Magnesium in PDB 3ksa: Detailed Structural Insight Into the Dna Cleavage Complex of Type Iia Topoisomerases (Cleaved Form)

The structure of Detailed Structural Insight Into the Dna Cleavage Complex of Type Iia Topoisomerases (Cleaved Form), PDB code: 3ksa 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)	29.40 / 3.30
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	116.911, 116.911, 183.759, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 21.8

The binding sites of Magnesium atom in the Detailed Structural Insight Into the Dna Cleavage Complex of Type Iia Topoisomerases (Cleaved Form) (pdb code 3ksa). 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 Dna Cleavage Complex of Type Iia Topoisomerases (Cleaved Form), PDB code: 3ksa:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Detailed Structural Insight Into the Dna Cleavage Complex of Type Iia Topoisomerases (Cleaved Form)


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 Dna Cleavage Complex of Type Iia Topoisomerases (Cleaved Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg742 b:0.5 occ:1.00 OE1 C:GLU433 2.8 0.5 1.0 OD2 C:ASP506 2.9 0.3 1.0 OP2 H:DG1 3.2 0.6 1.0 CB C:ASP506 3.2 0.6 1.0 OE2 C:GLU433 3.3 0.2 1.0 CG C:ASP506 3.4 0.1 1.0 O3' E:DT15 3.4 1.0 1.0 CD C:GLU433 3.4 0.9 1.0 OD2 C:ASP508 3.5 0.6 1.0 OD1 C:ASP508 3.8 0.1 1.0 C3' E:DT15 3.8 0.8 1.0 CG C:ASP508 4.1 0.5 1.0 OD1 C:ASP506 4.4 0.0 1.0 C4' E:DT15 4.5 0.2 1.0 CB C:ASP510 4.5 0.5 1.0 C5' E:DT15 4.6 0.4 1.0 P H:DG1 4.6 0.3 1.0 CA C:ASP506 4.6 0.1 1.0 N C:GLY511 4.8 0.3 1.0 CA C:GLY582 4.9 0.2 1.0 CG C:GLU433 4.9 0.9 1.0 N C:ASP506 5.0 0.4 1.0

Magnesium binding site 2 out of 2 in the Detailed Structural Insight Into the Dna Cleavage Complex of Type Iia Topoisomerases (Cleaved Form)


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 Dna Cleavage Complex of Type Iia Topoisomerases (Cleaved Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg742 b:0.2 occ:1.00 OE1 D:GLU433 2.6 0.9 1.0 OD2 D:ASP506 3.0 0.7 1.0 O3' G:DT15 3.0 0.2 1.0 OE2 D:GLU433 3.0 0.3 1.0 CD D:GLU433 3.2 0.2 1.0 OP2 F:DA1 3.2 0.3 1.0 CB D:ASP506 3.3 0.4 1.0 CG D:ASP506 3.3 1.0 1.0 OD2 D:ASP508 3.8 0.7 1.0 OD1 D:ASP508 4.0 0.9 1.0 C3' G:DT15 4.2 0.9 1.0 CG D:ASP508 4.3 0.8 1.0 OD1 D:ASP506 4.3 0.6 1.0 C4' G:DT15 4.4 0.6 1.0 C5' G:DT15 4.5 0.0 1.0 P F:DA1 4.6 0.5 1.0 CB D:ASP510 4.6 0.5 1.0 CA D:ASP506 4.6 0.1 1.0 CG D:GLU433 4.7 0.5 1.0 N D:GLY511 4.7 0.9 1.0 N D:ASP506 4.9 0.9 1.0 C5' F:DA1 5.0 0.6 1.0 O5' F:DA1 5.0 0.6 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