Magnesium in PDB 4gfh: Topoisomerase II-Dna-Amppnp Complex

All present enzymatic activity of Topoisomerase II-Dna-Amppnp Complex:
5.99.1.3;

The structure of Topoisomerase II-Dna-Amppnp Complex, PDB code: 4gfh was solved by B.H.Schmidt, N.Osheroff, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.99 / 4.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	169.135, 169.884, 169.212, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 27.5

The binding sites of Magnesium atom in the Topoisomerase II-Dna-Amppnp Complex (pdb code 4gfh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Topoisomerase II-Dna-Amppnp Complex, PDB code: 4gfh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Topoisomerase II-Dna-Amppnp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Topoisomerase II-Dna-Amppnp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:1.0 occ:1.00 O1B A:ANP1202 2.2 0.9 1.0 O2G A:ANP1202 2.4 0.7 1.0 O1A A:ANP1202 2.5 0.7 1.0 OD1 A:ASN70 2.7 0.2 1.0 CG A:ASN70 3.2 0.8 1.0 ND2 A:ASN70 3.4 0.7 1.0 O1G A:ANP1202 3.4 0.1 1.0 PG A:ANP1202 3.4 0.2 1.0 PB A:ANP1202 3.5 0.2 1.0 O A:GLU66 3.6 0.8 1.0 OE1 A:GLU66 3.8 0.3 1.0 PA A:ANP1202 3.8 1.0 1.0 N3B A:ANP1202 4.1 0.3 1.0 O3A A:ANP1202 4.1 0.8 1.0 OD2 A:ASP73 4.2 0.7 1.0 CB A:ASN70 4.3 0.9 1.0 N A:ASN70 4.3 0.7 1.0 CA A:ASN70 4.4 0.4 1.0 CA A:GLY140 4.4 0.9 1.0 CA A:GLY145 4.5 0.2 1.0 NZ A:LYS367 4.5 0.5 1.0 O5' A:ANP1202 4.6 0.6 1.0 C A:GLU66 4.7 0.9 1.0 O2B A:ANP1202 4.7 0.2 1.0 CG1 A:VAL69 4.7 0.3 1.0 O3G A:ANP1202 4.7 0.4 1.0 C A:VAL69 4.7 0.9 1.0 N A:GLY140 4.8 0.0 1.0 CB A:VAL69 4.8 0.6 1.0 N A:GLY145 4.8 0.0 1.0 O2A A:ANP1202 4.8 0.2 1.0 N A:ALA146 4.9 0.8 1.0 CA A:GLU66 4.9 0.9 1.0 C A:GLY145 5.0 1.0 1.0

Magnesium binding site 2 out of 2 in the Topoisomerase II-Dna-Amppnp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Topoisomerase II-Dna-Amppnp Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1201 b:0.7 occ:1.00 O1B F:ANP1202 2.3 0.1 1.0 O1A F:ANP1202 2.4 0.9 1.0 O2G F:ANP1202 2.6 0.1 1.0 OD1 F:ASN70 2.7 0.5 1.0 CG F:ASN70 3.1 1.0 1.0 ND2 F:ASN70 3.2 0.5 1.0 O1G F:ANP1202 3.4 0.8 1.0 PG F:ANP1202 3.5 0.5 1.0 O F:GLU66 3.5 0.2 1.0 PB F:ANP1202 3.6 0.8 1.0 OE1 F:GLU66 3.7 0.9 1.0 PA F:ANP1202 3.7 0.2 1.0 O3A F:ANP1202 4.1 0.1 1.0 N3B F:ANP1202 4.2 0.2 1.0 CB F:ASN70 4.2 0.9 1.0 CA F:GLY145 4.3 0.8 1.0 N F:ASN70 4.4 0.9 1.0 OD2 F:ASP73 4.4 0.1 1.0 CA F:ASN70 4.4 0.8 1.0 C F:GLU66 4.5 0.3 1.0 O5' F:ANP1202 4.6 0.5 1.0 CA F:GLY140 4.6 0.6 1.0 N F:GLY145 4.6 0.1 1.0 NZ F:LYS367 4.7 0.1 1.0 N F:ALA146 4.7 0.8 1.0 O2A F:ANP1202 4.7 0.4 1.0 CA F:GLU66 4.7 0.0 1.0 C F:GLY145 4.8 0.2 1.0 O3G F:ANP1202 4.8 0.0 1.0 O2B F:ANP1202 4.8 0.2 1.0 CG1 F:VAL69 4.8 0.1 1.0 C F:VAL69 4.8 0.7 1.0 CB F:VAL69 4.8 0.2 1.0 CD F:GLU66 4.9 0.9 1.0 CB F:GLU66 5.0 1.0 1.0

B.H.Schmidt, N.Osheroff, J.M.Berger. Structure of A Topoisomerase II-Dna-Nucleotide Complex Reveals A New Control Mechanism For Atpase Activity. Nat.Struct.Mol.Biol. V. 19 1147 2012.
ISSN: ISSN 1545-9993
PubMed: 23022727
DOI: 10.1038/NSMB.2388