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Magnesium in PDB 4kpe: Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate

Enzymatic activity of Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate

All present enzymatic activity of Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate:
5.99.1.3;

Protein crystallography data

The structure of Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate, PDB code: 4kpe was solved by I.Laponogov, X.-S.Pan, D.A.Vesekov, R.T.Cirz, A.S.Wagman, H.E.Moser, 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) 41.82 / 3.43
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.830, 157.830, 210.710, 90.00, 90.00, 120.00
R / Rfree (%) 15.4 / 19.5

Other elements in 4kpe:

The structure of Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate (pdb code 4kpe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate, PDB code: 4kpe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4kpe

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Magnesium binding site 1 out of 6 in the Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:43.0
occ:1.00
 O A:GLN322 2.0 50.0 1.0
O A:THR319 2.0 65.0 1.0
O A:PHE316 2.9 37.9 1.0
O A:LYS317 3.1 40.1 1.0
C A:GLN322 3.3 39.0 1.0
C A:THR319 3.3 56.0 1.0
C A:LYS317 3.8 38.6 1.0
C A:PHE316 4.0 38.5 1.0
N A:THR319 4.0 38.9 1.0
N A:ASP320 4.2 53.8 1.0
CA A:ASP320 4.2 50.4 1.0
N A:ILE323 4.2 45.6 1.0
N A:GLN322 4.2 36.7 1.0
CA A:GLN322 4.2 36.4 1.0
CA A:THR319 4.3 43.8 1.0
CA A:ILE323 4.4 44.9 1.0
CA A:LYS317 4.4 40.2 1.0
OD1 A:ASP320 4.5 58.7 1.0
N A:TYR318 4.5 35.8 1.0
CB A:GLN322 4.6 41.2 1.0
N A:LYS317 4.6 38.6 1.0
CG2 A:ILE323 4.7 48.2 1.0
C A:TYR318 4.7 43.6 1.0
C A:ASP320 4.8 46.0 1.0
O A:LEU315 4.8 40.2 1.0
CG A:GLN322 4.9 47.8 1.0
CA A:TYR318 5.0 33.0 1.0
N A:LEU321 5.0 37.8 1.0

Magnesium binding site 2 out of 6 in 4kpe

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Magnesium binding site 2 out of 6 in the Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:53.5
occ:1.00
 O08 F:AF5101 2.0 88.2 1.0
O11 F:AF5101 2.0 84.3 1.0
C07 F:AF5101 3.0 83.8 1.0
C10 F:AF5101 3.0 80.3 1.0
C06 F:AF5101 3.4 78.9 1.0
O09 F:AF5101 4.1 82.2 1.0
H271 F:AF5101 4.2 87.8 1.0
C12 F:AF5101 4.3 74.5 1.0
OD2 A:ASP83 4.4 59.2 1.0
OG A:SER79 4.5 71.9 1.0
O6 H:DG1 4.5 70.1 1.0
CB A:SER79 4.5 66.6 1.0
O4 E:DT15 4.5 77.8 1.0
C27 F:AF5101 4.7 73.2 1.0
C05 F:AF5101 4.7 72.0 1.0

Magnesium binding site 3 out of 6 in 4kpe

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Magnesium binding site 3 out of 6 in the Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:54.1
occ:1.00
 O B:THR319 2.0 57.1 1.0
O B:GLN322 2.0 58.8 1.0
O B:PHE316 3.0 51.3 1.0
O B:LYS317 3.2 38.5 1.0
C B:THR319 3.3 45.4 1.0
C B:GLN322 3.3 44.7 1.0
C B:LYS317 3.9 39.5 1.0
N B:THR319 4.2 42.5 1.0
C B:PHE316 4.2 45.9 1.0
N B:ASP320 4.2 39.9 1.0
CA B:ASP320 4.2 43.1 1.0
CA B:GLN322 4.2 41.6 1.0
N B:ILE323 4.2 48.5 1.0
N B:GLN322 4.3 40.3 1.0
CA B:THR319 4.3 40.7 1.0
CA B:ILE323 4.4 45.7 1.0
OD1 B:ASP320 4.4 59.1 1.0
CG2 B:ILE323 4.5 74.5 1.0
CB B:GLN322 4.5 46.3 1.0
CA B:LYS317 4.6 37.4 1.0
N B:TYR318 4.6 43.8 1.0
C B:TYR318 4.7 45.2 1.0
C B:ASP320 4.8 44.5 1.0
N B:LYS317 4.9 38.0 1.0
CA B:TYR318 5.0 43.6 1.0

Magnesium binding site 4 out of 6 in 4kpe

Go back to Magnesium Binding Sites List in 4kpe
Magnesium binding site 4 out of 6 in the Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:64.5
occ:1.00
 O09 H:AF5101 2.0 83.5 1.0
O11 H:AF5101 2.0 90.7 1.0
C07 H:AF5101 3.0 82.2 1.0
C10 H:AF5101 3.0 92.8 1.0
C06 H:AF5101 3.3 91.5 1.0
OG B:SER79 3.9 62.2 1.0
O4 G:DT15 4.0 50.9 1.0
O08 H:AF5101 4.1 72.5 1.0
H271 H:AF5101 4.2 0.7 1.0
C12 H:AF5101 4.2 93.1 1.0
OD2 B:ASP83 4.5 58.2 1.0
C27 H:AF5101 4.6 88.9 1.0
CB B:SER79 4.7 57.5 1.0
C05 H:AF5101 4.7 95.6 1.0
N6 H:DA5 4.8 58.5 1.0
N6 F:DA1 4.9 67.1 1.0

Magnesium binding site 5 out of 6 in 4kpe

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Magnesium binding site 5 out of 6 in the Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:59.7
occ:1.00
 OD2 C:ASP508 2.0 89.2 1.0
OD2 C:ASP506 2.8 94.7 1.0
CG C:ASP508 3.1 83.8 1.0
OD1 C:ASP508 3.5 83.5 1.0
CG C:ASP506 3.7 91.2 1.0
OP1 E:DT15 3.8 56.0 1.0
CB C:ASP506 4.0 81.1 1.0
OE1 C:GLU433 4.0 73.1 1.0
C5' E:DT15 4.2 57.1 1.0
CB C:ASP508 4.4 78.6 1.0
O C:LYS581 4.7 90.9 1.0
OD1 C:ASP506 4.8 93.1 1.0
CD C:GLU433 4.9 74.9 1.0

Magnesium binding site 6 out of 6 in 4kpe

Go back to Magnesium Binding Sites List in 4kpe
Magnesium binding site 6 out of 6 in the Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:52.8
occ:1.00
 OD2 D:ASP508 2.0 93.5 1.0
OD2 D:ASP506 2.9 96.0 1.0
CG D:ASP508 3.1 94.7 1.0
OD1 D:ASP508 3.5 94.9 1.0
OP1 G:DT15 3.6 59.0 1.0
CG D:ASP506 3.9 95.2 1.0
OE1 D:GLU433 4.2 77.3 1.0
CB D:ASP506 4.2 85.0 1.0
C5' G:DT15 4.3 55.7 1.0
CB D:ASP508 4.4 94.8 1.0
NH2 A:ARG117 4.7 42.5 0.5
P G:DT15 4.9 55.2 1.0
OD1 D:ASP506 5.0 99.9 1.0

Reference:

I.Laponogov, X.-S.Pan, D.A.Vesekov, R.T.Cirz, A.S.Wagman, H.E.Moser, L.M.Fisher, M.R.Sanderson. Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate To Be Published.
Page generated: Mon Aug 11 17:46:33 2025

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