Atomistry » Magnesium » PDB 5gre-5h1y » 5gvc
Atomistry »
  Magnesium »
    PDB 5gre-5h1y »
      5gvc »

Magnesium in PDB 5gvc: Human Topoisomerase Iiib Topo Domain

Enzymatic activity of Human Topoisomerase Iiib Topo Domain

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

Protein crystallography data

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

Magnesium Binding Sites:

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 5gvc

Go back to Magnesium Binding Sites List in 5gvc
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 5gvc

Go back to Magnesium Binding Sites List in 5gvc
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

Reference:

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
Page generated: Sun Sep 29 15:27:04 2024

Last articles

Na in 7Q78
Na in 7Q77
Na in 7Q76
Na in 7Q6Q
Na in 7Q75
Na in 7Q5F
Na in 7Q47
Na in 7Q3Z
Na in 7Q5E
Na in 7Q36
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy