Magnesium in PDB 5bs8: 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: 5bs8 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)	102.25 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.357, 83.070, 129.856, 90.00, 109.33, 90.00
R / Rfree (%)	19.6 / 23.3

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 5bs8). 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: 5bs8:
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:47.9 occ:1.00 O B:HOH804 2.1 53.1 1.0 O B:HOH816 2.1 54.0 1.0 O B:HOH811 2.1 36.6 1.0 O B:HOH812 2.1 40.8 1.0 OD2 B:ASP532 2.1 50.1 1.0 OD2 B:ASP534 2.1 53.6 1.0 CG B:ASP534 3.1 51.3 1.0 CG B:ASP532 3.1 51.7 1.0 HB2 B:ASP532 3.3 62.6 1.0 HB3 B:ASP532 3.3 62.6 1.0 OD1 B:ASP534 3.4 49.0 1.0 CB B:ASP532 3.4 52.2 1.0 H5'' E:DT10 3.9 0.3 0.5 O B:LYS611 3.9 66.5 1.0 H5'' G:DT10 3.9 65.7 0.5 OE2 B:GLU459 3.9 60.8 1.0 O B:HOH833 4.0 40.4 1.0 HA3 B:GLY612 4.0 61.7 1.0 OD1 B:ASP532 4.2 53.8 1.0 HB2 B:ASP536 4.3 62.7 1.0 OP1 E:DT10 4.4 0.1 0.5 OP1 G:DT10 4.4 49.3 0.5 CB B:ASP534 4.4 54.0 1.0 HA2 B:GLY612 4.5 61.7 1.0 HB3 B:ASP534 4.5 64.9 1.0 CA B:GLY612 4.7 51.4 1.0 H3' E:DT10 4.8 0.5 0.5 HB2 B:ASP534 4.8 64.9 1.0 C5' E:DT10 4.8 0.9 0.5 C5' G:DT10 4.9 54.8 0.5 H B:ASP534 4.9 69.3 1.0 CD B:GLU459 4.9 60.3 1.0 H3' G:DT10 5.0 71.1 0.5 C B:LYS611 5.0 62.1 1.0 CA B:ASP532 5.0 51.8 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:35.3 occ:1.00 O D:HOH802 2.1 44.9 1.0 OD2 D:ASP534 2.1 51.7 1.0 O D:HOH831 2.1 48.0 1.0 OD2 D:ASP532 2.1 48.7 1.0 O D:HOH807 2.1 31.3 1.0 O D:HOH809 2.1 45.8 1.0 CG D:ASP534 3.0 48.4 1.0 CG D:ASP532 3.1 49.4 1.0 HB2 D:ASP532 3.3 60.0 1.0 OD1 D:ASP534 3.3 45.8 1.0 HB3 D:ASP532 3.3 60.0 1.0 CB D:ASP532 3.5 50.0 1.0 H5'' F:DT10 3.7 84.4 0.5 OE2 D:GLU459 3.8 58.6 1.0 H5'' H:DT10 3.8 40.2 0.5 O D:HOH842 3.9 41.0 1.0 O D:LYS611 3.9 67.3 1.0 HA3 D:GLY612 4.0 67.1 1.0 O D:HOH806 4.1 40.0 1.0 HB2 D:ASP536 4.2 53.5 1.0 OD1 D:ASP532 4.2 49.8 1.0 CB D:ASP534 4.4 50.1 1.0 OP1 F:DT10 4.4 69.5 0.5 OP1 H:DT10 4.5 28.1 0.5 HB3 D:ASP534 4.5 60.1 1.0 HA2 D:GLY612 4.5 67.1 1.0 O C:HOH680 4.5 53.6 1.0 C5' F:DT10 4.7 70.3 0.5 CA D:GLY612 4.7 55.9 1.0 HB2 D:ASP534 4.7 60.1 