Magnesium in PDB 5gvc: Human Topoisomerase Iiib Topo Domain

All present enzymatic activity of Human Topoisomerase Iiib Topo Domain:
5.99.1.2;

The structure of Human Topoisomerase Iiib Topo Domain, PDB code: 5gvc was solved by S.Goto-Ito, A.Yamagata, Y.Sato, T.S.Takahashi, S.Fukai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.72 / 2.44
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	176.088, 93.665, 91.608, 90.00, 91.88, 90.00
R / Rfree (%)	18.2 / 22.9

The binding sites of Magnesium atom in the Human Topoisomerase Iiib Topo Domain (pdb code 5gvc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Topoisomerase Iiib Topo Domain, PDB code: 5gvc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Topoisomerase Iiib Topo Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Topoisomerase Iiib Topo Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:31.6 occ:1.00 O A:HOH866 2.1 22.0 1.0 O A:HOH907 2.1 33.0 1.0 O A:HOH857 2.1 22.7 1.0 O A:HOH990 2.2 38.1 1.0 O A:HOH845 2.2 22.7 1.0 OE2 A:GLU9 2.3 23.5 1.0 CD A:GLU9 3.2 30.8 1.0 OE1 A:GLU9 3.5 28.5 1.0 OD2 A:ASP119 4.2 32.1 1.0 OH A:TYR336 4.3 33.2 1.0 NH2 A:ARG338 4.3 37.9 1.0 O A:HOH1011 4.4 44.5 1.0 OD2 A:ASP117 4.4 55.0 1.0 OD1 A:ASP119 4.4 27.5 1.0 OE2 A:GLU326 4.5 42.6 1.0 CB A:GLU121 4.5 31.6 1.0 CG A:GLU9 4.6 30.6 1.0 CD1 A:ILE125 4.7 21.5 1.0 CG A:GLU121 4.7 42.2 1.0 O A:HOH996 4.7 33.4 1.0 CB A:ASP117 4.7 21.6 1.0 CG A:ASP119 4.8 33.8 1.0 CZ A:ARG338 4.9 33.9 1.0

Magnesium binding site 2 out of 2 in the Human Topoisomerase Iiib Topo Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Topoisomerase Iiib Topo Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:28.8 occ:1.00 O B:HOH936 2.0 26.9 1.0 O B:HOH954 2.1 34.7 1.0 O B:HOH837 2.1 26.2 1.0 OE1 B:GLU9 2.1 32.8 1.0 O B:HOH843 2.1 28.7 1.0 O B:HOH830 2.2 29.5 1.0 CD B:GLU9 3.1 36.6 1.0 OE2 B:GLU9 3.3 40.0 1.0 O B:HOH961 4.1 41.8 1.0 O B:HOH947 4.2 34.7 1.0 OH B:TYR336 4.2 35.3 1.0 OD2 B:ASP117 4.3 35.9 1.0 OE2 B:GLU326 4.3 28.6 1.0 CG B:GLU9 4.5 30.2 1.0 OD2 B:ASP119 4.5 41.1 1.0 OD1 B:ASP119 4.6 37.0 1.0 CD1 B:ILE125 4.6 41.5 1.0 O B:HOH953 4.6 36.7 1.0 CB B:ASP117 4.7 31.1 1.0 CB B:GLU121 4.7 31.0 1.0 CG B:ASP117 5.0 33.7 1.0 CG B:ASP119 5.0 39.7 1.0

S.Goto-Ito, A.Yamagata, T.S.Takahashi, Y.Sato, S.Fukai. Structural Basis of the Interaction Between Topoisomerase III Beta and the TDRD3 Auxiliary Factor Sci Rep V. 7 42123 2017.
ISSN: ESSN 2045-2322
PubMed: 28176834
DOI: 10.1038/SREP42123