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Magnesium in PDB 8qmc: High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin

Enzymatic activity of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin

All present enzymatic activity of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin:
5.6.2.2;

Protein crystallography data

The structure of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin, PDB code: 8qmc 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) 64.86 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.14, 157.14, 211.636, 90, 90, 120
R / Rfree (%) 24.1 / 29.9

Other elements in 8qmc:

The structure of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin (pdb code 8qmc). 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-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin, PDB code: 8qmc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8qmc

Go back to Magnesium Binding Sites List in 8qmc
Magnesium binding site 1 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and 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-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1505

b:11.6
occ:1.00
 O1 F:TE9101 2.5 26.5 1.0
O3 F:TE9101 2.7 27.0 1.0
HG A:SER1079 3.2 30.0 0.0
C5 F:TE9101 3.5 25.6 1.0
C6 F:TE9101 3.6 26.0 1.0
OG A:SER1079 3.8 20.0 1.0
HB2 A:SER1079 3.8 18.8 1.0
C4 F:TE9101 4.0 25.1 1.0
O4 E:DT15 4.1 21.7 1.0
O E:HOH104 4.3 13.6 1.0
CB A:SER1079 4.3 19.0 1.0
H73 E:DT15 4.4 21.7 1.0
OD2 A:ASP1083 4.5 12.8 1.0
O2 F:TE9101 4.5 24.6 1.0
H62 F:DA5 4.6 23.3 1.0
H4 F:TE9101 4.8 27.9 1.0
HB3 A:SER1079 4.8 19.2 1.0
H62 H:DA1 4.8 52.1 1.0
H62 E:DA14 4.8 18.5 1.0
C7 F:TE9101 4.9 25.6 1.0

Magnesium binding site 2 out of 6 in 8qmc

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Magnesium binding site 2 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and 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-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1506

b:8.1
occ:1.00
 O A:THR1319 2.6 17.8 1.0
O A:GLN1322 2.7 17.1 1.0
O A:LYS1317 3.0 19.0 1.0
O A:PHE1316 3.2 18.3 1.0
HA A:ILE1323 3.6 16.5 1.0
HA A:ASP1320 3.7 16.2 1.0
C A:THR1319 3.8 17.3 1.0
C A:LYS1317 3.9 19.3 1.0
C A:GLN1322 3.9 16.6 1.0
HA A:LYS1317 4.1 19.4 1.0
HG22 A:ILE1323 4.2 16.2 1.0
OD1 A:ASP1320 4.2 15.9 1.0
H A:GLN1322 4.3 17.3 1.0
C A:PHE1316 4.3 19.0 1.0
O A:HOH1634 4.4 8.0 1.0
CA A:ILE1323 4.5 16.1 1.0
CA A:LYS1317 4.5 19.7 1.0
CA A:ASP1320 4.5 16.2 1.0
HB3 A:GLN1322 4.5 17.7 1.0
H A:THR1319 4.6 18.4 1.0
N A:ILE1323 4.6 16.0 1.0
N A:THR1319 4.6 18.3 1.0
N A:ASP1320 4.6 16.8 1.0
O A:HOH1623 4.7 15.0 1.0
N A:TYR1318 4.7 19.5 1.0
O A:HOH1668 4.7 14.0 1.0
HG2 A:GLN1322 4.8 17.1 1.0
HA A:TYR1318 4.8 19.4 1.0
CA A:THR1319 4.9 17.8 1.0
CA A:GLN1322 4.9 16.7 1.0
N A:LYS1317 4.9 19.5 1.0
N A:GLN1322 5.0 17.0 1.0
C A:TYR1318 5.0 18.6 1.0

Magnesium binding site 3 out of 6 in 8qmc

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Magnesium binding site 3 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and 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-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1507

b:17.7
occ:1.00
 OD2 A:ASP508 2.0 25.5 1.0
OD2 A:ASP506 2.5 30.9 1.0
CG A:ASP508 3.1 26.5 1.0
HB3 A:ASP508 3.5 26.7 1.0
CG A:ASP506 3.6 32.4 1.0
HB3 A:ASP506 3.8 31.3 1.0
CB A:ASP508 3.8 26.4 1.0
HB2 A:ASP506 3.9 31.4 1.0
H5'' E:DT15 3.9 17.6 1.0
HB2 A:ASP508 3.9 25.8 1.0
O A:HOH1776 4.0 13.4 1.0
OD1 A:ASP508 4.0 27.0 1.0
CB A:ASP506 4.0 31.7 1.0
O A:LYS581 4.1 37.1 1.0
O A:HOH1790 4.2 6.4 1.0
OP1 E:DT15 4.4 18.0 1.0
OE2 A:GLU433 4.4 32.0 1.0
HA3 A:GLY582 4.5 39.4 1.0
OD1 A:ASP506 4.6 33.8 1.0
HB2 A:ASP510 4.8 23.5 1.0
HE1 B:TYR1118 4.9 19.7 1.0
C5' E:DT15 4.9 17.2 1.0
O A:HOH1771 4.9 12.7 1.0
HD1 A:HIS1076 5.0 30.0 0.0

