1374 4.6 24.0 1.0
HG21 B:ILE1374 4.6 24.1 1.0
CZ B:ARG1426 4.7 61.3 1.0
CD2 B:LEU1422 4.7 24.4 1.0
O B:HOH2093 4.7 43.2 1.0
HD23 B:LEU1378 4.8 30.0 1.0
HH21 B:ARG1371 4.8 25.8 1.0
HD22 B:LEU1422 4.9 24.5 1.0
O B:HOH1916 4.9 29.2 1.0

Chlorine binding site 3 out of 4 in 8qmb

Go back to Chlorine Binding Sites List in 8qmb
Chlorine binding site 3 out of 4 in the Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl101

b:44.6
occ:1.00
 CL1 F:TE9101 0.0 44.6 1.0
C14 F:TE9101 1.8 32.9 1.0
C10 F:TE9101 2.7 35.0 1.0
H9 F:TE9101 2.7 34.4 1.0
C2 F:TE9101 2.7 29.7 1.0
N2 F:TE9101 2.7 25.4 1.0
H10 F:TE9101 2.8 34.3 1.0
C15 F:TE9101 2.8 29.3 1.0
HB3 A:ARG456 2.8 39.7 1.0
C13 F:TE9101 2.8 32.5 1.0
N4 F:TE9101 2.9 35.3 1.0
N3 F:TE9101 3.1 34.2 1.0
C1 F:TE9101 3.3 27.6 1.0
O A:ARG456 3.4 34.5 1.0
C16 F:TE9101 3.5 34.9 1.0
C2 F:DA5 3.5 29.3 1.0
N3 F:DA5 3.6 30.8 1.0
H2 F:DA5 3.6 30.2 1.0
CB A:ARG456 3.7 39.1 1.0
N1 F:DA5 3.9 31.5 1.0
HB2 A:ARG456 3.9 40.1 1.0
C4 F:DA5 4.0 29.3 1.0
C18 F:TE9101 4.0 28.7 1.0
N1 F:TE9101 4.0 34.0 1.0
C9 F:TE9101 4.0 39.0 1.0
C17 F:TE9101 4.0 34.4 1.0
C A:ARG456 4.0 33.3 1.0
O F:HOH215 4.1 38.3 1.0
H1 F:TE9101 4.1 32.0 1.0
C7 F:TE9101 4.1 29.2 1.0
HD3 A:ARG456 4.1 46.0 1.0
C6 F:DA5 4.3 30.4 1.0
F2 F:TE9101 4.3 44.7 1.0
C12 F:TE9101 4.3 38.3 1.0
C11 F:TE9101 4.3 34.8 1.0
C5 F:DA5 4.4 28.0 1.0
CA A:ARG456 4.4 38.6 1.0
C3 F:TE9101 4.5 40.6 1.0
H1' F:DA5 4.5 40.5 1.0
C8 F:TE9101 4.5 36.1 1.0
HA A:ARG456 4.5 37.1 1.0
HA3 A:GLY457 4.6 36.2 1.0
H3 E:DT15 4.7 28.2 1.0
N9 F:DA5 4.7 36.4 1.0
H2 F:TE9101 4.7 31.9 1.0
H5 F:TE9101 4.8 35.8 1.0
CG A:ARG456 4.8 44.7 1.0
CD A:ARG456 4.8 46.8 1.0
N A:GLY457 4.8 33.7 1.0
H11 F:TE9101 4.9 33.1 1.0
H7 F:TE9101 4.9 37.5 1.0
H8 F:TE9101 5.0 33.1 0.0

Chlorine binding site 4 out of 4 in 8qmb

Go back to Chlorine Binding Sites List in 8qmb
Chlorine binding site 4 out of 4 in the Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl101

b:46.5
occ:1.00
 CL1 H:TE9101 0.0 46.5 1.0
C14 H:TE9101 1.8 34.9 1.0
C10 H:TE9101 2.7 36.8 1.0
H10 H:TE9101 2.7 37.2 1.0
N2 H:TE9101 2.7 29.8 1.0
C2 H:TE9101 2.7 33.5 1.0
C15 H:TE9101 2.8 31.9 1.0
H9 H:TE9101 2.8 37.3 1.0
HB3 B:ARG456 2.8 45.0 1.0
C13 H:TE9101 2.9 35.1 1.0
N4 H:TE9101 3.0 37.6 1.0
N3 H:TE9101 3.1 33.3 1.0
C1 H:TE9101 3.3 34.2 1.0
O B:ARG456 3.3 36.7 1.0
C2 H:DG5 3.4 35.7 1.0
C16 H:TE9101 3.5 39.1 1.0
N2 H:DG5 3.5 48.5 1.0
H21 H:DG5 3.5 43.7 1.0
N3 H:DG5 3.6 27.1 1.0
CB B:ARG456 3.7 44.6 1.0
C B:ARG456 3.9 38.4 1.0
N1 H:TE9101 3.9 38.5 1.0
C18 H:TE9101 3.9 32.2 1.0
H22 H:DG5 4.0 43.7 1.0
C17 H:TE9101 4.0 34.8 1.0
C9 H:TE9101 4.0 37.4 1.0
HB2 B:ARG456 4.0 45.3 1.0
N1 H:DG5 4.0 36.1 1.0
C7 H:TE9101 4.1 33.8 1.0
H1 H:TE9101 4.1 37.2 1.0
C4 H:DG5 4.1 30.1 1.0
HD3 B:ARG456 4.1 53.0 1.0
F2 H:TE9101 4.2 44.1 1.0
CA B:ARG456 4.3 40.3 1.0
H1 H:DG5 4.3 35.9 1.0
H1' H:DG5 4.4 44.2 1.0
HA3 B:GLY457 4.4 46.4 1.0
C12 H:TE9101 4.4 42.9 1.0
HA B:ARG456 4.4 40.6 1.0
C11 H:TE9101 4.4 38.0 1.0
C3 H:TE9101 4.5 33.2 1.0
C8 H:TE9101 4.6 36.6 1.0
H2 H:TE9101 4.6 37.1 1.0
C6 H:DG5 4.7 35.9 1.0
C5 H:DG5 4.7 34.2 1.0
H8 H:TE9101 4.7 33.1 0.0
N B:GLY457 4.7 43.6 1.0
H5 H:TE9101 4.8 39.0 1.0
CG B:ARG456 4.8 53.0 1.0
H11 H:TE9101 4.8 35.1 1.0
N9 H:DG5 4.9 38.9 1.0
H7 H:TE9101 4.9 41.4 1.0
CD B:ARG456 4.9 54.9 1.0

Reference:

S.Najmudin, X.S.Pan, B.Wang, N.E.Chayen, L.M.Fisher, M.R.Sanderson. The Nature of the Molecular Interactions at High Resolution of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin. To Be Published.
Page generated: Thu Oct 31 17:57:32 2024

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