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

The structure of Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate, PDB code: 4kpf 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)	41.83 / 3.24
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	157.860, 157.860, 210.780, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 18.4

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

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 4kpf). 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: 4kpf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

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:77.9 occ:1.00 O A:THR319 2.0 95.1 1.0 O A:GLN322 2.0 69.2 1.0 O A:PHE316 2.9 66.0 1.0 O A:LYS317 2.9 71.4 1.0 C A:GLN322 3.3 59.6 1.0 C A:THR319 3.3 82.2 1.0 C A:LYS317 3.7 70.0 1.0 C A:PHE316 3.9 68.1 1.0 N A:THR319 3.9 63.4 1.0 N A:ASP320 4.2 74.8 1.0 CA A:LYS317 4.2 69.0 1.0 CA A:GLN322 4.2 62.8 1.0 N A:ILE323 4.2 73.0 1.0 CA A:THR319 4.3 72.0 1.0 CA A:ASP320 4.3 76.5 1.0 N A:GLN322 4.3 72.6 1.0 CA A:ILE323 4.4 72.4 1.0 CB A:GLN322 4.5 63.7 1.0 N A:LYS317 4.5 69.0 1.0 N A:TYR318 4.5 65.6 1.0 OD1 A:ASP320 4.7 84.0 1.0 O A:LEU315 4.8 73.9 1.0 C A:TYR318 4.8 66.5 1.0 C A:ASP320 4.8 78.3 1.0 CA A:TYR318 5.0 65.4 1.0

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:0.6 occ:1.00 O08 H:1UV102 2.0 0.8 1.0 O11 H:1UV102 2.0 0.7 1.0 C07 H:1UV102 3.0 0.6 1.0 C10 H:1UV102 3.0 0.0 1.0 C06 H:1UV102 3.3 0.6 1.0 H271 H:1UV102 4.1 0.4 1.0 O09 H:1UV102 4.2 0.4 1.0 O4 E:DT15 4.2 89.6 1.0 C12 H:1UV102 4.2 0.7 1.0 OD2 A:ASP83 4.3 83.2 1.0 N6 F:DA5 4.6 98.3 1.0 C27 H:1UV102 4.6 1.0 1.0 OG A:SER79 4.7 0.5 1.0 C05 H:1UV102 4.7 0.1 1.0 O6 H:DG1 4.7 0.9 1.0 CB A:SER79 4.9 99.1 1.0

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:Mg700 b:92.0 occ:1.00 O B:THR319 2.0 93.7 1.0 O B:GLN322 2.0 84.1 1.0 O B:PHE316 2.8 82.0 1.0 O B:LYS317 3.0 74.1 1.0 C B:GLN322 3.3 72.5 1.0 C B:THR319 3.3 79.4 1.0 C B:LYS317 3.7 76.2 1.0 C B:PHE316 3.9 71.5 1.0 N B:THR319 4.1 75.6 1.0 CA B:ASP320 4.1 79.3 1.0 N B:ASP320 4.2 73.4 1.0 N B:GLN322 4.2 72.6 1.0 CA B:GLN322 4.2 73.0 1.0 N B:ILE323 4.3 76.3 1.0 CA B:LYS317 4.3 68.8 1.0 CA B:THR319 4.3 72.7 1.0 CA B:ILE323 4.4 77.2 1.0 OD1 B:ASP320 4.5 83.9 1.0 CB B:GLN322 4.5 80.2 1.0 N B:TYR318 4.6 82.2 1.0 N B:LYS317 4.6 63.9 1.0 C B:ASP320 4.7 81.6 1.0 C B:TYR318 4.8 77.5 1.0 O B:LEU315 4.8 85.2 1.0 CG B:GLN322 4.8 83.1 1.0 CG2 B:ILE323 4.9 78.7 1.0 N B:LEU321 5.0 84.1 1.0

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 C:Mg701 b:0.1 occ:1.00 OD2 C:ASP508 2.0 0.2 1.0 OD2 C:ASP506 2.6 0.8 1.0 CG C:ASP508 3.1 0.1 1.0 OD1 C:ASP508 3.5 0.1 1.0 CG C:ASP506 3.6 0.6 1.0 OP1 E:DT15 4.0 90.6 1.0 CB C:ASP506 4.0 0.8 1.0 OE1 C:GLU433 4.1 95.3 1.0 CB C:ASP508 4.4 0.6 1.0 O C:LYS581 4.6 0.7 1.0 OD1 C:ASP506 4.7 0.3 1.0 C5' E:DT15 4.7 82.5 1.0

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 D:Mg701 b:73.9 occ:1.00 OD2 D:ASP508 2.0 0.5 1.0 OD2 D:ASP506 2.9 0.8 1.0 CG D:ASP508 3.1 0.9 1.0 OD1 D:ASP508 3.5 0.1 1.0 OE1 D:GLU433 3.8 0.4 1.0 CG D:ASP506 3.8 1.0 1.0 OP1 G:DT15 3.9 90.8 1.0 CB D:ASP506 4.0 0.6 1.0 CB D:ASP508 4.4 0.9 1.0 C5' G:DT15 4.6 86.3 1.0 CD D:GLU433 4.8 0.5 1.0 O D:LYS581 4.8 0.6 1.0 OD1 D:ASP506 5.0 0.6 1.0

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 G:Mg100 b:0.7 occ:1.00 O08 H:1UV101 2.0 0.4 1.0 O11 H:1UV101 2.0 0.2 1.0 C10 H:1UV101 2.9 0.0 1.0 C07 H:1UV101 3.0 0.4 1.0 C06 H:1UV101 3.3 0.7 1.0 O4 G:DT15 3.8 74.2 1.0 O09 H:1UV101 4.1 0.8 1.0 C12 H:1UV101 4.2 0.8 1.0 H271 H:1UV101 4.2 0.0 1.0 OD2 B:ASP83 4.5 80.5 1.0 N6 H:DA5 4.5 88.8 1.0 C05 H:1UV101 4.6 0.0 1.0 C27 H:1UV101 4.6 0.2 1.0 OG B:SER79 4.8 0.0 1.0 N6 F:DA1 4.9 0.4 1.0 N6 G:DA14 4.9 79.1 1.0 C4 G:DT15 5.0 78.8 1.0

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.