Magnesium in PDB 9bq8: Human Topoisomerase 2 Beta Atpase Domain Bound to Non-Hydrolyzable Atp Analog Amppnp

All present enzymatic activity of Human Topoisomerase 2 Beta Atpase Domain Bound to Non-Hydrolyzable Atp Analog Amppnp:
5.6.2.2;

The structure of Human Topoisomerase 2 Beta Atpase Domain Bound to Non-Hydrolyzable Atp Analog Amppnp, PDB code: 9bq8 was solved by A.T.Q.Cong, C.A.Austin, J.Kubes, G.Karabanovich, I.Melnikova, O.Lencova, P.Kollarova, H.B.Piskackova, V.Kerestes, L.Applova, L.Arrouye, J.A.Alvey, J.Paluncic, T.L.Witter, A.Jirkovska, J.Kunes, P.Sterbova, M.Sterba, T.Simunek, J.Roh, M.J.Schellenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.33 / 1.25
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.766, 83.766, 127.108, 90, 90, 90
R / Rfree (%)	13 / 15.9

The binding sites of Magnesium atom in the Human Topoisomerase 2 Beta Atpase Domain Bound to Non-Hydrolyzable Atp Analog Amppnp (pdb code 9bq8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Human Topoisomerase 2 Beta Atpase Domain Bound to Non-Hydrolyzable Atp Analog Amppnp, PDB code: 9bq8:

Magnesium binding site 1 out of 1 in the Human Topoisomerase 2 Beta Atpase Domain Bound to Non-Hydrolyzable Atp Analog Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Topoisomerase 2 Beta Atpase Domain Bound to Non-Hydrolyzable Atp Analog Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:11.8 occ:1.00 O1G A:ANP701 2.0 12.0 1.0 O A:HOH851 2.0 12.2 1.0 OD1 A:ASN107 2.1 11.4 1.0 O1B A:ANP701 2.1 11.3 1.0 O2A A:ANP701 2.1 11.7 1.0 O A:HOH949 2.2 12.7 1.0 CG A:ASN107 3.1 11.3 1.0 HD21 A:ASN107 3.1 14.1 1.0 PB A:ANP701 3.1 11.8 1.0 PA A:ANP701 3.3 11.8 1.0 PG A:ANP701 3.3 11.6 1.0 ND2 A:ASN107 3.4 11.7 1.0 O3A A:ANP701 3.5 11.7 1.0 N3B A:ANP701 3.6 11.3 1.0 HA3 A:GLY182 3.7 14.4 1.0 HA2 A:GLY177 3.8 16.1 1.0 HA3 A:GLY177 3.8 16.1 1.0 HNB1 A:ANP701 3.9 13.5 1.0 O A:HOH993 4.0 18.2 1.0 O A:HOH924 4.1 15.4 1.0 O5' A:ANP701 4.1 12.2 1.0 H A:GLY182 4.1 13.7 1.0 OE1 A:GLU103 4.1 13.4 1.0 HA A:ASN107 4.2 12.3 1.0 O A:GLU103 4.3 11.1 1.0 O2G A:ANP701 4.3 11.8 1.0 CA A:GLY177 4.3 13.4 1.0 HD22 A:ASN107 4.3 14.1 1.0 H A:ALA183 4.4 14.4 1.0 O3G A:ANP701 4.4 11.8 1.0 CB A:ASN107 4.4 11.4 1.0 O2B A:ANP701 4.5 13.2 1.0 O1A A:ANP701 4.5 11.9 1.0 CA A:GLY182 4.5 12.0 1.0 H3' A:ANP701 4.6 15.2 1.0 HB3 A:GLU103 4.6 14.0 1.0 HZ2 A:LYS394 4.6 12.9 0.6 HZ1 A:LYS394 4.6 12.9 0.6 N A:GLY182 4.7 11.4 1.0 H A:ASN107 4.7 13.2 1.0 CA A:ASN107 4.7 10.2 1.0 OD2 A:ASP110 4.7 14.3 1.0 N A:ASN107 4.8 11.0 1.0 N A:ALA183 4.8 12.0 1.0 HG12 A:VAL106 4.9 14.6 1.0 HB2 A:ASN107 4.9 13.7 1.0 HA A:GLU103 4.9 12.4 1.0 HB3 A:ASN107 4.9 13.7 1.0

J.Kubes, G.Karabanovich, A.T.Q.Cong, I.Melnikova, O.Lencova, P.Kollarova, H.Bavlovic Piskackova, V.Kerestes, L.Applova, L.C.M.Arrouye, J.R.Alvey, J.Paluncic, T.L.Witter, A.Jirkovska, J.Kunes, P.Sterbova-Kovarikova, C.A.Austin, M.Sterba, T.Simunek, J.Roh, M.J.Schellenberg. Topobexin Targets the Topoisomerase II Atpase Domain For Beta Isoform-Selective Inhibition and Anthracycline Cardioprotection. Nat Commun V. 16 4928 2025.
ISSN: ESSN 2041-1723
PubMed: 40425539
DOI: 10.1038/S41467-025-60167-9