Magnesium 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:

Fluorine	(F)	6 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 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 Magnesium with other atoms in the Mg 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:Mg1503 b:20.0 occ:1.00 O F:HOH202 2.2 32.5 1.0 O E:HOH101 2.3 43.2 1.0 O3 F:TE9101 2.5 57.4 1.0 O1 F:TE9101 2.5 60.2 1.0 O A:HOH1739 2.6 24.3 1.0 C6 F:TE9101 3.5 59.0 1.0 C5 F:TE9101 3.6 61.2 1.0 HG A:SER1079 3.6 48.6 0.0 HB2 A:SER1079 3.8 45.1 1.0 C4 F:TE9101 4.0 60.0 1.0 OG A:SER1079 4.1 46.4 1.0 OD2 A:ASP1083 4.2 30.6 1.0 O4 E:DT7 4.4 44.7 1.0 H4 F:TE9101 4.5 60.6 1.0 CB A:SER1079 4.5 45.0 1.0 O6 H:DG1 4.6 77.6 1.0 H62 E:DA6 4.7 41.1 1.0 C7 F:TE9101 4.7 59.0 1.0 O2 F:TE9101 4.7 59.1 1.0 H62 F:DA5 4.8 61.2 1.0 H41 F:DC4 4.9 68.4 1.0 HB3 A:SER1079 5.0 45.1 1.0 H72 E:DT7 5.0 44.8 1.0

Magnesium binding site 2 out of 6 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 Magnesium with other atoms in the Mg 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 A:Mg1504 b:8.6 occ:1.00 O A:HOH1684 2.1 22.9 1.0 O A:HOH1777 2.4 27.2 1.0 O A:THR1319 2.5 32.8 1.0 O A:GLN1322 2.6 29.5 1.0 O A:PHE1316 2.7 30.2 1.0 O A:LYS1317 2.9 34.0 1.0 C A:LYS1317 3.5 33.7 1.0 HA A:ASP1320 3.6 29.5 1.0 C A:THR1319 3.7 31.1 1.0 C A:GLN1322 3.8 29.4 1.0 HA A:LYS1317 3.8 33.3 1.0 C A:PHE1316 3.8 30.5 1.0 HA A:ILE1323 3.9 29.1 1.0 H A:GLN1322 3.9 29.8 1.0 CA A:LYS1317 4.1 33.4 1.0 H A:THR1319 4.2 32.3 1.0 N A:TYR1318 4.3 33.8 1.0 HB3 A:GLN1322 4.3 29.9 1.0 HG2 A:GLN1322 4.3 29.6 1.0 N A:THR1319 4.3 32.4 1.0 HG22 A:ILE1323 4.4 29.0 1.0 N A:LYS1317 4.4 32.4 1.0 CA A:ASP1320 4.5 29.5 1.0 OD1 A:ASP1320 4.5 29.3 1.0 N A:ASP1320 4.5 29.7 1.0 N A:GLN1322 4.6 29.7 1.0 CA A:THR1319 4.6 30.2 1.0 CA A:GLN1322 4.6 29.6 1.0 HA A:TYR1318 4.6 33.2 1.0 N A:ILE1323 4.7 29.2 1.0 CA A:ILE1323 4.7 29.0 1.0 C A:TYR1318 4.7 32.8 1.0 O A:HOH1768 4.8 22.8 1.0 H A:TYR1318 4.8 33.8 1.0 CB A:GLN1322 4.8 29.8 1.0 CA A:TYR1318 4.8 33.3 1.0 HA A:PHE1316 4.9 30.4 1.0 O A:LEU1315 4.9 32.7 1.0 O A:HOH1648 4.9 19.5 1.0

Magnesium binding site 3 out of 6 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 Magnesium with other atoms in the Mg 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 A:Mg1505 b:39.1 occ:1.00 O A:HOH1601 2.3 36.4 1.0 O A:HOH1612 2.4 25.4 1.0 O A:HOH1645 2.4 31.9 1.0 OD2 A:ASP506 2.5 58.1 1.0 OD2 A:ASP508 3.0 45.6 1.0 H5'' E:DT7 3.1 50.0 1.0 O A:HOH1723 3.1 30.4 1.0 O E:HOH110 3.3 35.9 1.0 OP1 E:DT7 3.6 50.7 1.0 CG A:ASP506 3.7 57.7 1.0 O A:HOH1767 3.9 37.8 1.0 H3' E:DT7 3.9 52.0 1.0 CG A:ASP508 4.0 47.0 1.0 OE2 A:GLU433 4.0 66.2 1.0 C5' E:DT7 4.1 48.9 1.0 HE1 B:TYR1118 4.2 53.8 1.0 HB2 A:ASP506 4.3 56.4 1.0 OD1 A:ASP508 4.3 47.8 1.0 HB3 A:ASP506 4.4 56.3 1.0 CB A:ASP506 4.5 56.0 1.0 H5' E:DT7 4.5 28.0 1.0 HB2 A:ASP510 4.6 45.3 1.0 C3' E:DT7 4.6 50.9 1.0 OD1 A:ASP506 4.7 59.8 1.0 O5' E:DT7 4.8 49.4 1.0 CD A:GLU433 4.8 64.8 1.0 O3' E:DT7 4.8 54.0 1.0 P E:DT7 4.8 47.3 1.0 C4' E:DT7 4.8 48.4 1.0 HA3 A:GLY582 4.9 65.2 1.0 O A:HOH1649 4.9 26.1 1.0 H4' E:DT7 5.0 48.1 1.0 OE1 A:GLU433 5.0 63.8 1.0

