Zinc in PDB 9cah: Human TOP3B-TDRD3 Complex

All present enzymatic activity of Human TOP3B-TDRD3 Complex:
5.6.2.1;

The structure of Human TOP3B-TDRD3 Complex also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Zinc atom in the Human TOP3B-TDRD3 Complex (pdb code 9cah). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Human TOP3B-TDRD3 Complex, PDB code: 9cah:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Human TOP3B-TDRD3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human TOP3B-TDRD3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:85.7 occ:1.00 SG A:CYS706 2.4 105.1 1.0 SG A:CYS714 2.4 105.9 1.0 SG A:CYS709 2.5 107.6 1.0 CB A:CYS714 3.4 105.9 1.0 CB A:CYS709 3.5 107.6 1.0 CB A:CYS706 3.8 105.1 1.0 CA A:CYS706 4.5 105.1 1.0 CA A:CYS714 4.9 105.9 1.0 CA A:CYS709 4.9 107.6 1.0 O A:CYS714 5.0 105.9 1.0 CB A:SER717 5.0 104.7 1.0 SG A:CYS666 5.0 86.5 1.0

Zinc binding site 2 out of 3 in the Human TOP3B-TDRD3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human TOP3B-TDRD3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:84.0 occ:1.00 SG A:CYS646 2.3 68.4 1.0 SG A:CYS643 2.3 67.0 1.0 SG A:CYS627 2.3 72.5 1.0 SG A:CYS624 2.3 75.2 1.0 CB A:CYS627 3.2 72.5 1.0 CB A:CYS624 3.3 75.2 1.0 CB A:CYS643 3.4 67.0 1.0 CB A:CYS646 3.6 68.4 1.0 N A:CYS646 3.8 68.4 1.0 N A:CYS627 4.2 72.5 1.0 CA A:CYS646 4.3 68.4 1.0 CA A:CYS627 4.3 72.5 1.0 O A:CYS646 4.4 68.4 1.0 CB A:HIS645 4.5 64.7 1.0 CA A:CYS624 4.8 75.2 1.0 CB A:LYS626 4.8 72.5 1.0 CA A:CYS643 4.8 67.0 1.0 C A:CYS646 4.8 68.4 1.0 C A:LYS626 4.9 72.5 1.0 C A:HIS645 4.9 64.7 1.0

Zinc binding site 3 out of 3 in the Human TOP3B-TDRD3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human TOP3B-TDRD3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:98.3 occ:1.00 OD2 A:ASP669 2.1 85.8 1.0 SG A:CYS688 2.3 84.1 1.0 SG A:CYS666 2.3 86.5 1.0 SG A:CYS691 2.3 85.6 1.0 CG A:ASP669 2.4 85.8 1.0 OD1 A:ASP669 2.7 85.8 1.0 CB A:CYS666 3.2 86.5 1.0 CB A:ASP669 3.4 85.8 1.0 CB A:CYS688 3.5 84.1 1.0 N A:ASP669 3.9 85.8 1.0 CB A:CYS691 4.0 85.6 1.0 CA A:ASP669 4.2 85.8 1.0 N A:CYS691 4.3 85.6 1.0 NH1 B:ARG172 4.5 95.4 1.0 CA A:CYS666 4.6 86.5 1.0 CB A:LEU668 4.7 88.7 1.0 NH2 B:ARG172 4.7 95.4 1.0 CA A:CYS691 4.8 85.6 1.0 CB A:TYR690 4.8 83.6 1.0 C A:LEU668 4.8 88.7 1.0 CA A:CYS688 4.9 84.1 1.0 C A:ASP669 5.0 85.8 1.0 N A:LEU668 5.0 88.7 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