1.0 H3' H:DT10 4.8 41.1 0.5 C5' H:DT10 4.8 33.5 0.5 CD D:GLU459 4.8 57.1 1.0 O3' F:DT10 4.8 74.0 0.5 H D:ASP534 4.9 63.6 1.0 CA D:ASP532 5.0 49.7 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:Mg101 b:53.8 occ:1.00 O H:HOH209 2.1 83.0 1.0 O H:HOH202 2.1 67.7 1.0 O A:HOH615 2.1 0.8 1.0 O H:HOH203 2.1 50.7 1.0 O03 H:MFX101 2.1 44.8 1.0 O02 H:MFX101 2.2 42.6 1.0 C20 H:MFX101 3.2 45.1 1.0 C19 H:MFX101 3.2 41.8 1.0 C18 H:MFX101 3.6 40.7 1.0 HB1 A:ALA90 3.7 47.4 1.0 N6 G:DA11 3.9 29.2 0.5 H61 G:DA11 4.0 35.0 0.5 O6 E:DG11 4.0 0.7 0.5 HB3 A:ALA90 4.1 47.4 1.0 O4 E:DT10 4.2 1.0 0.5 O H:MFX101 4.2 50.8 1.0 OD2 A:ASP94 4.3 57.5 1.0 H17 H:MFX101 4.3 55.0 1.0 CB A:ALA90 4.3 39.5 1.0 O4 G:DT10 4.4 56.8 0.5 H71 G:DT10 4.5 71.1 0.5 H61 H:DA15 4.5 40.8 0.5 O G:HOH211 4.5 64.4 1.0 C14 H:MFX101 4.5 43.0 1.0 HB3 A:SER91 4.7 64.5 1.0 H71 E:DT10 4.7 0.2 0.5 H62 H:DA15 4.7 40.8 0.5 C6 E:DG11 4.9 0.1 0.5 HB2 A:ALA90 4.9 47.4 1.0 C6 G:DA11 4.9 29.4 0.5 C17 H:MFX101 4.9 45.8 1.0 O4 H:DT14 4.9 50.2 0.5 HA A:SER91 4.9 57.2 1.0 N6 H:DA15 4.9 34.0 0.5 O E:HOH207 5.0 68.8 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 F:Mg101 b:44.5 occ:1.00 O G:MFX101 2.0 49.2 1.0 O G:HOH203 2.1 38.9 1.0 O G:HOH206 2.1 46.3 1.0 O G:HOH210 2.1 51.6 1.0 O G:HOH205 2.1 46.5 1.0 O02 G:MFX101 2.1 42.6 1.0 C20 G:MFX101 3.0 48.2 1.0 C19 G:MFX101 3.1 42.9 1.0 C18 G:MFX101 3.5 45.2 1.0 HB1 C:ALA90 3.9 44.1 1.0 N6 F:DA11 4.0 0.5 0.5 O6 H:DG11 4.0 36.8 0.5 H61 E:DA15 4.1 83.3 0.5 H61 F:DA11 4.1 0.8 0.5 O03 G:MFX101 4.1 48.9 1.0 O4 H:DT10 4.1 40.2 0.5 O4 F:DT10 4.1 97.2 0.5 HB3 C:ALA90 4.2 44.1 1.0 H61 G:DA15 4.3 49.2 0.5 H17 G:MFX101 4.3 53.0 1.0 OD2 C:ASP94 4.4 50.7 1.0 C14 G:MFX101 4.4 43.0 1.0 H42 G:DC14 4.4 42.8 0.5 H62 E:DA15 4.5 83.3 0.5 CB C:ALA90 4.5 36.8 1.0 H71 H:DT10 4.6 50.9 0.5 N6 E:DA15 4.6 69.4 0.5 H41 G:DC14 4.6 42.8 0.5 HB3 C:SER91 4.6 70.9 1.0 O F:HOH204 4.7 0.5 1.0 N6 G:DA15 4.7 41.0 0.5 H73 F:DT10 4.8 0.6 0.5 N4 G:DC14 4.8 35.7 0.5 C17 G:MFX101 4.8 44.2 1.0 C6 H:DG11 4.8 39.5 0.5 HA C:SER91 4.9 62.2 1.0 C6 F:DA11 4.9 0.8 0.5 C16 G:MFX101 4.9 45.8 1.0 H62 F:DA9 5.0 0.5 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