Manganese in PDB 9caj: Human TOP3B-TDRD3 Core Complex in Pre-Cleavage State with Ssdna 5'- Acagatatt-3

All present enzymatic activity of Human TOP3B-TDRD3 Core Complex in Pre-Cleavage State with Ssdna 5'- Acagatatt-3:
5.6.2.1;

The binding sites of Manganese atom in the Human TOP3B-TDRD3 Core Complex in Pre-Cleavage State with Ssdna 5'- Acagatatt-3 (pdb code 9caj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Human TOP3B-TDRD3 Core Complex in Pre-Cleavage State with Ssdna 5'- Acagatatt-3, PDB code: 9caj:

Manganese binding site 1 out of 1 in the Human TOP3B-TDRD3 Core Complex in Pre-Cleavage State with Ssdna 5'- Acagatatt-3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human TOP3B-TDRD3 Core Complex in Pre-Cleavage State with Ssdna 5'- Acagatatt-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:78.8 occ:1.00 OE2 A:GLU9 2.1 73.0 1.0 OP1 C:DA5 2.2 72.6 1.0 OD2 A:ASP117 2.4 74.8 1.0 CD A:GLU9 3.2 73.0 1.0 P C:DA5 3.4 72.6 1.0 CG A:ASP117 3.6 74.8 1.0 OE1 A:GLU9 3.9 73.0 1.0 OP2 C:DA5 3.9 72.6 1.0 NZ A:LYS10 4.0 75.2 1.0 CG A:GLU9 4.2 73.0 1.0 OD1 A:ASP117 4.4 74.8 1.0 O5' C:DA5 4.4 72.6 1.0 O3' C:DT4 4.5 66.6 1.0 CB A:ASP117 4.6 74.8 1.0 CE A:LYS10 4.7 75.2 1.0 CD1 A:ILE125 4.7 65.5 1.0

X.Yang, X.Chen, W.Yang, Y.Pommier. Structural Insights Into Human Topoisomerase 3 Beta Dna and Rna Catalysis and Nucleic Acid Gate Dynamics. Nat Commun V. 16 834 2025.
ISSN: ESSN 2041-1723
PubMed: 39828754
DOI: 10.1038/S41467-025-55959-Y