Magnesium in PDB 3k9f: Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases

The structure of Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases, PDB code: 3k9f 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)	26.73 / 2.90
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	122.407, 122.407, 178.287, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 21.8

The structure of Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Magnesium atom in the Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases (pdb code 3k9f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases, PDB code: 3k9f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg742 b:70.5 occ:1.00 OD2 C:ASP508 2.0 0.0 1.0 OD2 C:ASP506 2.6 77.4 1.0 CG C:ASP508 3.2 92.9 1.0 OD1 C:ASP508 3.5 85.7 1.0 CG C:ASP506 3.7 82.4 1.0 O C:LYS581 3.9 70.9 1.0 CB C:ASP506 4.0 88.4 1.0 OP1 E:DT15 4.1 83.3 1.0 CB C:ASP508 4.5 59.5 1.0 OE1 C:GLU433 4.6 80.9 1.0 C5' E:DT15 4.8 52.2 1.0 OD1 C:ASP506 4.8 81.4 1.0

Magnesium binding site 2 out of 2 in the Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg742 b:70.3 occ:1.00 OD2 D:ASP508 2.0 0.2 1.0 OD2 D:ASP506 2.6 79.8 1.0 CG D:ASP508 3.2 95.2 1.0 OD1 D:ASP508 3.5 83.5 1.0 CG D:ASP506 3.7 82.8 1.0 O D:LYS581 3.9 69.4 1.0 CB D:ASP506 4.0 88.8 1.0 OP1 G:DT15 4.3 74.6 1.0 CB D:ASP508 4.5 60.6 1.0 OE1 D:GLU433 4.6 85.6 1.0 C5' G:DT15 4.8 47.2 1.0 OD1 D:ASP506 4.8 83.9 1.0

I.Laponogov, X.-S.Pan, D.A.Veselkov, K.E.Mcauley, L.M.Fisher, M.R.Sanderson. Structural Basis of Gate-Dna Breakage and Resealing By Type II Topoisomerases Plos One V. 5 E1133 2010.
ISSN: ESSN 1932-6203
PubMed: 20596531
DOI: 10.1371/JOURNAL.PONE.0011338