Manganese in PDB 9cag: Human TOP3B-TDRD3 Core Complex in Rna Pre-Cleavage State

All present enzymatic activity of Human TOP3B-TDRD3 Core Complex in Rna Pre-Cleavage State:
5.6.2.1;

The binding sites of Manganese atom in the Human TOP3B-TDRD3 Core Complex in Rna Pre-Cleavage State (pdb code 9cag). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human TOP3B-TDRD3 Core Complex in Rna Pre-Cleavage State, PDB code: 9cag:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human TOP3B-TDRD3 Core Complex in Rna Pre-Cleavage State


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 Rna Pre-Cleavage State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:78.1 occ:1.00 OD2 A:ASP511 2.1 67.6 1.0 OE2 A:GLU340 2.1 68.9 1.0 CG A:ASP511 2.9 67.6 1.0 OD2 A:ASP386 2.9 67.4 1.0 OD1 A:ASP511 3.3 67.6 1.0 CD A:GLU340 3.3 68.9 1.0 OP1 E:A2 3.9 65.4 1.0 CG A:ASP386 4.0 67.4 1.0 OE1 A:GLU340 4.0 68.9 1.0 CB A:ASP511 4.1 67.6 1.0 CG A:GLU340 4.4 68.9 1.0 CB A:GLU340 4.4 68.9 1.0 OD2 A:ASP119 4.5 69.4 1.0 OD1 A:ASP386 4.5 67.4 1.0 OP2 E:A2 4.6 65.4 1.0 P E:A2 4.7 65.4 1.0 N A:ASP511 4.7 67.6 1.0

Manganese binding site 2 out of 2 in the Human TOP3B-TDRD3 Core Complex in Rna Pre-Cleavage State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human TOP3B-TDRD3 Core Complex in Rna Pre-Cleavage State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:62.1 occ:1.00 OP1 E:A3 2.1 65.8 1.0 OD2 A:ASP117 2.1 66.9 1.0 OE2 A:GLU9 2.1 66.9 1.0 O3' E:A2 2.8 65.4 1.0 P E:A3 3.0 65.8 1.0 CG A:ASP117 3.1 66.9 1.0 CD A:GLU9 3.3 66.9 1.0 CB A:ASP117 3.4 66.9 1.0 OE1 A:GLU9 3.8 66.9 1.0 OD2 A:ASP119 3.8 69.4 1.0 NE2 A:HIS387 4.0 66.9 1.0 O5' E:A3 4.0 65.8 1.0 C3' E:A2 4.1 65.4 1.0 OP2 E:A3 4.1 65.8 1.0 OD1 A:ASP117 4.3 66.9 1.0 C4' E:A2 4.3 65.4 1.0 OD1 A:ASP119 4.3 69.4 1.0 O2' E:A2 4.4 65.4 1.0 CG A:ASP119 4.5 69.4 1.0 CG A:GLU9 4.5 66.9 1.0 CE1 A:HIS387 4.6 66.9 1.0 NZ A:LYS10 4.7 66.9 1.0 C5' E:A2 4.7 65.4 1.0 C2' E:A2 4.9 65.4 1.0 O5' E:A2 4.9 65.4 1.0 CA A:ASP117 5.0 66.9 1.0 OD1 A:ASP386 5.0 67.4 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