Magnesium in PDB 5btf: 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: 5btf 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)	49.78 / 2.61
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.955, 84.019, 130.590, 90.00, 108.87, 90.00
R / Rfree (%)	23 / 26.1

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 5btf). 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: 5btf:
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:41.6 occ:1.00 O B:HOH801 2.1 47.2 1.0 O B:HOH821 2.1 30.5 1.0 O B:HOH802 2.1 30.5 1.0 O B:HOH808 2.1 64.1 1.0 OD2 B:ASP532 2.1 40.3 1.0 OD2 B:ASP534 2.1 44.5 1.0 CG B:ASP534 3.1 45.0 1.0 CG B:ASP532 3.1 42.4 1.0 HB2 B:ASP532 3.3 51.9 1.0 HB3 B:ASP532 3.4 51.9 1.0 OD1 B:ASP534 3.4 43.4 1.0 CB B:ASP532 3.5 43.2 1.0 H5'' E:DT10 3.7 84.9 0.5 H5'' G:DT10 3.8 46.6 0.5 OE2 B:GLU459 4.0 54.8 1.0 O B:HOH823 4.0 30.5 1.0 O B:LYS611 4.2 74.5 1.0 HB2 B:ASP536 4.2 57.6 1.0 OP1 G:DT10 4.2 37.5 0.5 OD1 B:ASP532 4.3 43.9 1.0 HA3 B:GLY612 4.3 71.9 1.0 OP1 E:DT10 4.5 69.3 0.5 CB B:ASP534 4.5 47.7 1.0 H3' E:DT10 4.5 85.7 0.5 HB3 B:ASP534 4.5 57.2 1.0 HA2 B:GLY612 4.7 71.9 1.0 C5' E:DT10 4.7 70.8 0.5 C5' G:DT10 4.8 38.8 0.5 HB2 B:ASP534 4.8 57.2 1.0 CD B:GLU459 4.9 54.1 1.0 H B:ASP534 4.9 61.8 1.0 CA B:GLY612 5.0 60.0 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:83.1 occ:1.00 O G:HOH204 2.1 30.5 1.0 O F:HOH202 2.1 30.5 1.0 O G:HOH202 2.1 30.5 1.0 O20 G:GFN101 2.2 55.4 1.0 O22 G:GFN101 2.2 57.0 1.0 C21 G:GFN101 3.2 54.8 1.0 C19 G:GFN101 3.3 52.2 1.0 H62 F:DA11 3.5 0.3 0.5 HG C:SER90 3.6 50.8 1.0 C18 G:GFN101 3.7 52.5 1.0 H61 F:DA11 3.7 0.3 0.5 N6 F:DA11 3.8 1.0 0.5 O6 H:DG11 3.9 57.1 0.5 H61 E:DA15 4.0 91.5 0.5 OG C:SER90 4.1 42.4 1.0 O4 F:DT10 4.1 90.5 0.5 H101 G:GFN101 4.2 58.3 1.0 O4 H:DT10 4.2 52.1 0.5 H62 E:DA15 4.2 91.5 0.5 O23 G:GFN101 4.3 54.2 1.0 N6 E:DA15 4.4 76.2 0.5 C11 G:GFN101 4.5 49.3 1.0 HB3 C:SER90 4.6 50.4 1.0 O4 E:DT14 4.6 0.5 0.5 N4 G:DC14 4.6 67.2 0.5 N6 G:DA15 4.6 43.0 0.5 OD2 C:ASP94 4.6 53.5 1.0 C6 F:DA11 4.7 1.0 0.5 C10 G:GFN101 4.7 48.6 1.0 H71 H:DT10 4.7 57.3 0.5 C6 H:DG11 4.8 57.3 0.5 