Magnesium in PDB 5btg: Crystal Structure of A Topoisomerase II Complex

All present enzymatic activity of Crystal Structure of A Topoisomerase II Complex:
5.99.1.3;

The structure of Crystal Structure of A Topoisomerase II Complex, PDB code: 5btg was solved by T.R.Blower, B.H.Williamson, R.J.Kerns, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.33 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.094, 82.989, 129.101, 90.00, 108.76, 90.00
R / Rfree (%)	22.6 / 24.9

The structure of Crystal Structure of A Topoisomerase II Complex also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of A Topoisomerase II Complex (pdb code 5btg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Topoisomerase II Complex, PDB code: 5btg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of A Topoisomerase II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Topoisomerase II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:32.7 occ:1.00 O B:HOH806 2.1 25.9 1.0 O B:HOH803 2.1 35.7 1.0 O G:HOH102 2.1 50.8 1.0 OD2 B:ASP534 2.1 40.5 1.0 O B:HOH808 2.1 44.7 1.0 OD2 B:ASP532 2.1 44.3 1.0 CG B:ASP534 3.1 39.9 1.0 CG B:ASP532 3.2 44.9 1.0 HB2 B:ASP532 3.4 54.3 1.0 OD1 B:ASP534 3.4 38.1 1.0 HB3 B:ASP532 3.5 54.3 1.0 H5'' G:DT10 3.5 23.4 0.5 CB B:ASP532 3.6 45.2 1.0 H5'' E:DT10 3.7 75.3 0.5 O B:HOH817 3.8 29.1 1.0 OE2 B:GLU459 3.8 40.0 1.0 OP1 G:DT10 4.0 16.2 0.5 HB2 B:ASP536 4.1 42.1 1.0 O B:LYS611 4.2 47.4 1.0 HA3 B:GLY612 4.3 50.0 1.0 OD1 B:ASP532 4.3 45.6 1.0 H3' E:DT10 4.4 77.8 0.5 CB B:ASP534 4.4 41.8 1.0 HB3 B:ASP534 4.5 50.2 1.0 C5' G:DT10 4.5 19.5 0.5 OP1 E:DT10 4.5 59.2 0.5 C5' E:DT10 4.6 62.8 0.5 HB2 B:ASP534 4.7 50.2 1.0 HA2 B:GLY612 4.7 50.0 1.0 CD B:GLU459 4.8 39.9 1.0 H5' G:DT10 4.8 23.4 0.5 H B:ASP534 4.9 55.2 1.0 CA B:GLY612 4.9 41.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of A Topoisomerase II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Topoisomerase II Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:21.7 occ:1.00 O D:HOH801 2.1 35.2 1.0 OD2 D:ASP534 2.1 38.8 1.0 OD2 D:ASP532 2.1 44.9 1.0 O D:HOH808 2.1 42.6 1.0 O D:HOH806 2.1 34.2 1.0 O D:HOH807 2.1 20.0 1.0 CG D:ASP534 3.1 38.8 1.0 CG D:ASP532 3.1 45.4 1.0 HB2 D:ASP532 3.3 54.0 1.0 HB3 D:ASP532 3.4 54.0 1.0 OD1 D:ASP534 3.4 37.1 1.0 CB D:ASP532 3.5 45.0 1.0 H5'' F:DT10 3.7 74.2 0.5 H5'' H:DT10 3.7 25.2 0.5 OE2 D:GLU459 3.8 43.8 1.0 O D:LYS611 4.0 47.5 1.0 O D:HOH818 4.0 35.1 1.0 HA3 D:GLY612 4.1 55.4 1.0 O D:HOH804 4.1 42.6 1.0 HB2 D:ASP536 4.2 39.8 1.0 OD1 D:ASP532 4.2 46.3 1.0 OP1 H:DT10 4.3 18.2 0.5 CB D:ASP534 4.4 40.5 1.0 HA2 D:GLY612 4.4 55.4 1.0 HB3 D:ASP534 4.5 48.6 1.0 O3' F:DT10 4.6 64.0 0.5 C5' F:DT10 4.6 61.8 0.5 OP1 F:DT10 4.6 62.2 0.5 C5' H:DT10 4.7 21.0 0.5 H3' H:DT10 4.7 27.3 0.5 CA D:GLY612 4.7 46.2 1.0 HB2 D:ASP534 4.7 48.6 1.0 CD D:GLU459 4.8 42.7 1.0 H D:ASP534 4.9 51.1 1.0 H5' H:DT10 5.0 25.2 0.5 CA D:ASP532 5.0 43.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of A Topoisomerase II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Topoisomerase II Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg102 b:31.0 occ:1.00 O A:HOH603 2.1 47.3 1.0 O E:HOH202 2.1 47.1 1.0 O E:HOH204 2.1 34.1 1.0 O03 E:LFX101 2.1 32.0 1.0 O02 E:LFX101 2.2 30.5 1.0 C E:LFX101 3.2 31.3 1.0 C15 E:LFX101 3.3 31.0 1.0 HB1 A:ALA90 3.7 35.9 1.0 C17 E:LFX101 3.7 30.2 1.0 O6 E:DG11 3.8 0.2 0.5 O4 E:DT10 3.8 69.2 0.5 N6 G:DA11 4.1 24.6 0.5 HB3 A:ALA90 4.2 35.9 1.0 OD2 A:ASP94 4.2 33.2 1.0 O E:LFX101 4.3 31.5 1.0 O4 G:DT10 4.3 24.6 0.5 H61 H:DA15 4.4 16.8 0.5 CB A:ALA90 4.4 29.9 1.0 H13 E:LFX101 4.4 40.2 1.0 O A:HOH643 4.6 53.1 1.0 C6 E:DG11 4.6 0.5 0.5 H71 E:DT10 4.6 80.7 0.5 H62 H:DA15 4.6 16.8 0.5 C10 E:LFX101 4.6 32.2 1.0 H71 G:DT10 4.6 28.7 0.5 HB3 A:SER91 4.8 44.7 1.0 N6 H:DA15 4.8 14.0 0.5 HA A:SER91 4.9 41.7 1.0 HB2 A:ALA90 4.9 35.9 1.0 C13 E:LFX101 5.0 33.5 1.0 C4 E:DT10 5.0 68.3 0.5 O4 H:DT14 5.0 36.5 0.5 N4 F:DC14 5.0 0.8 0.5

