Magnesium in PDB 5btd: 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: 5btd 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)	47.39 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.907, 83.158, 129.203, 90.00, 108.65, 90.00
R / Rfree (%)	21.5 / 24.6

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 5btd). 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: 5btd:
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:34.3 occ:1.00 O B:HOH821 2.1 48.4 1.0 O B:HOH804 2.1 30.3 1.0 O B:HOH807 2.1 36.7 1.0 OD2 B:ASP532 2.1 38.2 1.0 O B:HOH810 2.1 30.6 1.0 OD2 B:ASP534 2.1 38.2 1.0 CG B:ASP534 3.0 36.9 1.0 CG B:ASP532 3.1 39.0 1.0 HB2 B:ASP532 3.2 46.4 1.0 HB3 B:ASP532 3.3 46.4 1.0 OD1 B:ASP534 3.3 35.6 1.0 CB B:ASP532 3.4 38.6 1.0 H5'' G:DT10 3.7 38.3 0.5 OE2 B:GLU459 3.8 46.6 1.0 H5'' E:DT10 3.9 59.0 0.5 O B:HOH826 3.9 44.3 1.0 O B:LYS611 4.1 58.9 1.0 O B:HOH808 4.1 59.6 1.0 HA3 B:GLY612 4.2 51.5 1.0 HB2 B:ASP536 4.2 44.7 1.0 OP1 G:DT10 4.2 31.8 0.5 OD1 B:ASP532 4.2 40.9 1.0 CB B:ASP534 4.4 37.4 1.0 HB3 B:ASP534 4.5 44.9 1.0 H3' E:DT10 4.6 59.4 0.5 HA2 B:GLY612 4.6 51.5 1.0 OP1 E:DT10 4.6 48.8 0.5 C5' G:DT10 4.7 31.9 0.5 CD B:GLU459 4.7 47.1 1.0 HB2 B:ASP534 4.7 44.9 1.0 H B:ASP534 4.8 53.5 1.0 C5' E:DT10 4.8 49.1 0.5 CA B:GLY612 4.8 42.9 1.0 CA B:ASP532 4.9 42.0 1.0 H B:GLY537 5.0 49.8 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:31.8 occ:1.00 O D:HOH801 2.1 31.8 1.0 O D:HOH812 2.1 66.0 1.0 OD2 D:ASP532 2.1 38.6 1.0 O D:HOH805 2.1 30.6 1.0 OD2 D:ASP534 2.1 38.0 1.0 O D:HOH806 2.1 29.6 1.0 CG D:ASP534 3.1 32.6 1.0 CG D:ASP532 3.1 40.7 1.0 HB2 D:ASP532 3.2 48.8 1.0 OD1 D:ASP534 3.3 29.5 1.0 H5'' F:DT10 3.4 70.2 0.5 HB3 D:ASP532 3.5 48.8 1.0 CB D:ASP532 3.5 40.7 1.0 H5'' H:DT10 3.6 32.8 0.5 OE2 D:GLU459 3.6 44.9 1.0 O D:HOH809 4.0 48.1 1.0 HB2 D:ASP536 4.0 38.7 1.0 HA3 D:GLY612 4.2 50.0 1.0 OP1 F:DT10 4.2 59.2 0.5 OD1 D:ASP532 4.3 42.1 1.0 O D:LYS611 4.3 53.3 1.0 O D:HOH816 4.3 40.8 1.0 OP1 H:DT10 4.4 26.5 0.5 C5' F:DT10 4.4 58.5 0.5 CB D:ASP534 4.4 31.1 1.0 H3' H:DT10 4.5 36.6 0.5 O3' F:DT10 4.5 60.9 0.5 HB3 D:ASP534 4.5 37.3 1.0 C5' H:DT10 4.5 27.4 0.5 CD D:GLU459 4.6 45.9 1.0 HA2 D:GLY612 4.7 50.0 1.0 HB2 D:ASP534 4.8 37.3 1.0 H5' F:DT10 4.8 70.2 0.5 CB D:ASP536 4.9 32.3 1.0 CA D:GLY612 4.9 41.7 1.0 H5' H:DT10 4.9 32.8 0.5 HB3 