Magnesium binding site 4 out of 6 in 8qmc

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Magnesium binding site 4 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and 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-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1502

b:15.3
occ:1.00
 O3 H:TE9101 2.2 44.5 1.0
O2 H:TE9101 2.7 43.7 1.0
C6 H:TE9101 3.4 43.4 1.0
O B:HOH1782 3.5 11.8 1.0
C5 H:TE9101 3.6 42.6 1.0
HB2 B:SER1079 3.7 15.2 1.0
O6 F:DG1 3.9 41.0 1.0
C4 H:TE9101 3.9 42.5 1.0
HG B:SER1079 4.1 30.0 0.0
HB3 B:SER1079 4.2 15.6 1.0
H4 H:TE9101 4.2 45.2 1.0
CB B:SER1079 4.2 15.3 1.0
OG B:SER1079 4.3 16.1 1.0
H42 H:DC4 4.3 54.6 1.0
H41 G:DC15 4.4 21.0 1.0
C7 H:TE9101 4.6 43.3 1.0
H41 H:DC4 4.6 55.9 1.0
O1 H:TE9101 4.6 41.9 1.0
N4 H:DC4 4.7 55.2 1.0
C6 F:DG1 4.8 42.9 1.0
C8 H:TE9101 4.8 44.4 1.0

Magnesium binding site 5 out of 6 in 8qmc

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Magnesium binding site 5 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and 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-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1503

b:12.9
occ:1.00
 O B:THR1319 2.2 20.0 1.0
O B:GLN1322 2.4 19.5 1.0
O B:PHE1316 2.8 21.4 1.0
O B:LYS1317 2.8 22.2 1.0
C B:THR1319 3.4 20.2 1.0
C B:GLN1322 3.6 19.1 1.0
HA B:ASP1320 3.6 19.4 1.0
HB3 B:GLN1322 3.6 20.2 1.0
C B:LYS1317 3.6 22.6 1.0
H B:GLN1322 3.7 19.6 1.0
C B:PHE1316 3.9 21.9 1.0
H B:THR1319 4.0 21.4 1.0
HA B:ILE1323 4.0 18.9 1.0
N B:THR1319 4.1 21.2 1.0
HA B:LYS1317 4.1 23.1 1.0
N B:ASP1320 4.3 19.9 1.0
CA B:LYS1317 4.4 23.1 1.0
CA B:GLN1322 4.4 19.3 1.0
N B:TYR1318 4.4 22.6 1.0
N B:GLN1322 4.4 19.5 1.0
CA B:ASP1320 4.4 19.4 1.0
CB B:GLN1322 4.4 19.9 1.0
CA B:THR1319 4.4 20.4 1.0
OD1 B:ASP1320 4.5 19.7 1.0
N B:LYS1317 4.6 22.7 1.0
HG22 B:ILE1323 4.6 18.3 1.0
N B:ILE1323 4.6 18.7 1.0
C B:TYR1318 4.6 21.6 1.0
HA B:TYR1318 4.6 22.2 1.0
HG2 B:GLN1322 4.8 19.8 1.0
CA B:ILE1323 4.8 18.6 1.0
CA B:TYR1318 4.8 22.1 1.0
HA B:THR1319 4.9 20.4 1.0
O B:LEU1315 4.9 20.7 1.0
HA B:PHE1316 4.9 21.1 1.0
H B:TYR1318 5.0 22.8 1.0
H B:LEU1321 5.0 19.7 1.0

Magnesium binding site 6 out of 6 in 8qmc

Go back to Magnesium Binding Sites List in 8qmc
Magnesium binding site 6 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and 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-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1504

b:9.6
occ:1.00
 OD2 B:ASP508 2.3 23.6 1.0
OD2 B:ASP506 2.7 28.1 1.0
O F:HOH207 3.4 14.0 1.0
CG B:ASP508 3.5 24.6 1.0
H5'' G:DC15 3.5 18.9 1.0
O G:HOH106 3.6 12.2 1.0
O B:HOH1759 3.8 11.7 1.0
CG B:ASP506 3.8 28.1 1.0
OP1 G:DC15 3.8 17.3 1.0
O B:LYS581 4.1 40.0 1.0
OD1 B:ASP508 4.1 25.4 1.0
HB3 B:ASP508 4.3 24.5 1.0
HB3 B:ASP506 4.4 27.3 1.0
C5' G:DC15 4.5 18.0 1.0
H3' G:DC15 4.5 22.6 1.0
OD1 B:ASP506 4.5 28.2 1.0
HB2 B:ASP506 4.5 27.4 1.0
CB B:ASP508 4.5 24.5 1.0
CB B:ASP506 4.6 27.6 1.0
H5' G:DC15 4.8 16.8 1.0
HE2 A:TYR1118 4.8 20.7 1.0
HB2 B:ASP508 4.8 23.9 1.0
HA3 B:GLY582 4.8 42.7 1.0
OE2 B:GLU433 4.9 25.8 1.0
HD1 B:HIS1076 5.0 30.0 0.0
O B:PRO1075 5.0 15.2 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 21:59:11 2024

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