Magnesium in PDB 7yq8: Cryo-Em Structure of Human Topoisomerase II Beta in Complex with Dna and Etoposide

All present enzymatic activity of Cryo-Em Structure of Human Topoisomerase II Beta in Complex with Dna and Etoposide:
5.6.2.2;

The binding sites of Magnesium atom in the Cryo-Em Structure of Human Topoisomerase II Beta in Complex with Dna and Etoposide (pdb code 7yq8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of Human Topoisomerase II Beta in Complex with Dna and Etoposide, PDB code: 7yq8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Human Topoisomerase II Beta in Complex with Dna and Etoposide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Human Topoisomerase II Beta in Complex with Dna and Etoposide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1701 b:132.2 occ:1.00 OD2 A:ASP564 2.0 149.0 1.0 OD2 A:ASP562 2.1 159.4 1.0 CG A:ASP562 2.7 159.4 1.0 CG A:ASP564 2.8 149.0 1.0 CB A:ASP562 2.9 159.4 1.0 OD1 A:ASP564 3.0 149.0 1.0 OD1 A:ASP562 3.8 159.4 1.0 CB A:ASP564 4.2 149.0 1.0 O A:LYS635 4.4 161.8 1.0 CA A:ASP562 4.4 159.4 1.0 O3' C:DG23 4.9 150.8 1.0 OD2 A:ASP566 4.9 135.6 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Human Topoisomerase II Beta in Complex with Dna and Etoposide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Human Topoisomerase II Beta in Complex with Dna and Etoposide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1701 b:138.4 occ:1.00 OD2 B:ASP564 2.0 150.3 1.0 OD2 B:ASP562 2.1 162.9 1.0 CG B:ASP562 2.7 162.9 1.0 CG B:ASP564 2.7 150.3 1.0 OD1 B:ASP564 2.9 150.3 1.0 CB B:ASP562 2.9 162.9 1.0 OD1 B:ASP562 3.9 162.9 1.0 CB B:ASP564 4.2 150.3 1.0 CA B:ASP562 4.4 162.9 1.0 O B:LYS635 4.5 161.2 1.0 N B:ASP564 4.9 150.3 1.0 OE2 B:GLU482 5.0 155.7 1.0

H.Bunch, D.Kim, M.Naganuma, R.Nakagawa, A.Cong, J.Jeong, H.Ehara, H.Vu, J.H.Chang, M.J.Schellenberg, S.I.Sekine. ERK2-Topoisomerase II Regulatory Axis Is Important For Gene Activation in Immediate Early Genes. Nat Commun V. 14 8341 2023.
ISSN: ESSN 2041-1723
PubMed: 38097570
DOI: 10.1038/S41467-023-44089-Y