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Magnesium 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:

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

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 6 in 8qmb

Go back to Magnesium Binding Sites List in 8qmb
Magnesium binding site 1 out of 6 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 Magnesium with other atoms in the Mg 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:Mg1501

b:50.6
occ:1.00
 O F:HOH201 1.9 50.5 1.0
O1 F:TE9101 2.2 55.3 1.0
O3 F:TE9101 2.2 44.6 1.0
C6 F:TE9101 3.2 35.2 1.0
C5 F:TE9101 3.3 42.2 1.0
C4 F:TE9101 3.7 43.7 1.0
HG A:SER1079 3.7 30.0 0.0
HB2 A:SER1079 3.9 39.8 1.0
O4 E:DT15 4.2 27.5 1.0
OG A:SER1079 4.2 47.5 1.0
H4 F:TE9101 4.4 35.3 1.0
C7 F:TE9101 4.5 29.2 1.0
CB A:SER1079 4.5 38.6 1.0
O2 F:TE9101 4.5 49.8 1.0
H62 H:DA1 4.6 34.8 1.0
H62 F:DA5 4.6 31.3 1.0
H72 E:DT15 4.7 33.1 0.0
H61 F:DA5 4.7 31.2 1.0
OD2 A:ASP1083 4.8 30.8 1.0
HB3 A:SER1079 4.8 40.1 1.0
C8 F:TE9101 4.9 36.1 1.0
H62 E:DA14 4.9 27.4 1.0
H61 H:DA1 5.0 34.9 1.0
O H:HOH214 5.0 46.0 1.0
N6 F:DA5 5.0 31.8 1.0
N6 H:DA1 5.0 35.7 1.0

Magnesium binding site 2 out of 6 in 8qmb

Go back to Magnesium Binding Sites List in 8qmb
Magnesium binding site 2 out of 6 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 Magnesium with other atoms in the Mg 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
A:Mg1502

b:17.6
occ:1.00
 O A:HOH1773 2.1 59.1 1.0
O A:HOH1926 2.3 51.6 1.0
O A:THR1319 2.5 34.1 1.0
O A:GLN1322 2.6 25.9 1.0
O A:PHE1316 2.6 28.6 1.0
O A:LYS1317 2.9 35.1 1.0
C A:LYS1317 3.4 30.4 1.0
C A:THR1319 3.6 28.3 1.0
HA A:LYS1317 3.7 29.8 1.0
C A:PHE1316 3.7 27.8 1.0
C A:GLN1322 3.7 24.4 1.0
H A:GLN1322 3.9 29.1 1.0
H A:THR1319 3.9 26.9 1.0
HA A:ASP1320 3.9 25.9 1.0
CA A:LYS1317 4.0 29.6 1.0
HA A:ILE1323 4.0 26.1 1.0
HB3 A:GLN1322 4.0 29.4 1.0
N A:THR1319 4.1 26.6 1.0
N A:TYR1318 4.1 30.9 1.0
N A:LYS1317 4.3 28.4 1.0
HG2 A:GLN1322 4.5 30.7 1.0
CA A:THR1319 4.5 27.0 1.0
N A:ASP1320 4.5 25.2 1.0
HG23 A:ILE1323 4.6 25.7 1.0
N A:GLN1322 4.6 29.7 1.0
O A:HOH1883 4.6 57.4 1.0
CA A:GLN1322 4.6 27.5 1.0
HA A:TYR1318 4.6 29.6 1.0
C A:TYR1318 4.6 26.5 1.0
H A:TYR1318 4.6 30.7 1.0
CB A:GLN1322 4.6 28.7 1.0
N A:ILE1323 4.7 24.4 1.0
CA A:ASP1320 4.7 25.1 1.0
HE22 A:GLN1322 4.7 28.3 1.0
CA A:TYR1318 4.7 30.0 1.0
O A:HOH1740 4.7 37.7 1.0
HA A:PHE1316 4.7 28.7 1.0
CA A:ILE1323 4.8 27.3 1.0
OD1 A:ASP1320 4.8 32.8 1.0
O A:LEU1315 4.8 31.3 1.0
CA A:PHE1316 4.9 29.5 1.0
HA A:THR1319 4.9 26.6 1.0

