Magnesium in PDB 9bq6: Human Topoisomerase 2 Alpha Atpase Domain Bound to Non-Hydrolyzable Atp Analog Amppnp

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

The structure of Human Topoisomerase 2 Alpha Atpase Domain Bound to Non-Hydrolyzable Atp Analog Amppnp, PDB code: 9bq6 was solved by J.Paluncic, T.L.Witter, J.Kubes, G.Karabanovich, A.T.Q.Cong, I.Melnikova, O.Lencova, P.Kollarova, H.B.Piskackova, V.Kerestes, L.Applova, L.Arrouye, J.A.Alvey, A.Jirkovska, J.Kunes, C.A.Austin, 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)	46.65 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.781, 92.699, 125.464, 90, 90, 90
R / Rfree (%)	17.6 / 19.6

The binding sites of Magnesium atom in the Human Topoisomerase 2 Alpha Atpase Domain Bound to Non-Hydrolyzable Atp Analog Amppnp (pdb code 9bq6). 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 Topoisomerase 2 Alpha Atpase Domain Bound to Non-Hydrolyzable Atp Analog Amppnp, PDB code: 9bq6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Topoisomerase 2 Alpha 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 Alpha Atpase Domain Bound to Non-Hydrolyzable Atp Analog Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:27.8 occ:1.00 O1G A:ANP901 2.0 25.3 1.0 O1B A:ANP901 2.1 21.4 1.0 O1A A:ANP901 2.1 26.2 1.0 OD1 A:ASN91 2.1 26.9 1.0 O A:HOH1110 2.2 24.3 1.0 O A:HOH1013 2.2 23.3 1.0 PB A:ANP901 3.1 28.7 1.0 HD21 A:ASN91 3.1 35.7 1.0 CG A:ASN91 3.1 29.4 1.0 PA A:ANP901 3.2 28.9 1.0 PG A:ANP901 3.3 27.1 1.0 O3A A:ANP901 3.4 29.3 1.0 ND2 A:ASN91 3.5 29.7 1.0 HA3 A:GLY166 3.5 34.9 1.0 N3B A:ANP901 3.6 27.1 1.0 HA2 A:GLY161 3.8 39.5 1.0 HNB1 A:ANP901 3.9 32.5 1.0 O A:HOH1072 3.9 26.7 1.0 HA3 A:GLY161 4.0 39.5 1.0 O5' A:ANP901 4.0 33.7 1.0 O A:HOH1054 4.0 34.1 1.0 H A:GLY166 4.1 32.8 1.0 OE1 A:GLU87 4.1 28.4 1.0 H A:ALA167 4.2 31.2 1.0 O3G A:ANP901 4.2 23.4 1.0 HZ1 A:LYS378 4.3 40.5 1.0 O A:GLU87 4.3 26.8 1.0 HA A:ASN91 4.3 36.6 1.0 O2G A:ANP901 4.3 27.4 1.0 HD22 A:ASN91 4.3 35.7 1.0 CA A:GLY161 4.3 32.9 1.0 CA A:GLY166 4.4 29.1 1.0 O2B A:ANP901 4.5 30.1 1.0 O2A A:ANP901 4.5 27.3 1.0 CB A:ASN91 4.5 30.2 1.0 H3' A:ANP901 4.5 31.9 1.0 HZ2 A:LYS378 4.6 40.5 1.0 N A:GLY166 4.6 27.4 1.0 OD2 A:ASP94 4.6 34.1 1.0 HB3 A:GLU87 4.7 31.9 1.0 N A:ALA167 4.7 26.0 1.0 H A:ASN91 4.7 35.2 1.0 CA A:ASN91 4.8 30.5 1.0 NZ A:LYS378 4.8 33.8 1.0 N A:ASN91 4.9 29.4 1.0 HB2 A:ASN91 5.0 36.3 1.0 HG12 A:VAL90 5.0 34.8 1.0 C A:GLY166 5.0 30.9 1.0

Magnesium binding site 2 out of 2 in the Human Topoisomerase 2 Alpha 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 2 of Human Topoisomerase 2 Alpha Atpase Domain Bound to Non-Hydrolyzable Atp Analog Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:35.5 occ:1.00 O B:HOH1036 2.0 34.5 1.0 O1A B:ANP901 2.1 31.5 1.0 O B:HOH1048 2.1 31.7 1.0 O1B B:ANP901 2.1 31.5 1.0 O1G B:ANP901 2.1 31.9 1.0 OD1 B:ASN91 2.1 46.4 1.0 PB B:ANP901 3.0 33.4 1.0 HD21 B:ASN91 3.1 51.6 1.0 CG B:ASN91 3.1 47.8 1.0 PA B:ANP901 3.2 35.9 1.0 PG B:ANP901 3.2 32.5 1.0 O3A B:ANP901 3.5 33.6 1.0 ND2 B:ASN91 3.5 43.0 1.0 N3B B:ANP901 3.6 30.9 1.0 HA3 B:GLY166 3.6 42.9 1.0 HA2 B:GLY161 3.7 44.3 1.0 HA3 B:GLY161 3.8 44.3 1.0 HNB1 B:ANP901 3.8 37.1 1.0 O B:HOH1022 3.9 37.9 1.0 O5' B:ANP901 4.0 39.9 1.0 OE1 B:GLU87 4.1 39.6 1.0 H B:GLY166 4.1 45.1 1.0 O B:HOH1068 4.2 42.1 1.0 CA B:GLY161 4.2 36.9 1.0 O B:GLU87 4.3 45.2 1.0 O3G B:ANP901 4.3 27.7 1.0 O2G B:ANP901 4.3 31.4 1.0 H B:ALA167 4.3 47.9 1.0 HA B:ASN91 4.3 53.9 1.0 HD22 B:ASN91 4.4 51.6 1.0 O2B B:ANP901 4.4 31.0 1.0 HZ1 B:LYS378 4.4 56.4 1.0 CA B:GLY166 4.5 35.7 1.0 O2A B:ANP901 4.5 30.0 1.0 H3' B:ANP901 4.5 51.2 1.0 CB B:ASN91 4.5 47.9 1.0 OD2 B:ASP94 4.6 45.5 1.0 HB3 B:GLU87 4.7 50.0 1.0 N B:GLY166 4.7 37.6 1.0 HZ2 B:LYS378 4.7 56.4 1.0 H B:ASN91 4.8 52.1 1.0 CA B:ASN91 4.8 44.9 1.0 N B:ALA167 4.8 39.9 1.0 N B:ASN91 4.9 43.4 1.0 N B:GLY161 4.9 42.6 1.0 HG12 B:VAL90 4.9 44.8 1.0 HA B:GLU87 5.0 48.8 1.0 NZ B:LYS378 5.0 47.0 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