Magnesium in PDB 3raf: Quinazolinedione-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae

The structure of Quinazolinedione-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae, PDB code: 3raf 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)	114.98 / 3.24
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	158.550, 158.550, 210.330, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 20.6

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

Fluorine

(F)

2 atoms

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

Magnesium binding site 1 out of 4 in the Quinazolinedione-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 Quinazolinedione-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg700 b:41.8 occ:1.00 O A:GLN322 2.0 40.7 1.0 O A:THR319 2.1 47.6 1.0 O A:PHE316 2.8 30.1 1.0 C A:GLN322 3.3 31.5 1.0 C A:THR319 3.3 37.0 1.0 O A:LYS317 3.4 32.6 1.0 C A:LYS317 3.9 31.4 1.0 C A:PHE316 3.9 30.6 1.0 N A:THR319 4.1 27.7 1.0 N A:GLN322 4.1 32.0 1.0 CA A:GLN322 4.2 29.8 1.0 N A:ASP320 4.2 36.9 1.0 CA A:ASP320 4.2 35.0 1.0 N A:ILE323 4.2 21.9 1.0 CA A:THR319 4.3 27.4 1.0 CA A:LYS317 4.3 29.1 1.0 CA A:ILE323 4.4 24.7 1.0 CB A:GLN322 4.5 32.4 1.0 OD1 A:ASP320 4.5 48.2 1.0 N A:LYS317 4.5 29.9 1.0 N A:TYR318 4.5 29.1 1.0 O A:LEU315 4.7 37.4 1.0 C A:ASP320 4.8 34.6 1.0 C A:TYR318 4.8 27.0 1.0 CA A:PHE316 5.0 27.8 1.0 CG A:GLN322 5.0 37.8 1.0

Magnesium binding site 2 out of 4 in the Quinazolinedione-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 Quinazolinedione-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg700 b:42.0 occ:1.00 O B:GLN322 2.0 47.2 1.0 O B:THR319 2.0 44.5 1.0 O B:PHE316 2.9 34.5 1.0 C B:GLN322 3.3 37.5 1.0 C B:THR319 3.3 40.3 1.0 O B:LYS317 3.6 38.5 1.0 C B:LYS317 4.1 35.2 1.0 N B:THR319 4.1 36.6 1.0 C B:PHE316 4.1 31.6 1.0 CA B:GLN322 4.2 37.0 1.0 N B:ASP320 4.2 41.5 1.0 N B:GLN322 4.2 34.7 1.0 N B:ILE323 4.3 28.3 1.0 CA B:ASP320 4.3 44.4 1.0 CA B:THR319 4.3 36.0 1.0 OD1 B:ASP320 4.4 55.1 1.0 CB B:GLN322 4.4 38.8 1.0 CA B:ILE323 4.5 33.3 1.0 N B:TYR318 4.6 34.8 1.0 CG2 B:ILE323 4.6 41.6 1.0 CA B:LYS317 4.7 31.3 1.0 C B:TYR318 4.7 34.2 1.0 CG B:GLN322 4.8 40.2 1.0 O B:LEU315 4.9 48.5 1.0 N B:LYS317 4.9 30.3 1.0 C B:ASP320 4.9 44.7 1.0 CA B:TYR318 5.0 35.0 1.0

Magnesium binding site 3 out of 4 in the Quinazolinedione-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 Quinazolinedione-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg742 b:33.9 occ:1.00 OD2 C:ASP508 2.0 58.8 1.0 OD2 C:ASP506 2.6 65.4 1.0 CG C:ASP508 3.1 60.6 1.0 OD1 C:ASP508 3.5 61.1 1.0 CG C:ASP506 3.6 60.2 1.0 CB C:ASP506 4.0 48.7 1.0 OP1 E:DT15 4.0 41.7 1.0 OE1 C:GLU433 4.1 48.6 1.0 O H:HOH744 4.4 36.3 1.0 CB C:ASP508 4.4 24.6 1.0 O C:LYS581 4.4 48.7 1.0 OD1 C:ASP506 4.7 60.9 1.0 C5' E:DT15 4.7 38.1 1.0 O5' E:DT15 5.0 38.0 1.0

Magnesium binding site 4 out of 4 in the Quinazolinedione-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 Quinazolinedione-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg742 b:23.4 occ:1.00 OD2 D:ASP508 2.0 65.7 1.0 OD2 D:ASP506 2.7 69.6 1.0 CG D:ASP508 3.1 66.2 1.0 OD1 D:ASP508 3.6 66.8 1.0 CG D:ASP506 3.9 63.4 1.0 OP1 G:DT15 3.9 33.6 1.0 OE1 D:GLU433 4.2 61.6 1.0 CB D:ASP506 4.4 54.9 1.0 O D:LYS581 4.4 56.3 1.0 CB D:ASP508 4.4 49.3 1.0 C5' G:DT15 4.7 36.4 1.0 OD1 D:ASP506 4.9 62.2 1.0

I.Laponogov, X.-S.Pan, D.A.Veselkov, K.E.Mcauley, 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.