Magnesium in PDB 5btn: 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: 5btn 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)	49.65 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.337, 82.914, 129.078, 90.00, 108.78, 90.00
R / Rfree (%)	22.3 / 25.1

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 5btn). 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: 5btn:
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:37.9 occ:1.00 O B:HOH802 2.1 44.4 1.0 O B:HOH801 2.1 97.7 1.0 O B:HOH803 2.1 47.2 1.0 O B:HOH810 2.1 38.9 1.0 OD2 B:ASP534 2.1 44.1 1.0 OD2 B:ASP532 2.1 46.1 1.0 CG B:ASP534 3.1 44.2 1.0 CG B:ASP532 3.1 45.8 1.0 HB2 B:ASP532 3.3 54.7 1.0 HB3 B:ASP532 3.4 54.7 1.0 OD1 B:ASP534 3.5 43.2 1.0 CB B:ASP532 3.5 45.6 1.0 OE2 B:GLU459 3.8 51.0 1.0 H5'' E:DT10 3.8 76.7 0.5 H5'' G:DT10 3.9 51.8 0.5 O B:LYS611 4.1 60.6 1.0 HA3 B:GLY612 4.1 54.5 1.0 HB2 B:ASP536 4.2 53.7 1.0 OP1 G:DT10 4.2 43.5 0.5 OD1 B:ASP532 4.3 46.5 1.0 CB B:ASP534 4.5 46.6 1.0 HB3 B:ASP534 4.5 56.0 1.0 H3' E:DT10 4.5 77.0 0.5 HA2 B:GLY612 4.6 54.5 1.0 OP1 E:DT10 4.6 64.2 0.5 CD B:GLU459 4.7 50.4 1.0 C5' E:DT10 4.8 63.9 0.5 CA B:GLY612 4.8 45.4 1.0 C5' G:DT10 4.8 43.1 0.5 HB2 B:ASP534 4.8 56.0 1.0 H B:ASP534 4.9 62.9 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 C:Mg601 b:46.8 occ:1.00 O G:HOH202 2.1 57.9 1.0 O G:HOH201 2.1 74.6 1.0 O G:HOH203 2.1 43.8 1.0 O28 G:8MX101 2.1 58.1 1.0 O19 G:8MX101 2.2 60.5 1.0 C26 G:8MX101 3.1 57.7 1.0 C18 G:8MX101 3.2 60.0 1.0 C20 G:8MX101 3.6 59.0 1.0 H62 F:DA11 3.8 77.1 0.5 HG C:SER90 3.9 61.9 1.0 H61 F:DA11 4.1 77.1 0.5 H61 E:DA15 4.1 80.3 0.5 H051 G:8MX101 4.1 75.0 1.0 N6 F:DA11 4.1 64.3 0.5 H61 G:DA15 4.2 51.6 0.5 O4 H:DT10 4.2 39.2 0.5 O27 G:8MX101 4.3 56.2 1.0 OD2 C:ASP94 4.3 46.9 1.0 O4 F:DT10 4.3 81.4 0.5 H42 G:DC14 4.3 68.5 0.5 O6 H:DG11 4.3 80.8 0.5 OG C:SER90 4.3 51.6 1.0 H62 E:DA15 4.3 80.3 0.5 H41 G:DC14 4.4 68.5 0.5 C04 G:8MX101 4.4 61.4 1.0 N6 G:DA15 4.5 43.0 0.5 N6 E:DA15 4.6 66.9 0.5 N4 G:DC14 4.6 57.1 0.5 HB3 C:SER90 4.7 61.0 1.0 H71 H:DT10 4.7 45.4 0.5 C05 G:8MX101 4.7 62.5 1.0 H62 F:DA9 4.8 97.9 0.5 O4 E:DT14 4.9 96.7 0.5 H62 H:DA9 5.0 37.0 0.5 C21 G:8MX101 5.0 60.9 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 D:Mg701 b:32.2 occ:1.00 OD2 D:ASP534 2.1 41.9 1.0 O D:HOH802 2.1 59.5 1.0 O D:HOH801 2.1 89.4 1.0 O D:HOH808 2.1 24.8 1.0 O D:HOH805 2.1 37.5 1.0 OD2 D:ASP532 2.1 44.9 1.0 CG D:ASP534 3.1 42.5 1.0 CG D:ASP532 3.2 45.1 1.0 HB2 D:ASP532 3.4 53.4 1.0 H5'' F:DT10 3.4 87.9 0.5 HB3 D:ASP532 3.5 53.4 1.0 OD1 D:ASP534 3.5 39.6 1.0 CB D:ASP532 3.6 44.5 1.0 OE2 D:GLU459 3.9 60.4 1.0 H5'' H:DT10 3.9 36.9 0.5 O D:LYS611 3.9 53.6 1.0 HA3 D:GLY612 4.0 50.8 1.0 OP1 F:DT10 4.1 71.5 0.5 HB2 D:ASP536 4.1 57.6 1.0 OD1 D:ASP532 4.3 46.2 1.0 C5' F:DT10 4.4 73.2 0.5 CB D:ASP534 4.4 46.6 1.0 HB3 D:ASP534 4.5 55.9 1.0 HA2 D:GLY612 4.5 50.8 1.0 OP1 H:DT10 4.6 23.9 0.5 CA D:GLY612 4.7 42.3 1.0 H3' H:DT10 4.7 40.0 0.5 H5' F:DT10 4.8 87.9 0.5 HB2 D:ASP534 4.8 55.9 1.0 O3' F:DT10 4.8 78.9 0.5 CD D:GLU459 4.9 59.1 1.0 C5' H:DT10 4.9 30.8 0.5 H D:ASP534 5.0 59.8 1.0

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 E:Mg101 b:74.6 occ:1.00 O H:HOH201 2.1 41.2 1.0 O H:HOH203 2.1 49.3 1.0 O H:HOH204 2.1 78.8 1.0 O19 H:8MX101 2.2 50.7 1.0 O27 H:8MX101 2.2 51.6 1.0 C18 H:8MX101 3.2 50.1 1.0 C26 H:8MX101 3.2 49.9 1.0 C20 H:8MX101 3.6 50.1 1.0 O4 E:DT10 3.8 67.9 0.5 H61 H:DA15 3.9 32.0 0.5 HG A:SER90 4.0 49.6 1.0 H62 H:DA15 4.0 32.0 0.5 O6 E:DG11 4.0 0.3 0.5 H051 H:8MX101 4.1 59.2 1.0 N6 G:DA11 4.1 49.9 0.5 O4 G:DT10 4.2 44.9 0.5 N6 H:DA15 4.3 26.7 0.5 O28 H:8MX101 4.3 47.3 1.0 OG A:SER90 4.4 41.4 1.0 OD2 A:ASP94 4.4 50.0 1.0 C04 H:8MX101 4.4 50.2 1.0 O4 H:DT14 4.6 65.3 0.5 H62 E:DA9 4.6 83.4 0.5 N6 F:DA15 4.6 86.3 0.5 H71 G:DT10 4.7 49.5 0.5 C05 H:8MX101 4.7 49.3 1.0 H41 F:DC14 4.7 0.7 0.5 N4 F:DC14 4.7 91.4 0.5 HB3 A:SER90 4.7 49.5 1.0 C6 E:DG11 4.8 0.4 0.5 H71 E:DT10 4.9 78.8 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