Manganese in PDB 9c9y: Human TOP3B-TDRD3 Core Complex in Dna Pre-Cleavage State

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

The binding sites of Manganese atom in the Human TOP3B-TDRD3 Core Complex in Dna Pre-Cleavage State (pdb code 9c9y). 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 Pre-Cleavage State, PDB code: 9c9y:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human TOP3B-TDRD3 Core Complex in Dna 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 Dna Pre-Cleavage State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:81.6 occ:1.00 OP1 C:DA5 2.1 72.9 1.0 OD2 A:ASP117 2.1 80.2 1.0 OE2 A:GLU9 2.2 80.2 1.0 O3' C:DA4 2.8 74.3 1.0 P C:DA5 3.0 72.9 1.0 CG A:ASP117 3.3 80.2 1.0 CD A:GLU9 3.4 80.2 1.0 O5' C:DA5 3.6 72.9 1.0 NZ A:LYS10 3.8 80.2 1.0 OD2 A:ASP119 3.9 82.6 1.0 OE1 A:GLU9 4.0 80.2 1.0 CB A:ASP117 4.0 80.2 1.0 C3' C:DA4 4.2 74.3 1.0 NE2 A:HIS387 4.2 80.2 1.0 OD1 A:ASP117 4.3 80.2 1.0 OP2 C:DA5 4.3 72.9 1.0 CE1 A:HIS387 4.5 80.2 1.0 CG A:GLU9 4.6 80.2 1.0 C4' C:DA4 4.7 74.3 1.0 C2' C:DA4 4.9 74.3 1.0 CG A:ASP119 4.9 82.6 1.0 C5' C:DA5 5.0 72.9 1.0

Manganese binding site 2 out of 2 in the Human TOP3B-TDRD3 Core Complex in Dna 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 Dna Pre-Cleavage State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:83.7 occ:1.00 OD2 A:ASP511 2.0 82.5 1.0 OE2 A:GLU340 2.2 80.2 1.0 CG A:ASP511 3.0 82.5 1.0 CD A:GLU340 3.0 80.2 1.0 OE1 A:GLU340 3.2 80.2 1.0 OD1 A:ASP511 3.6 82.5 1.0 OD1 A:ASP386 3.9 81.3 1.0 CB A:ASP511 4.1 82.5 1.0 CG A:ASP386 4.5 81.3 1.0 CG A:GLU340 4.5 80.2 1.0 OD2 A:ASP386 4.5 81.3 1.0 OP1 C:DA4 4.8 74.3 1.0 N A:ASP511 4.9 82.5 1.0

X.Yang, X.Chen, W.Yang, Y.Pommier. Structural Insights Into Human Topoisomerase 3-Beta Dna and Rna Catalytic Cycles and Topo-Gate Dynamics To Be Published.