Magnesium in PDB 5btl: 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: 5btl 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)	49.60 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.938, 83.047, 128.737, 90.00, 108.88, 90.00
R / Rfree (%)	23 / 25.6

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 5btl). 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: 5btl:
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:48.5 occ:1.00 OD2 B:ASP534 2.1 50.2 1.0 O B:HOH804 2.1 76.5 1.0 O B:HOH809 2.1 46.4 1.0 O B:HOH811 2.1 51.8 1.0 O B:HOH807 2.1 30.8 1.0 OD2 B:ASP532 2.1 45.6 1.0 CG B:ASP534 3.1 48.9 1.0 CG B:ASP532 3.1 46.5 1.0 HB2 B:ASP532 3.3 57.3 1.0 OD1 B:ASP534 3.4 47.1 1.0 HB3 B:ASP532 3.5 57.3 1.0 CB B:ASP532 3.5 47.8 1.0 H5'' G:DT10 3.7 39.0 0.5 H5'' E:DT10 3.7 78.8 0.5 OE2 B:GLU459 3.8 54.4 1.0 O B:HOH823 3.8 36.4 1.0 O B:LYS611 4.1 57.6 1.0 O B:HOH802 4.1 37.0 1.0 OP1 G:DT10 4.1 30.8 0.5 HA3 B:GLY612 4.2 66.8 1.0 HB2 B:ASP536 4.2 49.5 1.0 OD1 B:ASP532 4.3 47.5 1.0 CB B:ASP534 4.4 50.0 1.0 HB3 B:ASP534 4.5 60.0 1.0 H3' E:DT10 4.5 80.9 0.5 OP1 E:DT10 4.6 63.9 0.5 HA2 B:GLY612 4.6 66.8 1.0 C5' G:DT10 4.6 32.5 0.5 C5' E:DT10 4.7 65.7 0.5 HB2 B:ASP534 4.7 60.0 1.0 CD B:GLU459 4.8 54.7 1.0 CA B:GLY612 4.8 55.7 1.0 H B:ASP534 4.9 64.0 1.0 O3' G:DT10 5.0 37.0 0.5

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:40.1 occ:1.00 O D:HOH801 2.1 57.6 1.0 O D:HOH807 2.1 0.7 1.0 O D:HOH811 2.1 34.9 1.0 O D:HOH803 2.1 43.6 1.0 OD2 D:ASP532 2.1 50.1 1.0 OD2 D:ASP534 2.1 51.3 1.0 CG D:ASP534 3.1 49.2 1.0 CG D:ASP532 3.1 50.3 1.0 HB2 D:ASP532 3.4 60.5 1.0 HB3 D:ASP532 3.5 60.5 1.0 OD1 D:ASP534 3.5 45.8 1.0 CB D:ASP532 3.6 50.5 1.0 H5'' F:DT10 3.6 71.7 0.5 H5'' H:DT10 3.8 48.7 0.5 OE2 D:GLU459 3.9 60.2 1.0 O D:LYS611 4.0 54.1 1.0 O D:HOH817 4.0 44.1 1.0 HA3 D:GLY612 4.0 58.3 1.0 HB2 D:ASP536 4.2 58.0 1.0 OD1 D:ASP532 4.3 50.8 1.0 OP1 H:DT10 4.3 39.2 0.5 CB D:ASP534 4.4 51.5 1.0 HB3 D:ASP534 4.5 61.8 1.0 O3' F:DT10 4.5 60.6 0.5 HA2 D:GLY612 4.5 58.3 1.0 C5' F:DT10 4.6 59.8 0.5 OP1 F:DT10 4.6 62.4 0.5 H3' H:DT10 4.7 52.4 0.5 C5' H:DT10 4.7 40.6 0.5 CA D:GLY612 4.7 48.6 1.0 HB2 D:ASP534 4.8 61.8 1.0 CD D:GLU459 4.9 59.0 1.0 H3' F:DT10 5.0 71.7 0.5 H5' F:DT10 5.0 71.7 0.5 HH22 A:ARG128 5.0 64.4 0.5 HH21 A:ARG128 5.0 64.4 0.5

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:65.8 occ:1.00 O H:HOH204 2.1 57.4 1.0 O H:HOH201 2.1 0.1 1.0 O H:HOH203 2.1 0.2 1.0 O27 H:8MX101 2.1 50.3 1.0 O19 H:8MX101 2.2 45.7 1.0 C26 H:8MX101 3.1 47.5 1.0 C18 H:8MX101 3.3 44.0 1.0 C20 H:8MX101 3.6 45.0 1.0 O6 E:DG11 3.9 1.0 0.5 O4 E:DT10 4.0 73.3 0.5 H61 H:DA15 4.1 41.4 0.5 N6 G:DA11 4.2 50.8 0.5 HB1 A:ALA90 4.2 55.8 1.0 O28 H:8MX101 4.2 46.2 1.0 H051 H:8MX101 4.3 49.3 1.0 H62 H:DA15 4.3 41.4 0.5 OD2 A:ASP94 4.4 49.2 1.0 O4 G:DT10 4.4 41.0 0.5 C04 H:8MX101 4.5 41.9 1.0 N6 H:DA15 4.5 34.5 0.5 HB3 A:ALA90 4.6 55.8 1.0 O4 H:DT14 4.7 62.5 0.5 C6 E:DG11 4.7 0.9 0.5 H71 E:DT10 4.8 85.5 0.5 C05 H:8MX101 4.8 41.0 1.0 O A:HOH645 4.8 59.8 1.0 CB A:ALA90 4.9 46.5 1.0 H71 G:DT10 4.9 45.7 0.5 N4 F:DC14 4.9 0.8 0.5 H62 E:DA9 4.9 85.0 0.5 N6 F:DA15 5.0 92.3 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:47.2 occ:1.00 O F:HOH205 2.1 0.9 1.0 O C:HOH607 2.1 0.0 1.0 O E:HOH205 2.1 43.7 1.0 O19 E:8MX101 2.3 41.7 1.0 O27 E:8MX101 2.3 47.4 1.0 C18 E:8MX101 3.3 41.5 1.0 C26 E:8MX101 3.3 45.2 1.0 C20 E:8MX101 3.7 42.7 1.0 O4 F:DT10 3.8 62.8 0.5 H62 F:DA11 3.8 98.5 0.5 H61 E:DA15 4.0 96.4 0.5 H051 E:8MX101 4.2 50.0 1.0 O4 H:DT10 4.2 42.4 0.5 HB1 C:ALA90 4.2 55.5 1.0 OD2 C:ASP94 4.2 52.5 1.0 N6 F:DA11 4.2 82.0 0.5 H61 F:DA11 4.2 98.5 0.5 H62 E:DA15 4.3 96.4 0.5 O28 E:8MX101 4.4 44.8 1.0 H62 F:DA9 4.4 72.0 0.5 N6 E:DA15 4.5 80.3 0.5 C04 E:8MX101 4.5 41.2 1.0 H73 F:DT10 4.5 76.6 0.5 HB3 C:ALA90 4.5 55.5 1.0 H71 H:DT10 4.5 48.7 0.5 O6 H:DG11 4.5 75.2 0.5 N6 G:DA15 4.6 52.9 0.5 HB3 C:SER91 4.6 58.9 1.0 C05 E:8MX101 4.7 41.7 1.0 CB C:ALA90 4.8 46.2 1.0 HA C:SER91 4.8 54.6 1.0 N6 F:DA9 4.9 60.0 0.5

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