Atomistry » Magnesium » PDB 4knx-4kvi » 4kpe
Atomistry »
  Magnesium »
    PDB 4knx-4kvi »
      4kpe »

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

Go back to Magnesium Binding Sites List in 4kpe
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

Go back to Magnesium Binding Sites List in 4kpe
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

Go back to Magnesium Binding Sites List in 4kpe
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

Go back to Magnesium Binding Sites List in 4kpe
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: Sat Aug 17 03:53:00 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy