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Magnesium in PDB 4koe: Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae

Enzymatic activity of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae

All present enzymatic activity of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae:
5.99.1.3;

Protein crystallography data

The structure of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae, PDB code: 4koe was solved by I.Laponogov, X.-S.Pan, D.A.Veselkov, 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) 62.42 / 3.02
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.040, 158.040, 210.420, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 21

Other elements in 4koe:

The structure of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae (pdb code 4koe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae, PDB code: 4koe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4koe

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Magnesium binding site 1 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:82.0
occ:1.00
 O A:THR319 2.0 81.3 1.0
O A:GLN322 2.0 66.4 1.0
O A:PHE316 2.9 51.9 1.0
C A:THR319 3.3 56.9 1.0
C A:GLN322 3.3 51.5 1.0
O A:LYS317 3.4 62.7 1.0
C A:LYS317 3.9 58.2 1.0
CA A:ASP320 4.0 60.3 1.0
C A:PHE316 4.1 56.5 1.0
N A:ASP320 4.1 55.8 1.0
N A:THR319 4.1 51.4 1.0
OD1 A:ASP320 4.1 74.4 1.0
N A:GLN322 4.2 57.4 1.0
N A:ILE323 4.2 57.4 1.0
CA A:GLN322 4.2 53.5 1.0
CA A:THR319 4.3 44.0 1.0
CA A:ILE323 4.3 61.4 1.0
CA A:LYS317 4.5 61.0 1.0
CB A:GLN322 4.5 60.6 1.0
N A:TYR318 4.6 52.7 1.0
C A:ASP320 4.6 56.8 1.0
N A:LYS317 4.7 55.7 1.0
C A:TYR318 4.8 56.3 1.0
CG2 A:ILE323 4.8 61.0 1.0
O A:LEU315 4.8 53.4 1.0
N A:LEU321 4.9 55.1 1.0

Magnesium binding site 2 out of 6 in 4koe

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Magnesium binding site 2 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:74.4
occ:1.00
 O27 F:TR6101 2.0 0.8 1.0
O29 F:TR6101 2.0 90.2 1.0
C26 F:TR6101 3.0 0.5 1.0
C23 F:TR6101 3.0 83.1 1.0
C24 F:TR6101 3.4 86.2 1.0
O4 E:DT15 4.1 73.0 1.0
O28 F:TR6101 4.1 75.3 1.0
H211 F:TR6101 4.2 89.6 1.0
C22 F:TR6101 4.2 73.4 1.0
OG A:SER79 4.2 81.5 1.0
OD2 A:ASP83 4.3 74.6 1.0
O6 H:DG1 4.4 0.3 1.0
CB A:SER79 4.6 69.1 1.0
C21 F:TR6101 4.6 74.7 1.0
C25 F:TR6101 4.8 72.6 1.0
N6 F:DA5 4.9 63.7 1.0

Magnesium binding site 3 out of 6 in 4koe

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Magnesium binding site 3 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:90.8
occ:1.00
 O B:THR319 2.0 91.8 1.0
O B:GLN322 2.0 59.6 1.0
O B:PHE316 2.8 67.9 1.0
O B:LYS317 3.2 61.6 1.0
C B:GLN322 3.3 52.5 1.0
C B:THR319 3.3 61.9 1.0
C B:LYS317 3.9 56.8 1.0
C B:PHE316 4.0 56.6 1.0
CA B:ASP320 4.1 60.7 1.0
N B:ASP320 4.1 58.3 1.0
CA B:GLN322 4.1 48.4 1.0
N B:GLN322 4.1 56.7 1.0
N B:THR319 4.2 63.6 1.0
N B:ILE323 4.2 54.8 1.0
CA B:THR319 4.3 55.9 1.0
CB B:GLN322 4.3 58.9 1.0
CA B:LYS317 4.4 43.6 1.0
CA B:ILE323 4.5 66.7 1.0
OD1 B:ASP320 4.5 82.8 1.0
N B:LYS317 4.6 39.2 1.0
N B:TYR318 4.7 58.6 1.0
C B:ASP320 4.7 61.1 1.0
C B:TYR318 4.8 63.2 1.0
O B:LEU315 4.8 57.0 1.0
NE2 B:GLN322 4.9 69.0 1.0
N B:LEU321 4.9 62.0 1.0

Magnesium binding site 4 out of 6 in 4koe

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Magnesium binding site 4 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:74.0
occ:1.00
 O28 H:TR6101 2.0 98.8 1.0
O29 H:TR6101 2.0 82.7 1.0
C26 H:TR6101 3.0 84.5 1.0
C23 H:TR6101 3.0 81.1 1.0
C24 H:TR6101 3.4 82.3 1.0
O4 G:DT15 3.8 58.9 1.0
O27 H:TR6101 4.0 73.3 1.0
C22 H:TR6101 4.2 84.7 1.0
H211 H:TR6101 4.2 0.5 1.0
OG B:SER79 4.3 86.4 1.0
OD2 B:ASP83 4.3 75.8 1.0
CB B:SER79 4.5 65.1 1.0
N6 F:DA1 4.6 98.7 1.0
C21 H:TR6101 4.7 92.0 1.0
C25 H:TR6101 4.7 65.5 1.0
N6 H:DA5 4.8 65.0 1.0
C4 G:DT15 4.9 65.7 1.0
C7 G:DT15 4.9 68.4 1.0

Magnesium binding site 5 out of 6 in 4koe

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Magnesium binding site 5 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:59.4
occ:1.00
 OD2 C:ASP508 2.0 92.1 1.0
OD2 C:ASP506 2.6 98.2 1.0
CG C:ASP508 3.1 80.2 1.0
OD1 C:ASP508 3.5 69.6 1.0
CG C:ASP506 3.6 98.6 1.0
CB C:ASP506 4.0 82.2 1.0
OP1 E:DT15 4.2 70.9 1.0
O C:LYS581 4.2 89.7 1.0
OE1 C:GLU433 4.3 89.2 1.0
CB C:ASP508 4.4 77.4 1.0
OD1 C:ASP506 4.7 0.0 1.0
C5' E:DT15 4.9 76.2 1.0

Magnesium binding site 6 out of 6 in 4koe

Go back to Magnesium Binding Sites List in 4koe
Magnesium binding site 6 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:58.4
occ:1.00
 OD2 D:ASP508 2.0 0.8 1.0
OD2 D:ASP506 2.5 0.8 1.0
CG D:ASP508 3.1 87.9 1.0
CG D:ASP506 3.5 0.0 1.0
OD1 D:ASP508 3.5 75.1 1.0
CB D:ASP506 3.9 98.1 1.0
OP1 G:DT15 4.1 65.5 1.0
O D:LYS581 4.2 93.2 1.0
CB D:ASP508 4.4 78.3 1.0
OD1 D:ASP506 4.6 0.6 1.0
OE1 D:GLU433 4.7 91.5 1.0
C5' G:DT15 4.8 61.2 1.0

Reference:

I.Laponogov, X.-S.Pan, D.A.Veselkov, L.M.Fisher, M.R.Sanderson. Inhibitor-Stabilised Cleavage Complexes of Topoisomerase Iia: Structural Analysis of Drug-Dependent Inter- and Intramolecular Interactions To Be Published.
Page generated: Mon Aug 11 17:46:07 2025

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