Magnesium binding site 4 out of 4 in the Crystal Structure of A Topoisomerase II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Topoisomerase II Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg102 b:31.1 occ:1.00 O F:HOH202 2.1 39.2 1.0 O C:HOH607 2.1 33.8 1.0 O F:HOH204 2.1 25.3 1.0 O F:LFX101 2.2 30.1 1.0 O02 F:LFX101 2.2 29.2 1.0 C F:LFX101 3.3 30.1 1.0 C15 F:LFX101 3.3 29.4 1.0 H62 F:DA11 3.4 0.6 0.5 C17 F:LFX101 3.8 29.6 1.0 N6 F:DA11 3.8 0.7 0.5 H61 F:DA11 3.9 0.6 0.5 O4 F:DT10 3.9 75.4 0.5 HB1 C:ALA90 4.0 39.9 1.0 H61 E:DA15 4.1 75.3 0.5 O6 H:DG11 4.2 64.9 0.5 O4 H:DT10 4.2 28.3 0.5 H61 G:DA15 4.2 27.3 0.5 OD2 C:ASP94 4.4 36.1 1.0 O03 F:LFX101 4.4 30.4 1.0 H13 F:LFX101 4.4 36.7 1.0 HB3 C:ALA90 4.4 39.9 1.0 H62 E:DA15 4.5 75.3 0.5 N6 E:DA15 4.6 62.8 0.5 N6 G:DA15 4.6 22.7 0.5 C10 F:LFX101 4.6 29.9 1.0 CB C:ALA90 4.7 33.3 1.0 H71 H:DT10 4.7 32.5 0.5 H73 F:DT10 4.7 89.7 0.5 C6 F:DA11 4.8 0.6 0.5 H62 F:DA9 4.8 83.4 0.5 HB3 C:SER91 4.8 48.0 1.0 O4 E:DT14 4.8 0.1 0.5 N4 G:DC14 4.9 26.2 0.5 C13 F:LFX101 5.0 30.6 1.0

T.R.Blower, B.H.Williamson, R.J.Kerns, J.M.Berger. Crystal Structure and Stability of Gyrase-Fluoroquinolone Cleaved Complexes From Mycobacterium Tuberculosis. Proc.Natl.Acad.Sci.Usa V. 113 1706 2016.
ISSN: ESSN 1091-6490
PubMed: 26792525
DOI: 10.1073/PNAS.1525047113