Magnesium binding site 3 out of 6 in 8qmb

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Magnesium binding site 3 out of 6 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 Magnesium with other atoms in the Mg 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
A:Mg1503

b:40.9
occ:1.00
 O A:HOH1765 2.0 43.1 1.0
O A:HOH1684 2.0 35.3 1.0
O E:HOH106 2.0 33.4 1.0
OD2 A:ASP508 2.1 38.6 1.0
OD2 A:ASP506 2.3 39.3 1.0
O A:HOH1609 2.3 27.6 1.0
CG A:ASP508 3.1 39.3 1.0
CG A:ASP506 3.4 41.5 1.0
HB2 A:ASP506 3.5 40.9 1.0
OD1 A:ASP508 3.5 39.9 1.0
H5'' E:DT15 3.6 32.8 1.0
HB3 A:ASP506 3.6 40.9 1.0
CB A:ASP506 3.8 42.0 1.0
O A:HOH1833 3.9 52.8 1.0
O A:HOH1639 4.0 41.2 1.0
O A:HOH1925 4.1 39.2 1.0
OE2 A:GLU433 4.1 44.5 1.0
HB2 A:ASP510 4.3 32.5 1.0
O A:LYS581 4.4 45.7 1.0
CB A:ASP508 4.4 35.5 1.0
OP1 E:DT15 4.4 24.6 1.0
HB3 A:ASP508 4.5 37.3 1.0
OD1 A:ASP506 4.5 44.4 1.0
O A:HOH1900 4.6 42.8 1.0
C5' E:DT15 4.6 34.3 1.0
HB2 A:ASP508 4.6 36.6 1.0
HA3 A:GLY582 4.6 41.8 1.0
H3' E:DT15 4.6 34.6 1.0
OE1 A:GLU433 4.7 38.9 1.0
H A:GLY511 4.8 36.3 1.0
CD A:GLU433 4.8 44.0 1.0
HA2 A:GLY582 4.9 42.3 1.0
H5' E:DT15 4.9 32.7 1.0

Magnesium binding site 4 out of 6 in 8qmb

Go back to Magnesium Binding Sites List in 8qmb
Magnesium binding site 4 out of 6 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 Magnesium with other atoms in the Mg 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
B:Mg1501

b:50.8
occ:1.00
 O H:HOH201 1.9 43.8 1.0
O2 H:TE9101 2.1 46.2 1.0
O3 H:TE9101 2.2 34.2 1.0
C5 H:TE9101 3.2 39.2 1.0
C6 H:TE9101 3.2 32.6 1.0
C4 H:TE9101 3.7 35.9 1.0
HG B:SER1079 3.7 30.0 0.0
H42 G:DC15 3.7 28.6 1.0
HB2 B:SER1079 3.9 37.3 1.0
OG B:SER1079 4.3 46.8 1.0
O1 H:TE9101 4.3 44.6 1.0
N4 G:DC15 4.4 29.6 1.0
H4 H:TE9101 4.5 36.1 1.0
CB B:SER1079 4.5 35.1 1.0
C7 H:TE9101 4.5 33.8 1.0
H41 G:DC15 4.6 28.7 1.0
O6 F:DG1 4.7 40.1 1.0
HB3 B:SER1079 4.8 37.5 1.0
H42 H:DC4 4.8 46.7 1.0
OD2 B:ASP1083 4.9 26.9 1.0
O6 H:DG5 4.9 39.3 1.0
C8 H:TE9101 5.0 36.6 1.0

