Chlorine in PDB 8c41: High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin

The structure of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin, PDB code: 8c41 was solved by S.Najmudin, X.S.Pan, B.Wang, N.E.Cheyen, 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)	115.01 / 2.39
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	157.471, 157.471, 212.339, 90, 90, 120
R / Rfree (%)	19.2 / 24.3

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

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

The binding sites of Chlorine atom in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin (pdb code 8c41). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin, PDB code: 8c41:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-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 High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1506 b:51.4 occ:1.00 HH21 A:ARG1426 1.9 55.0 1.0 NH2 A:ARG1426 2.6 55.4 1.0 HH12 A:ARG1371 2.6 19.2 0.0 HH22 A:ARG1426 2.8 54.8 1.0 HH21 A:ARG1371 2.9 30.1 1.0 O A:HOH1785 3.2 8.7 1.0 NH1 A:ARG1371 3.4 30.0 1.0 NH2 A:ARG1371 3.6 30.2 1.0 HH12 A:ARG1426 3.6 62.1 0.0 HD11 A:LEU1378 3.6 36.0 1.0 CZ A:ARG1426 3.8 53.8 1.0 HD12 A:LEU1378 3.9 36.2 1.0 CZ A:ARG1371 4.0 30.0 1.0 HH11 A:ARG1371 4.1 19.2 0.0 CD1 A:LEU1378 4.1 36.2 1.0 NH1 A:ARG1426 4.3 55.4 1.0 HD13 A:LEU1378 4.3 36.2 1.0 HH22 A:ARG1371 4.3 30.3 1.0 H12 A:MPD1501 4.5 48.7 1.0 HE A:ARG1426 4.8 48.0 1.0 NE A:ARG1426 4.8 48.0 1.0 HD23 A:LEU1422 4.9 30.7 1.0 HH11 A:ARG1426 4.9 62.1 0.0

Chlorine binding site 2 out of 4 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-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 High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1505 b:47.3 occ:1.00 O B:HOH1770 2.3 26.7 1.0 HH12 B:ARG1371 2.6 12.2 0.0 HH12 B:ARG1426 3.0 52.7 0.0 O B:HOH1751 3.0 17.0 1.0 HD11 B:LEU1378 3.3 29.1 1.0 NH1 B:ARG1371 3.4 28.6 1.0 NH1 B:ARG1426 3.7 45.6 1.0 H53 B:MPD1501 3.7 31.2 1.0 HD12 B:LEU1378 3.8 29.2 1.0 HH11 B:ARG1371 3.8 12.2 0.0 HD23 B:LEU1422 3.8 29.2 1.0 HH11 B:ARG1426 3.8 52.7 0.0 CD1 B:LEU1378 4.0 29.2 1.0 HH21 B:ARG1371 4.0 28.8 1.0 HD21 B:LEU1422 4.2 29.1 1.0 HG23 B:ILE1374 4.2 28.9 1.0 CD2 B:LEU1422 4.4 29.2 1.0 CZ B:ARG1371 4.4 28.7 1.0 HD13 B:LEU1378 4.4 29.2 1.0 HD23 B:LEU1378 4.4 29.4 1.0 NH2 B:ARG1371 4.5 28.8 1.0 HG22 B:ILE1374 4.5 29.0 1.0 C5 B:MPD1501 4.5 31.3 1.0 HD22 B:LEU1422 4.5 29.2 1.0 H52 B:MPD1501 4.6 31.3 1.0 H51 B:MPD1501 4.7 31.2 1.0 O B:HOH1702 4.7 12.3 1.0 CG2 B:ILE1374 4.8 29.0 1.0 O B:HOH1674 4.8 22.8 1.0 CZ B:ARG1426 4.9 42.2 1.0 HH21 B:ARG1426 4.9 42.5 1.0

