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Magnesium in PDB 3rae: Quinolone(Levofloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae

Protein crystallography data

The structure of Quinolone(Levofloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae, PDB code: 3rae was solved by I.Laponogov, X.-S.Pan, D.A.Veselkov, K.E.Mcauley, 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 / 2.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.831, 157.831, 211.147, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 22.6

Other elements in 3rae:

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

Fluorine (F) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Quinolone(Levofloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae (pdb code 3rae). 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(Levofloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae, PDB code: 3rae:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3rae

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Magnesium binding site 1 out of 6 in the Quinolone(Levofloxacin)-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(Levofloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:72.2
occ:1.00
 O A:GLN322 2.0 74.7 1.0
O A:THR319 2.0 84.2 1.0
O A:PHE316 2.7 60.0 1.0
C A:GLN322 3.3 59.9 1.0
C A:THR319 3.3 67.9 1.0
O A:LYS317 3.3 62.2 1.0
C A:LYS317 3.7 58.4 1.0
C A:PHE316 3.7 60.4 1.0
N A:THR319 4.0 58.3 1.0
CA A:LYS317 4.1 60.1 1.0
CA A:GLN322 4.2 55.7 1.0
N A:GLN322 4.2 56.1 1.0
N A:ASP320 4.2 68.2 1.0
CA A:ASP320 4.2 62.9 1.0
N A:ILE323 4.3 54.9 1.0
CA A:THR319 4.3 57.7 1.0
N A:LYS317 4.3 56.0 1.0
N A:TYR318 4.4 48.6 1.0
CB A:GLN322 4.4 55.2 1.0
CA A:ILE323 4.5 57.5 1.0
OD1 A:ASP320 4.5 74.6 1.0
O A:LEU315 4.7 60.6 1.0
C A:TYR318 4.8 63.9 1.0
C A:ASP320 4.8 61.6 1.0
CA A:PHE316 4.9 59.9 1.0
CG A:GLN322 4.9 60.2 1.0
CA A:TYR318 4.9 57.4 1.0
N A:LEU321 5.0 56.3 1.0

Magnesium binding site 2 out of 6 in 3rae

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Magnesium binding site 2 out of 6 in the Quinolone(Levofloxacin)-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(Levofloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:89.5
occ:1.00
 O03 F:LFX101 2.0 0.8 1.0
O02 F:LFX101 2.0 0.3 1.0
C15 F:LFX101 3.0 99.6 1.0
C F:LFX101 3.1 1.0 1.0
C17 F:LFX101 3.4 0.3 1.0
O4 E:DT15 3.5 69.6 1.0
O F:LFX101 4.2 0.7 1.0
OG A:SER79 4.3 82.5 1.0
CB A:SER79 4.3 70.0 1.0
C10 F:LFX101 4.3 91.4 1.0
N6 F:DA5 4.4 78.8 1.0
H13 F:LFX101 4.5 0.5 1.0
C4 E:DT15 4.7 72.5 1.0
C12 F:LFX101 4.7 91.7 1.0
OD2 A:ASP83 4.8 70.9 1.0
O6 H:DG1 4.9 0.9 1.0
C13 F:LFX101 4.9 84.5 1.0

Magnesium binding site 3 out of 6 in 3rae

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Magnesium binding site 3 out of 6 in the Quinolone(Levofloxacin)-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(Levofloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg700

b:70.8
occ:1.00
 O B:GLN322 2.0 86.3 1.0
O B:THR319 2.0 75.3 1.0
O B:PHE316 2.8 69.8 1.0
O B:LYS317 3.1 66.2 1.0
C B:GLN322 3.3 72.8 1.0
C B:THR319 3.3 66.0 1.0
C B:LYS317 3.7 66.2 1.0
C B:PHE316 3.9 65.2 1.0
N B:THR319 4.1 66.6 1.0
N B:ASP320 4.2 71.2 1.0
CA B:GLN322 4.2 66.5 1.0
CA B:ASP320 4.2 67.8 1.0
N B:GLN322 4.2 55.0 1.0
N B:ILE323 4.3 71.2 1.0
CA B:THR319 4.3 55.6 1.0
CA B:LYS317 4.3 69.7 1.0
CA B:ILE323 4.5 68.0 1.0
CB B:GLN322 4.5 77.1 1.0
N B:TYR318 4.5 64.9 1.0
OD1 B:ASP320 4.5 82.8 1.0
N B:LYS317 4.6 60.9 1.0
C B:TYR318 4.7 72.0 1.0
C B:ASP320 4.8 64.9 1.0
O B:LEU315 4.8 74.8 1.0
CA B:TYR318 4.9 67.2 1.0

