Magnesium in PDB 1zxm: Human Topo Iia Atpase/Amp-Pnp

All present enzymatic activity of Human Topo Iia Atpase/Amp-Pnp:
5.99.1.3;

The structure of Human Topo Iia Atpase/Amp-Pnp, PDB code: 1zxm was solved by H.Wei, A.J.Ruthenburg, S.K.Bechis, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.772, 75.285, 164.887, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 24.3

The binding sites of Magnesium atom in the Human Topo Iia Atpase/Amp-Pnp (pdb code 1zxm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Topo Iia Atpase/Amp-Pnp, PDB code: 1zxm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Topo Iia Atpase/Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Topo Iia Atpase/Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:20.5 occ:1.00 O A:HOH928 2.0 17.3 1.0 O1G A:ANP901 2.0 20.6 1.0 O1B A:ANP901 2.0 21.6 1.0 OD1 A:ASN91 2.0 17.2 1.0 O A:HOH927 2.3 19.4 1.0 O1A A:ANP901 2.4 27.5 1.0 CG A:ASN91 3.0 21.8 1.0 PB A:ANP901 3.1 22.8 1.0 PG A:ANP901 3.3 22.5 1.0 ND2 A:ASN91 3.3 19.9 1.0 PA A:ANP901 3.5 25.1 1.0 O3A A:ANP901 3.5 25.9 1.0 N3B A:ANP901 3.7 20.2 1.0 O A:HOH992 4.0 21.5 1.0 O A:HOH948 4.1 30.5 1.0 OE2 A:GLU87 4.2 20.4 1.0 O A:GLU87 4.2 19.6 1.0 CA A:GLY161 4.3 21.9 1.0 CA A:GLY166 4.3 20.4 1.0 O3G A:ANP901 4.3 22.2 1.0 O2G A:ANP901 4.4 22.8 1.0 CB A:ASN91 4.4 19.6 1.0 O2B A:ANP901 4.4 22.1 1.0 O2A A:ANP901 4.5 28.1 1.0 OD2 A:ASP94 4.7 29.8 1.0 N A:ALA167 4.7 18.1 1.0 CA A:ASN91 4.7 19.5 1.0 N A:GLY166 4.7 22.2 1.0 O5' A:ANP901 4.8 35.3 1.0 N A:ASN91 4.9 19.8 1.0 C A:GLY166 4.9 19.1 1.0

Magnesium binding site 2 out of 2 in the Human Topo Iia Atpase/Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Topo Iia Atpase/Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg904 b:20.6 occ:1.00 O1B B:ANP902 2.0 24.7 1.0 O1G B:ANP902 2.0 23.2 1.0 O B:HOH923 2.0 18.6 1.0 O B:HOH922 2.1 21.3 1.0 OD1 B:ASN91 2.2 19.4 1.0 O1A B:ANP902 2.6 32.8 1.0 PB B:ANP902 3.1 26.0 1.0 CG B:ASN91 3.1 22.2 1.0 PG B:ANP902 3.3 25.0 1.0 ND2 B:ASN91 3.5 20.1 1.0 O3A B:ANP902 3.5 27.7 1.0 PA B:ANP902 3.6 28.2 1.0 N3B B:ANP902 3.7 23.2 1.0 O B:HOH915 4.0 20.6 1.0 O B:HOH926 4.0 31.0 1.0 OE1 B:GLU87 4.1 21.9 1.0 O B:GLU87 4.3 19.4 1.0 O2G B:ANP902 4.3 23.5 1.0 CA B:GLY166 4.3 23.9 1.0 O3G B:ANP902 4.3 24.9 1.0 CA B:GLY161 4.4 23.4 1.0 O2B B:ANP902 4.4 23.1 1.0 O2A B:ANP902 4.4 30.4 1.0 OD2 B:ASP94 4.4 25.6 1.0 CB B:ASN91 4.5 20.0 1.0 N B:ALA167 4.7 22.4 1.0 N B:GLY166 4.8 24.7 1.0 CA B:ASN91 4.8 20.0 1.0 NZ B:LYS378 4.9 27.7 1.0 O5' B:ANP902 4.9 35.3 1.0 N B:ASN91 4.9 20.6 1.0 C B:GLY166 5.0 23.5 1.0

H.Wei, A.J.Ruthenburg, S.K.Bechis, G.L.Verdine. Nucleotide-Dependent Domain Movement in the Atpase Domain of A Human Type Iia Dna Topoisomerase. J.Biol.Chem. V. 280 37041 2005.
ISSN: ISSN 0021-9258
PubMed: 16100112
DOI: 10.1074/JBC.M506520200