H73 F:DT10 4.9 0.1 0.5 O C:HOH724 4.9 72.7 1.0 CB C:SER90 4.9 42.0 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:41.6 occ:1.00 OD2 D:ASP532 2.0 47.6 1.0 O D:HOH810 2.0 30.5 1.0 O D:HOH801 2.1 30.5 1.0 O D:HOH809 2.1 30.5 1.0 O D:HOH804 2.1 30.5 1.0 OD2 D:ASP534 2.1 50.3 1.0 CG D:ASP534 2.9 48.5 1.0 CG D:ASP532 3.0 46.9 1.0 HB2 D:ASP532 3.1 53.1 1.0 OD1 D:ASP534 3.1 45.5 1.0 HB3 D:ASP532 3.3 53.1 1.0 CB D:ASP532 3.3 44.3 1.0 H5'' F:DT10 3.5 96.4 0.5 OE2 D:GLU459 3.6 54.6 1.0 HB2 D:ASP536 3.8 53.9 1.0 H5'' H:DT10 3.9 38.6 0.5 OD1 D:ASP532 4.2 48.6 1.0 O D:LYS611 4.3 59.7 1.0 CB D:ASP534 4.4 50.0 1.0 HA3 D:GLY612 4.4 58.1 1.0 C5' F:DT10 4.5 80.3 0.5 HB3 D:ASP534 4.5 59.9 1.0 OP1 F:DT10 4.5 78.0 0.5 CD D:GLU459 4.6 54.2 1.0 OP1 H:DT10 4.6 30.8 0.5 O3' F:DT10 4.6 84.4 0.5 HA2 D:GLY612 4.7 58.1 1.0 CB D:ASP536 4.7 44.9 1.0 H D:GLY537 4.7 56.1 1.0 HB2 D:ASP534 4.7 59.9 1.0 H D:ASP534 4.8 60.8 1.0 H3' H:DT10 4.8 41.4 0.5 OE1 D:GLU459 4.8 53.6 1.0 C5' H:DT10 4.8 32.1 0.5 H5' F:DT10 4.8 96.4 0.5 CA D:ASP532 4.8 44.7 1.0 HB3 D:ASP536 4.9 53.9 1.0 H D:ASP532 5.0 52.8 1.0 H4' F:DT10 5.0 97.5 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 E:Mg101 b:68.4 occ:1.00 O F:HOH203 2.1 30.5 1.0 O E:HOH203 2.1 30.5 1.0 O E:HOH202 2.1 30.5 1.0 O20 F:GFN101 2.2 48.2 1.0 O22 F:GFN101 2.3 51.4 1.0 C19 F:GFN101 3.3 47.4 1.0 C21 F:GFN101 3.4 49.4 1.0 C18 F:GFN101 3.8 47.0 1.0 O4 E:DT10 3.8 77.0 0.5 HG A:SER90 3.8 57.2 1.0 O6 E:DG11 3.8 0.7 0.5 N6 G:DA11 3.9 49.4 0.5 H61 H:DA15 4.0 41.2 0.5 O4 G:DT10 4.1 44.5 0.5 H101 F:GFN101 4.1 57.8 1.0 OG A:SER90 4.1 47.7 1.0 H62 H:DA15 4.2 41.2 0.5 N6 H:DA15 4.4 34.4 0.5 C11 F:GFN101 4.4 47.8 1.0 O23 F:GFN101 4.5 49.7 1.0 O4 H:DT14 4.6 63.0 0.5 HB3 A:SER90 4.6 57.0 1.0 C6 E:DG11 4.6 0.7 0.5 N6 F:DA15 4.6 0.8 0.5 C10 F:GFN101 4.7 48.2 1.0 H71 G:DT10 4.7 50.4 0.5 OD2 A:ASP94 4.7 48.2 1.0 N4 F:DC14 4.7 0.5 0.5 O A:HOH675 4.8 30.5 1.0 H41 F:DC14 4.8 0.2 0.5 C6 G:DA11 4.8 49.6 0.5 H71 E:DT10 4.8 89.9 0.5 H62 E:DA9 4.9 85.1 0.5 CB A:SER90 5.0 47.5 1.0 C4 E:DT10 5.0 76.2 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