Magnesium binding site 4 out of 6 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 Magnesium with other atoms in the Mg 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 B:Mg1502 b:31.1 occ:1.00 O H:HOH202 2.1 31.9 1.0 O G:HOH101 2.3 49.1 1.0 O B:HOH1602 2.4 53.2 1.0 O2 H:TE9101 2.6 56.1 1.0 O3 H:TE9101 2.8 50.2 1.0 HB2 B:SER1079 3.5 41.3 1.0 HG B:SER1079 3.6 45.7 0.0 C5 H:TE9101 3.7 57.4 1.0 C6 H:TE9101 3.8 53.2 1.0 O B:HOH1760 3.9 29.8 1.0 OD2 B:ASP1083 3.9 30.8 1.0 OG B:SER1079 4.1 42.0 1.0 H62 F:DA1 4.2 78.4 1.0 C4 H:TE9101 4.2 55.1 1.0 CB B:SER1079 4.2 41.0 1.0 HB3 B:SER1079 4.6 41.2 1.0 O4 G:DT7 4.7 40.2 1.0 H4 H:TE9101 4.8 54.4 1.0 O1 H:TE9101 4.8 60.4 1.0 N6 F:DA1 4.9 76.9 1.0 H62 G:DA6 5.0 35.6 1.0 H61 H:DA5 5.0 56.2 1.0

Magnesium binding site 5 out of 6 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 Magnesium with other atoms in the Mg binding site number 5 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:Mg1503 b:26.4 occ:1.00 O B:THR1319 2.4 44.4 1.0 O B:GLN1322 2.5 40.0 1.0 O B:HOH1754 2.6 39.8 1.0 O B:HOH1776 2.7 29.2 1.0 O B:PHE1316 2.7 41.0 1.0 O B:LYS1317 2.8 46.9 1.0 C B:LYS1317 3.5 46.9 1.0 C B:THR1319 3.5 43.2 1.0 HA B:ASP1320 3.7 43.0 1.0 C B:GLN1322 3.7 41.1 1.0 H B:GLN1322 3.8 41.4 1.0 C B:PHE1316 3.8 42.6 1.0 HB3 B:GLN1322 3.9 42.4 1.0 H B:THR1319 4.0 45.1 1.0 HA B:LYS1317 4.0 45.8 1.0 HA B:ILE1323 4.0 40.6 1.0 N B:THR1319 4.1 45.0 1.0 CA B:LYS1317 4.2 45.7 1.0 N B:TYR1318 4.3 48.1 1.0 N B:ASP1320 4.4 43.3 1.0 CA B:THR1319 4.4 43.1 1.0 CA B:ASP1320 4.4 43.0 1.0 N B:GLN1322 4.5 41.0 1.0 N B:LYS1317 4.5 43.7 1.0 HG2 B:GLN1322 4.5 42.5 1.0 CA B:GLN1322 4.5 41.5 1.0 HA B:TYR1318 4.5 47.3 1.0 C B:TYR1318 4.5 47.0 1.0 HG22 B:ILE1323 4.6 40.0 1.0 CB B:GLN1322 4.6 42.4 1.0 N B:ILE1323 4.7 40.6 1.0 CA B:TYR1318 4.7 47.3 1.0 O B:LEU1315 4.8 42.9 1.0 H B:TYR1318 4.8 47.8 1.0 HA B:PHE1316 4.8 42.6 1.0 CA B:ILE1323 4.8 40.5 1.0 HA B:THR1319 4.8 43.1 1.0 OD1 B:ASP1320 4.8 40.8 1.0 H B:LEU1321 4.9 42.8 1.0 CA B:PHE1316 5.0 42.7 1.0

Magnesium binding site 6 out of 6 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 Magnesium with other atoms in the Mg binding site number 6 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:Mg1504 b:27.2 occ:1.00 O B:HOH1621 2.2 15.7 1.0 O B:HOH1601 2.2 21.7 1.0 OD2 B:ASP506 2.5 50.2 1.0 O B:HOH1606 2.5 25.6 1.0 H5'' G:DT7 3.0 42.7 1.0 OD2 B:ASP508 3.0 47.0 1.0 O F:HOH206 3.1 32.9 1.0 OP1 G:DT7 3.6 43.6 1.0 O G:HOH105 3.6 29.5 1.0 H3' G:DT7 3.7 45.1 1.0 CG B:ASP506 3.7 49.8 1.0 C5' G:DT7 3.9 41.4 1.0 CG B:ASP508 4.0 48.2 1.0 HE1 A:TYR1118 4.0 55.5 1.0 OE2 B:GLU433 4.2 51.1 1.0 OD1 B:ASP508 4.3 48.4 1.0 HB2 B:ASP506 4.3 50.0 1.0 H5' G:DT7 4.4 32.9 1.0 C3' G:DT7 4.4 43.7 1.0 CB B:ASP506 4.5 49.8 1.0 HB3 B:ASP506 4.5 50.0 1.0 HB2 B:ASP510 4.6 43.0 1.0 OD1 B:ASP506 4.6 51.4 1.0 O5' G:DT7 4.6 41.6 1.0 C4' G:DT7 4.7 41.2 1.0 P G:DT7 4.7 41.9 1.0 O3' G:DT7 4.7 44.4 1.0 CD B:GLU433 4.8 52.0 1.0 O B:LYS581 4.8 67.8 1.0 H4' G:DT7 4.8 40.5 1.0 HO3' G:DT7 4.9 62.4 0.0 CE1 A:TYR1118 5.0 56.3 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.