Manganese in PDB 9cak: Human TOP3B-TDRD3 Core Complex in Dna Rejoining State with Ssdna 5'- Gacagatatt-3

All present enzymatic activity of Human TOP3B-TDRD3 Core Complex in Dna Rejoining State with Ssdna 5'- Gacagatatt-3:
5.6.2.1;

The binding sites of Manganese atom in the Human TOP3B-TDRD3 Core Complex in Dna Rejoining State with Ssdna 5'- Gacagatatt-3 (pdb code 9cak). 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 Dna Rejoining State with Ssdna 5'- Gacagatatt-3, PDB code: 9cak:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human TOP3B-TDRD3 Core Complex in Dna Rejoining State with Ssdna 5'- Gacagatatt-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 Dna Rejoining State with Ssdna 5'- Gacagatatt-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:56.0 occ:1.00 OD2 A:ASP117 2.1 55.6 1.0 OE2 A:GLU9 2.1 55.6 1.0 O1P A:PTR336 2.9 51.9 1.0 CG A:ASP117 3.1 55.6 1.0 CD A:GLU9 3.1 55.6 1.0 O2P A:PTR336 3.3 51.9 1.0 O3' D:DT4 3.4 57.0 1.0 P A:PTR336 3.5 51.9 1.0 OE1 A:GLU9 3.5 55.6 1.0 CB A:ASP117 3.6 55.6 1.0 OD2 A:ASP119 3.8 57.5 1.0 C3' D:DT4 3.8 57.0 1.0 O3P A:PTR336 3.9 51.9 1.0 OD1 A:ASP117 4.2 55.6 1.0 CG A:GLU9 4.5 55.6 1.0 NE2 A:HIS387 4.5 55.6 1.0 CG A:ASP119 4.7 57.5 1.0 C5' E:DA5 4.7 56.0 1.0 O5' D:DT4 4.7 57.0 1.0 OD1 A:ASP119 4.8 57.5 1.0 C4' D:DT4 4.8 57.0 1.0

Manganese binding site 2 out of 2 in the Human TOP3B-TDRD3 Core Complex in Dna Rejoining State with Ssdna 5'- Gacagatatt-3


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 Dna Rejoining State with Ssdna 5'- Gacagatatt-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:73.2 occ:1.00 OD2 A:ASP511 2.0 57.6 1.0 OE2 A:GLU340 2.1 55.6 1.0 CG A:ASP511 3.2 57.6 1.0 CD A:GLU340 3.3 55.6 1.0 OD1 A:ASP511 3.7 57.6 1.0 CG A:GLU340 3.9 55.6 1.0 OD2 A:ASP386 4.2 55.6 1.0 OE1 A:GLU340 4.3 55.6 1.0 CB A:ASP511 4.4 57.6 1.0 OP1 D:DT4 4.4 57.0 1.0 OD2 A:ASP119 4.5 57.5 1.0 N A:ASP511 4.8 57.6 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