Magnesium binding site 4 out of 6 in 3rae

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Magnesium binding site 4 out of 6 in the Quinolone(Levofloxacin)-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(Levofloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:98.1
occ:1.00
 OD2 C:ASP508 2.0 0.8 1.0
OD2 C:ASP506 2.6 0.4 1.0
CG C:ASP508 3.1 89.5 1.0
CG C:ASP506 3.5 0.5 1.0
OD1 C:ASP508 3.5 75.7 1.0
CB C:ASP506 3.9 87.0 1.0
O E:HOH101 3.9 66.9 1.0
OE1 C:GLU433 4.0 94.2 1.0
OP1 E:DT15 4.3 69.3 1.0
CB C:ASP508 4.4 82.5 1.0
OD1 C:ASP506 4.6 0.9 1.0
O C:LYS581 4.6 92.7 1.0
C5' E:DT15 4.8 72.0 1.0
CD C:GLU433 4.8 0.3 1.0
NH2 B:ARG117 4.8 44.8 0.5
O3' E:DT15 4.9 87.9 1.0
OE2 C:GLU433 5.0 0.9 1.0

Magnesium binding site 5 out of 6 in 3rae

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Magnesium binding site 5 out of 6 in the Quinolone(Levofloxacin)-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(Levofloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:72.8
occ:1.00
 OD2 D:ASP508 2.0 0.9 1.0
OD2 D:ASP506 2.5 0.8 1.0
CG D:ASP508 3.1 0.3 1.0
OD1 D:ASP508 3.5 99.2 1.0
CG D:ASP506 3.6 0.7 1.0
CB D:ASP506 4.1 95.1 1.0
OP1 G:DT15 4.1 68.9 1.0
O D:LYS581 4.3 0.3 1.0
CB D:ASP508 4.4 0.8 1.0
OE1 D:GLU433 4.4 0.4 1.0
NH2 A:ARG117 4.6 46.4 0.5
OD1 D:ASP506 4.7 0.9 1.0
O3' G:DT15 4.9 0.2 1.0
C5' G:DT15 5.0 63.6 1.0

Magnesium binding site 6 out of 6 in 3rae

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Magnesium binding site 6 out of 6 in the Quinolone(Levofloxacin)-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(Levofloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg101

b:0.5
occ:1.00
 O03 H:LFX101 2.0 0.9 1.0
O02 H:LFX101 2.0 0.4 1.0
C15 H:LFX101 2.9 0.9 1.0
C H:LFX101 3.0 0.2 1.0
C17 H:LFX101 3.3 0.6 1.0
O4 G:DT15 3.5 63.7 1.0
O H:LFX101 4.2 99.0 1.0
OG B:SER79 4.2 81.3 1.0
C10 H:LFX101 4.3 0.9 1.0
H13 H:LFX101 4.4 0.2 1.0
N6 H:DA5 4.4 79.9 1.0
CB B:SER79 4.5 71.7 1.0
C4 G:DT15 4.6 67.0 1.0
C12 H:LFX101 4.7 99.6 1.0
C13 H:LFX101 4.8 97.7 1.0
N6 F:DA1 4.8 89.0 1.0
C7 G:DT15 4.8 66.3 1.0
N6 G:DA14 5.0 56.9 1.0

Reference:

D.A.Veselkov, I.Laponogov, X.S.Pan, J.Selvarajah, G.B.Skamrova, A.Branstrom, J.Narasimhan, J.V.Prasad, L.M.Fisher, M.R.Sanderson. Structure of A Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae and Comparison with A Related Streptococcus Pneumoniae Complex. Acta Crystallogr.,Sect.D V. 72 488 2016.
ISSN: ISSN 0907-4449
PubMed: 27050128
DOI: 10.1107/S2059798316001212
Page generated: Thu Aug 15 10:21:57 2024

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