Magnesium in PDB 3ksb: Detailed Structural Insight Into the Dna Cleavage Complex of Type Iia Topoisomerases (Re-Sealed Form)

The structure of Detailed Structural Insight Into the Dna Cleavage Complex of Type Iia Topoisomerases (Re-Sealed Form), PDB code: 3ksb 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)	29.32 / 3.50
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	116.757, 116.757, 182.811, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 22.6

The binding sites of Magnesium atom in the Detailed Structural Insight Into the Dna Cleavage Complex of Type Iia Topoisomerases (Re-Sealed Form) (pdb code 3ksb). 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 (Re-Sealed Form), PDB code: 3ksb:
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 (Re-Sealed 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 (Re-Sealed Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg742 b:0.1 occ:1.00 OD2 C:ASP506 2.2 0.3 1.0 OE1 C:GLU433 2.6 0.5 1.0 CG C:ASP506 2.6 0.6 1.0 OP1 E:DG16 2.7 0.3 1.0 CB C:ASP506 2.9 0.7 1.0 CD C:GLU433 3.2 0.2 1.0 O3' E:DT15 3.4 0.4 1.0 OD1 C:ASP506 3.5 0.4 1.0 OE2 C:GLU433 3.6 1.0 1.0 P E:DG16 3.7 0.6 1.0 OD2 C:ASP508 3.9 0.2 1.0 CG C:GLU433 4.2 0.6 1.0 CA C:ASP506 4.3 0.2 1.0 C5' E:DG16 4.4 0.7 1.0 CA C:GLY582 4.4 0.3 1.0 OH B:TYR118 4.4 0.8 1.0 O C:LYS581 4.4 0.5 1.0 O5' E:DG16 4.5 88.5 1.0 N C:ASP506 4.7 0.9 1.0 CB C:GLU433 4.7 0.3 1.0 C3' E:DT15 4.7 0.4 1.0 CE1 B:TYR118 4.9 0.0 1.0 CG C:ASP508 4.9 0.8 1.0 OP2 E:DG16 4.9 0.1 1.0

Magnesium binding site 2 out of 2 in the Detailed Structural Insight Into the Dna Cleavage Complex of Type Iia Topoisomerases (Re-Sealed 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 (Re-Sealed Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg742 b:0.8 occ:1.00 OD2 D:ASP506 2.1 0.6 1.0 CG D:ASP506 2.4 0.6 1.0 OE1 D:GLU433 2.4 0.7 1.0 CB D:ASP506 2.7 0.2 1.0 OP1 F:DA16 2.7 0.4 1.0 CD D:GLU433 3.0 0.6 1.0 OD1 D:ASP506 3.2 0.4 1.0 OE2 D:GLU433 3.3 0.3 1.0 O3' F:DT15 3.6 0.9 1.0 P F:DA16 3.8 0.1 1.0 OD2 D:ASP508 4.0 0.5 1.0 CG D:GLU433 4.0 0.3 1.0 CA D:ASP506 4.1 0.8 1.0 CA D:GLY582 4.4 0.8 1.0 N D:ASP506 4.4 0.2 1.0 CB D:GLU433 4.5 0.6 1.0 OH A:TYR118 4.6 0.2 1.0 C5' F:DA16 4.6 0.9 1.0 O D:LYS581 4.6 0.1 1.0 O5' F:DA16 4.7 90.8 1.0 CG D:ASP508 4.9 0.5 1.0 C3' F:DT15 5.0 0.7 1.0 OP2 F:DA16 5.0 0.0 1.0 OD1 D:ASP508 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