D:ASP536 4.9 38.7 1.0 OE1 D:GLU459 4.9 50.5 1.0 H4' F:DT10 4.9 71.0 0.5 H D:ASP534 5.0 50.7 1.0 H D:GLY537 5.0 50.6 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:40.6 occ:1.00 O23 E:GFN101 2.0 39.4 1.0 O E:HOH202 2.1 66.3 1.0 O A:HOH615 2.1 48.5 1.0 O E:HOH210 2.1 41.0 1.0 O E:HOH203 2.1 49.2 1.0 O20 E:GFN101 2.2 40.0 1.0 C21 E:GFN101 3.1 37.1 1.0 C19 E:GFN101 3.2 39.3 1.0 C18 E:GFN101 3.5 38.0 1.0 O4 E:DT10 3.6 64.2 0.5 O6 E:DG11 3.8 0.7 0.5 HB1 A:ALA90 3.8 42.0 1.0 N6 G:DA11 3.9 32.6 0.5 O A:HOH634 4.0 59.4 1.0 O E:HOH209 4.0 87.0 1.0 HB3 A:ALA90 4.1 42.0 1.0 O4 G:DT10 4.1 42.9 0.5 H61 H:DA15 4.2 30.0 0.5 O22 E:GFN101 4.2 35.6 1.0 H101 E:GFN101 4.3 49.8 1.0 CB A:ALA90 4.4 35.0 1.0 H62 H:DA15 4.4 30.0 0.5 C11 E:GFN101 4.4 40.2 1.0 H71 E:DT10 4.5 71.9 0.5 C6 E:DG11 4.5 0.4 0.5 OD2 A:ASP94 4.5 47.5 1.0 H71 G:DT10 4.6 46.6 0.5 N6 H:DA15 4.6 25.0 0.5 HB3 A:SER91 4.6 61.5 1.0 H62 F:DA15 4.7 99.0 0.5 C4 E:DT10 4.8 60.7 0.5 C6 G:DA11 4.8 33.1 0.5 C10 E:GFN101 4.8 41.5 1.0 N7 E:DG11 4.8 0.9 0.5 N6 F:DA15 4.8 99.0 0.5 C17 E:GFN101 4.9 39.9 1.0 HB2 A:ALA90 4.9 42.0 1.0 O E:HOH208 4.9 53.4 1.0 O4 H:DT14 4.9 55.4 0.5 H62 E:DA9 4.9 63.2 0.5 C5 E:DG11 4.9 0.5 0.5 N7 G:DA11 4.9 34.3 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:Mg101 b:48.4 occ:1.00 O G:HOH202 2.1 45.2 1.0 O G:HOH204 2.1 40.5 1.0 O C:HOH612 2.1 45.9 1.0 O22 G:GFN101 2.1 41.0 1.0 O F:HOH203 2.1 39.9 1.0 O20 G:GFN101 2.2 41.7 1.0 C21 G:GFN101 3.1 40.2 1.0 C19 G:GFN101 3.2 40.1 1.0 H62 F:DA11 3.4 86.5 0.5 C18 G:GFN101 3.6 38.8 1.0 HB1 C:ALA90 3.8 40.3 1.0 N6 F:DA11 3.8 72.1 0.5 H61 F:DA11 3.9 86.5 0.5 O4 F:DT10 3.9 68.7 0.5 O6 H:DG11 4.0 51.0 0.5 HB3 C:ALA90 4.1 40.3 1.0 O4 H:DT10 4.1 33.4 0.5 O23 G:GFN101 4.2 39.9 1.0 H61 G:DA15 4.2 43.6 0.5 H101 G:GFN101 4.3 49.2 1.0 CB C:ALA90 4.4 33.6 1.0 H42 G:DC14 4.4 44.2 0.5 H71 H:DT10 4.4 40.8 0.5 C11 G:GFN101 4.5 40.6 1.0 OD2 C:ASP94 4.5 48.5 1.0 H73 F:DT10 4.6 81.0 0.5 N6 G:DA15 4.6 36.4 0.5 O F:HOH204 4.6 87.0 1.0 HB3 C:SER91 4.7 61.7 1.0 H62 E:DA15 4.7 91.3 0.5 C6 F:DA11 4.7 73.0 0.5 H41 G:DC14 4.7 44.2 0.5 N6 E:DA15 4.7 76.1 0.5 C6 H:DG11 4.8 52.6 0.5 C10 G:GFN101 4.8 41.0 1.0 N4 G:DC14 4.8 36.8 0.5 HB2 C:ALA90 4.9 40.3 1.0 N7 F:DA11 4.9 75.5 0.5 N7 H:DG11 5.0 54.3 0.5 C17 G:GFN101 5.0 40.1 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