Magnesium binding site 5 out of 6 in 8qmb

Go back to Magnesium Binding Sites List in 8qmb
Magnesium binding site 5 out of 6 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 Magnesium with other atoms in the Mg binding site number 5 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:Mg1502

b:32.6
occ:1.00
 O B:HOH1739 2.0 51.0 1.0
O B:PHE1316 2.3 44.6 1.0
O B:THR1319 2.3 39.0 1.0
O B:GLN1322 2.4 36.5 1.0
O B:LYS1317 3.1 44.9 1.0
C B:LYS1317 3.5 39.4 1.0
C B:PHE1316 3.5 37.8 1.0
C B:GLN1322 3.5 34.2 1.0
C B:THR1319 3.5 37.8 1.0
HB3 B:GLN1322 3.6 37.2 1.0
H B:GLN1322 3.6 34.5 1.0
HA B:LYS1317 3.7 38.4 1.0
H B:THR1319 3.8 40.3 1.0
HA B:ASP1320 3.9 34.5 1.0
CA B:LYS1317 4.0 38.4 1.0
HA B:ILE1323 4.1 33.1 1.0
N B:THR1319 4.1 40.6 1.0
N B:TYR1318 4.2 44.3 1.0
HG2 B:GLN1322 4.2 36.5 1.0
N B:LYS1317 4.2 36.4 1.0
CB B:GLN1322 4.3 38.1 1.0
CA B:GLN1322 4.3 34.0 1.0
N B:GLN1322 4.3 34.5 1.0
CA B:THR1319 4.5 36.4 1.0
HA B:PHE1316 4.5 37.5 1.0
N B:ASP1320 4.5 35.9 1.0
N B:ILE1323 4.5 31.3 1.0
HE22 B:GLN1322 4.6 34.6 1.0
HG23 B:ILE1323 4.6 35.8 1.0
H B:TYR1318 4.6 42.0 1.0
CA B:ASP1320 4.6 34.5 1.0
HA B:TYR1318 4.6 40.0 1.0
C B:TYR1318 4.7 42.7 1.0
CA B:PHE1316 4.7 37.4 1.0
O B:LEU1315 4.7 40.9 1.0
O B:HOH1704 4.7 46.2 1.0
CA B:TYR1318 4.8 39.2 1.0
CG B:GLN1322 4.8 37.2 1.0
CA B:ILE1323 4.8 32.5 1.0
HA B:THR1319 4.9 36.9 1.0
OD1 B:ASP1320 4.9 41.2 1.0
H B:LEU1321 5.0 35.1 1.0

Magnesium binding site 6 out of 6 in 8qmb

Go back to Magnesium Binding Sites List in 8qmb
Magnesium binding site 6 out of 6 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 Magnesium with other atoms in the Mg binding site number 6 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:Mg1503

b:33.8
occ:1.00
 O B:HOH1796 1.9 33.6 1.0
O B:HOH1789 2.0 27.7 1.0
O B:HOH1654 2.0 30.7 1.0
OD2 B:ASP508 2.1 49.4 1.0
O B:HOH1695 2.1 32.1 1.0
OD2 B:ASP506 2.2 38.4 1.0
CG B:ASP508 3.1 39.0 1.0
CG B:ASP506 3.3 39.6 1.0
HB2 B:ASP506 3.3 38.5 1.0
OD1 B:ASP508 3.4 42.2 1.0
HB3 B:ASP506 3.5 38.4 1.0
H5'' G:DC15 3.6 31.7 1.0
CB B:ASP506 3.6 38.4 1.0
OE2 B:GLU433 4.0 42.5 1.0
O B:HOH1722 4.1 38.9 1.0
HB2 B:ASP510 4.2 33.9 1.0
O F:HOH217 4.3 35.5 1.0
O B:LYS581 4.3 47.9 1.0
CB B:ASP508 4.4 37.6 1.0
OD1 B:ASP506 4.4 38.5 1.0
H3' G:DC15 4.5 33.0 1.0
OE1 B:GLU433 4.5 39.4 1.0
HB3 B:ASP508 4.5 38.4 1.0
C5' G:DC15 4.5 30.8 1.0
OP1 G:DC15 4.5 28.0 1.0
CD B:GLU433 4.6 47.9 1.0
HB2 B:ASP508 4.6 38.0 1.0
HA3 B:GLY582 4.6 49.4 1.0
HA2 B:GLY582 4.7 49.6 1.0
H B:GLY511 4.7 35.5 1.0
H5' G:DC15 4.8 31.6 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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