Chlorine binding site 3 out of 4 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-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 High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl101 b:65.9 occ:1.00 CL1 F:TE9101 0.0 65.9 1.0 C14 F:TE9101 1.7 61.9 1.0 H10 F:TE9101 2.2 62.8 1.0 N2 F:TE9101 2.5 53.6 1.0 C2 F:TE9101 2.6 56.7 1.0 C10 F:TE9101 2.7 62.4 1.0 C15 F:TE9101 2.7 60.2 1.0 C13 F:TE9101 2.8 62.9 1.0 N4 F:TE9101 2.9 62.6 1.0 HB3 A:ARG456 3.0 59.4 1.0 N3 F:TE9101 3.0 58.8 1.0 C1 F:TE9101 3.1 53.5 1.0 H9 F:TE9101 3.2 62.0 1.0 C16 F:TE9101 3.4 56.9 1.0 O A:ARG456 3.4 53.0 1.0 H2 F:TE9101 3.6 53.3 1.0 HD2 A:ARG456 3.8 62.0 1.0 C18 F:TE9101 3.8 53.8 1.0 N1 F:TE9101 3.8 53.1 1.0 C2 F:DA5 3.8 59.6 1.0 H8 F:TE9101 3.9 49.2 0.0 CB A:ARG456 3.9 59.5 1.0 C17 F:TE9101 3.9 55.6 1.0 H2 F:DA5 3.9 59.8 1.0 C9 F:TE9101 4.0 62.4 1.0 C A:ARG456 4.0 56.5 1.0 C7 F:TE9101 4.0 59.0 1.0 N3 F:DA5 4.0 59.4 1.0 N1 F:DA5 4.0 59.9 1.0 C12 F:TE9101 4.1 61.7 1.0 HA A:ARG456 4.2 57.9 1.0 F2 F:TE9101 4.2 61.3 1.0 C11 F:TE9101 4.2 61.7 1.0 O4 F:TE9101 4.3 61.8 1.0 CA A:ARG456 4.3 58.0 1.0 C4 F:DA5 4.4 60.3 1.0 HB2 A:ARG456 4.4 59.7 1.0 C6 F:DA5 4.5 59.6 1.0 C3 F:TE9101 4.5 59.6 1.0 C8 F:TE9101 4.5 60.3 1.0 H6 F:TE9101 4.6 62.6 1.0 CD A:ARG456 4.6 62.5 1.0 C5 F:DA5 4.6 59.1 1.0 H1 F:TE9101 4.6 54.2 1.0 H11 F:TE9101 4.7 55.6 1.0 CG A:ARG456 4.7 61.5 1.0 HA3 A:GLY457 4.8 55.8 1.0 H3 E:DT7 4.8 46.1 1.0 F3 F:TE9101 4.8 54.4 1.0 HE A:ARG456 4.8 62.9 1.0 H7 F:TE9101 4.9 61.5 1.0 HG3 A:ARG456 4.9 61.4 1.0 N A:GLY457 4.9 55.4 1.0 H5 F:TE9101 4.9 61.7 1.0 H3 F:TE9101 5.0 60.0 1.0 N3 H:DG1 5.0 82.2 1.0

Chlorine binding site 4 out of 4 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-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 High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl101 b:62.0 occ:1.00 CL1 H:TE9101 0.0 62.0 1.0 C14 H:TE9101 1.7 56.8 1.0 H10 H:TE9101 2.2 61.0 1.0 N2 H:TE9101 2.6 50.7 1.0 C10 H:TE9101 2.7 56.4 1.0 C2 H:TE9101 2.7 52.0 1.0 C15 H:TE9101 2.8 55.0 1.0 C13 H:TE9101 2.8 61.2 1.0 HB3 B:ARG456 2.9 73.0 1.0 N4 H:TE9101 2.9 59.3 1.0 N3 H:TE9101 3.1 53.5 1.0 H9 H:TE9101 3.2 60.0 1.0 C1 H:TE9101 3.2 51.2 1.0 O B:ARG456 3.2 56.7 1.0 C16 H:TE9101 3.6 51.7 1.0 C2 H:DA5 3.7 55.9 1.0 H2 H:DA5 3.7 56.0 1.0 C B:ARG456 3.8 63.5 1.0 CB B:ARG456 3.8 74.4 1.0 N1 H:TE9101 3.8 50.6 1.0 N3 H:DA5 3.8 55.9 1.0 C18 H:TE9101 3.9 52.7 1.0 C9 H:TE9101 4.0 54.2 1.0 H8 H:TE9101 4.0 50.2 0.0 C7 H:TE9101 4.0 54.0 1.0 C17 H:TE9101 4.1 52.4 1.0 HA B:ARG456 4.1 66.2 1.0 H2 H:TE9101 4.1 51.3 1.0 N1 H:DA5 4.1 54.7 1.0 CA B:ARG456 4.1 65.9 1.0 C12 H:TE9101 4.1 59.7 1.0 HB2 B:ARG456 4.2 73.2 1.0 H1 H:TE9101 4.2 51.5 1.0 HD2 B:ARG456 4.2 79.4 1.0 C11 H:TE9101 4.3 58.2 1.0 C4 H:DA5 4.3 56.3 1.0 HA3 B:GLY457 4.4 57.8 1.0 F2 H:TE9101 4.4 52.4 1.0 O4 H:TE9101 4.5 58.7 1.0 C3 H:TE9101 4.5 54.6 1.0 C8 H:TE9101 4.5 54.4 1.0 C6 H:DA5 4.6 55.1 1.0 H6 H:TE9101 4.6 59.4 1.0 N B:GLY457 4.6 60.6 1.0 C5 H:DA5 4.7 55.2 1.0 HH11 B:ARG456 4.8 76.9 0.0 H1' H:DA5 4.8 59.4 1.0 H11 H:TE9101 4.8 52.8 1.0 H3 G:DT7 4.8 40.2 1.0 CG B:ARG456 4.9 78.5 1.0 H7 H:TE9101 4.9 59.0 1.0 N3 F:DA1 4.9 80.2 1.0 F3 H:TE9101 4.9 53.6 1.0 CD B:ARG456 5.0 79.8 1.0 H5 H:TE9101 5.0 58.5 1.0 H3 H:TE9101 5.0 55.3 1.0

S.Najmudin, X.S.Pan, B.Wang, N.E.Cheyen, 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.