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

Protein crystallography data

The structure of Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae, PDB code: 3rad 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) 41.67 / 3.35
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.128, 157.128, 211.091, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 22.8

Other elements in 3rad:

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

Fluorine (F) 2 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 6 in 3rad

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

b:87.4
occ:1.00
 O A:GLN322 2.0 82.2 1.0
O A:THR319 2.0 0.0 1.0
O A:PHE316 2.9 85.1 1.0
O A:LYS317 3.3 81.7 1.0
C A:GLN322 3.3 68.0 1.0
C A:THR319 3.3 87.3 1.0
C A:LYS317 3.9 75.2 1.0
C A:PHE316 4.0 63.4 1.0
N A:THR319 4.1 77.5 1.0
CG A:GLN322 4.1 97.6 1.0
N A:ILE323 4.2 70.4 1.0
N A:ASP320 4.2 98.7 1.0
CA A:GLN322 4.2 65.6 1.0
CA A:ILE323 4.3 70.5 1.0
CA A:ASP320 4.3 0.4 1.0
N A:GLN322 4.3 75.5 1.0
CA A:THR319 4.3 73.6 1.0
CA A:LYS317 4.4 91.5 1.0
OD1 A:ASP320 4.5 92.2 1.0
CB A:GLN322 4.6 83.7 1.0
N A:TYR318 4.6 71.7 1.0
N A:LYS317 4.7 73.8 1.0
CG2 A:ILE323 4.8 70.6 1.0
C A:TYR318 4.8 83.2 1.0
C A:ASP320 4.9 90.7 1.0
O A:LEU315 4.9 87.0 1.0

Magnesium binding site 2 out of 6 in 3rad

Go back to Magnesium Binding Sites List in 3rad
Magnesium binding site 2 out of 6 in the Quinolone(Clinafloxacin)-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(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:0.7
occ:1.00
 O03 F:NFX101 2.0 0.4 1.0
O02 F:NFX101 2.0 0.3 1.0
C19 F:NFX101 2.9 0.9 1.0
C20 F:NFX101 2.9 1.0 1.0
C18 F:NFX101 3.3 0.2 1.0
O4 E:DT15 3.7 0.9 1.0
O F:NFX101 4.2 0.2 1.0
C14 F:NFX101 4.3 0.9 1.0
H17 F:NFX101 4.4 0.9 1.0
N6 F:DA5 4.4 0.9 1.0
CB A:SER79 4.5 76.5 1.0
O6 H:DG1 4.5 0.5 1.0
C16 F:NFX101 4.6 0.5 1.0
OG A:SER79 4.6 0.4 1.0
OD2 A:ASP83 4.7 86.6 1.0
N6 E:DA14 4.7 0.4 1.0
C17 F:NFX101 4.8 0.3 1.0
C4 E:DT15 4.8 0.3 1.0

Magnesium binding site 3 out of 6 in 3rad

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Magnesium binding site 3 out of 6 in the Quinolone(Clinafloxacin)-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(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:0.5
occ:1.00
 O B:GLN322 2.0 99.0 1.0
O B:THR319 2.0 0.9 1.0
O B:PHE316 2.9 91.5 1.0
C B:GLN322 3.3 80.6 1.0
C B:THR319 3.3 90.7 1.0
O B:LYS317 3.3 77.3 1.0
C B:LYS317 4.0 76.9 1.0
C B:PHE316 4.0 76.9 1.0
CA B:ASP320 4.1 96.1 1.0
N B:ASP320 4.1 97.6 1.0
N B:GLN322 4.2 82.8 1.0
N B:THR319 4.2 76.6 1.0
N B:ILE323 4.2 68.7 1.0
CA B:GLN322 4.2 67.5 1.0
CA B:ILE323 4.3 63.8 1.0
CA B:THR319 4.3 76.4 1.0
CA B:LYS317 4.6 92.4 1.0
CB B:GLN322 4.6 86.0 1.0
C B:ASP320 4.7 85.6 1.0
N B:TYR318 4.7 92.3 1.0
OD1 B:ASP320 4.7 96.8 1.0
N B:LEU321 4.8 70.9 1.0
CG2 B:ILE323 4.8 74.5 1.0
N B:LYS317 4.8 77.8 1.0
C B:TYR318 4.9 82.7 1.0
NE2 B:GLN322 4.9 92.7 1.0
O B:LEU315 4.9 96.9 1.0

Magnesium binding site 4 out of 6 in 3rad

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Magnesium binding site 4 out of 6 in the Quinolone(Clinafloxacin)-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(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:0.1
occ:1.00
 O02 H:NFX101 2.0 0.5 1.0
O03 H:NFX101 2.2 0.8 1.0
C19 H:NFX101 3.0 0.8 1.0
C20 H:NFX101 3.1 0.2 1.0
C18 H:NFX101 3.4 0.1 1.0
O H:NFX101 4.3 0.9 1.0
CB B:SER79 4.3 81.9 1.0
H17 H:NFX101 4.3 0.2 1.0
C14 H:NFX101 4.4 0.1 1.0
O4 G:DT15 4.4 75.1 1.0
OG B:SER79 4.7 0.1 1.0
N6 F:DA1 4.7 0.9 1.0
OD2 B:ASP83 4.7 83.8 1.0
C16 H:NFX101 4.8 0.8 1.0
C17 H:NFX101 4.8 0.6 1.0

Magnesium binding site 5 out of 6 in 3rad

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

b:87.9
occ:1.00
 OD2 C:ASP508 2.0 0.9 1.0
OD2 C:ASP506 2.6 0.9 1.0
CG C:ASP508 3.2 0.3 1.0
OD1 C:ASP508 3.6 0.8 1.0
CG C:ASP506 3.6 0.6 1.0
OP1 E:DT15 4.0 89.6 1.0
OE1 C:GLU433 4.1 0.4 1.0
CB C:ASP506 4.1 0.9 1.0
CB C:ASP508 4.4 0.3 1.0
C5' E:DT15 4.5 99.9 1.0
OD1 C:ASP506 4.7 0.0 1.0
O C:LYS581 4.7 0.7 1.0

Magnesium binding site 6 out of 6 in 3rad

Go back to Magnesium Binding Sites List in 3rad
Magnesium binding site 6 out of 6 in the Quinolone(Clinafloxacin)-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(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:78.4
occ:1.00
 OD2 D:ASP508 2.0 0.5 1.0
OD2 D:ASP506 2.9 0.7 1.0
CG D:ASP508 3.1 0.3 1.0
OD1 D:ASP508 3.5 0.7 1.0
OP1 G:DT15 3.8 85.7 1.0
CG D:ASP506 3.9 0.3 1.0
O D:LYS581 4.2 0.5 1.0
CB D:ASP506 4.2 0.3 1.0
CB D:ASP508 4.4 0.9 1.0
C5' G:DT15 4.4 94.7 1.0
OE1 D:GLU433 4.5 0.2 1.0
OD1 D:ASP506 4.9 0.1 1.0

Reference:

I.Laponogov, X.S.Pan, D.A.Veselkov, R.T.Cirz, A.Wagman, H.E.Moser, L.M.Fisher, M.R.Sanderson. Exploring the Active Site of the Streptococcus Pneumoniae Topoisomerase IV-Dna Cleavage Complex with Novel 7,8-Bridged Fluoroquinolones. Open Biol V. 6 2016.
ISSN: ESSN 2046-2441
PubMed: 27655731
DOI: 10.1098/RSOB.160157
Page generated: Thu Aug 15 10:21:53 2024

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