Magnesium in PDB 5bti: 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: 5bti 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)	49.43 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.390, 83.280, 129.701, 90.00, 108.73, 90.00
R / Rfree (%)	21.5 / 24

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 5bti). 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: 5bti:
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:49.6 occ:1.00 O B:HOH804 2.1 53.0 1.0 OD2 B:ASP534 2.1 44.3 1.0 O B:HOH809 2.1 92.0 1.0 O B:HOH808 2.1 37.9 1.0 O G:HOH102 2.1 32.6 1.0 OD2 B:ASP532 2.1 44.3 1.0 CG B:ASP534 3.1 44.7 1.0 CG B:ASP532 3.1 44.8 1.0 HB2 B:ASP532 3.2 54.3 1.0 HB3 B:ASP532 3.3 54.3 1.0 OD1 B:ASP534 3.4 44.2 1.0 CB B:ASP532 3.4 45.2 1.0 H5'' E:DT10 3.7 95.1 0.5 H5'' G:DT10 3.7 29.4 0.5 OE2 B:GLU459 3.8 57.2 1.0 O B:HOH834 4.0 31.9 1.0 O B:LYS611 4.1 56.6 1.0 HA3 B:GLY612 4.1 55.5 1.0 OD1 B:ASP532 4.2 45.8 1.0 HB2 B:ASP536 4.3 53.9 1.0 OP1 G:DT10 4.3 22.6 0.5 H3' E:DT10 4.4 94.5 0.5 CB B:ASP534 4.4 46.5 1.0 OP1 E:DT10 4.4 78.6 0.5 HB3 B:ASP534 4.5 55.8 1.0 HA2 B:GLY612 4.6 55.5 1.0 C5' E:DT10 4.6 79.2 0.5 C5' G:DT10 4.7 24.5 0.5 CD B:GLU459 4.8 56.0 1.0 HB2 B:ASP534 4.8 55.8 1.0 CA B:GLY612 4.8 46.3 1.0 H B:ASP534 4.8 61.3 1.0 CA B:ASP532 4.9 45.2 1.0 O3' G:DT10 4.9 27.8 0.5 H B:GLY537 4.9 52.5 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:38.5 occ:1.00 O F:HOH202 2.1 39.0 1.0 O F:HOH210 2.1 56.9 1.0 O C:HOH723 2.1 35.4 1.0 O F:HOH204 2.1 44.0 1.0 O F:LFX101 2.1 38.9 1.0 O02 F:LFX101 2.4 34.9 1.0 C F:LFX101 3.3 37.7 1.0 HG C:SER90 3.4 48.6 1.0 C15 F:LFX101 3.4 35.9 1.0 H62 F:DA11 3.6 0.8 0.5 OG C:SER90 3.8 40.5 1.0 C17 F:LFX101 3.8 36.9 1.0 O F:HOH211 3.9 0.4 1.0 O4 F:DT10 4.0 70.2 0.5 N6 F:DA11 4.1 84.8 0.5 H61 F:DA11 4.1 0.8 0.5 H61 E:DA15 4.2 69.6 0.5 O4 H:DT10 4.2 32.6 0.5 OD2 C:ASP94 4.2 50.1 1.0 H61 G:DA15 4.3 55.4 0.5 O03 F:LFX101 4.3 37.0 1.0 O6 H:DG11 4.4 34.1 0.5 H62 E:DA15 4.5 69.6 0.5 HB3 C:SER90 4.5 46.0 1.0 H71 H:DT10 4.5 38.1 0.5 H13 F:LFX101 4.6 44.4 1.0 H42 G:DC14 4.6 38.2 0.5 N6 E:DA15 4.7 58.0 0.5 N6 G:DA15 4.7 46.2 0.5 HB3 C:SER91 4.7 61.6 1.0 H73 F:DT10 4.7 82.3 0.5 H62 F:DA9 4.7 86.2 0.5 C10 F:LFX101 4.8 36.9 1.0 CB C:SER90 4.8 38.4 1.0 HA C:SER91 4.8 57.9 1.0 N4 G:DC14 5.0 31.8 0.5 C6 F:DA11 5.0 83.4 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 D:Mg701 b:31.5 occ:1.00 OD2 D:ASP532 2.1 46.2 1.0 O D:HOH805 2.1 33.4 1.0 O D:HOH807 2.1 28.4 1.0 O D:HOH829 2.1 44.6 1.0 OD2 D:ASP534 2.1 48.2 1.0 O D:HOH809 2.1 26.6 1.0 CG D:ASP534 3.0 48.0 1.0 CG D:ASP532 3.1 47.3 1.0 HB2 D:ASP532 3.2 55.8 1.0 OD1 D:ASP534 3.3 46.5 1.0 HB3 D:ASP532 3.4 55.8 1.0 CB D:ASP532 3.4 46.5 1.0 H5'' F:DT10 3.6 77.5 0.5 H5'' H:DT10 3.7 35.1 0.5 OE2 D:GLU459 3.7 53.6 1.0 HB2 D:ASP536 4.1 52.2 1.0 HA3 D:GLY612 4.1 57.1 1.0 O D:LYS611 4.1 55.7 1.0 O D:HOH803 4.2 52.4 1.0 OD1 D:ASP532 4.2 49.0 1.0 OP1 F:DT10 4.4 65.7 0.5 CB D:ASP534 4.4 49.8 1.0 O3' F:DT10 4.5 65.1 0.5 OP1 H:DT10 4.5 24.5 0.5 O C:HOH772 4.5 49.0 1.0 HB3 D:ASP534 4.5 59.8 1.0 C5' F:DT10 4.5 64.6 0.5 HA2 D:GLY612 4.5 57.1 1.0 H3' H:DT10 4.6 37.3 0.5 C5' H:DT10 4.6 29.2 0.5 O C:HOH751 4.7 0.7 1.0 CD D:GLU459 4.7 53.1 1.0 O A:HOH639 4.7 29.8 1.0 HB2 D:ASP534 4.8 59.8 1.0 CA D:GLY612 4.8 47.6 1.0 H D:ASP534 4.9 62.9 1.0 HH21 A:ARG128 4.9 48.4 0.5 H D:GLY537 4.9 53.1 1.0 CA D:ASP532 5.0 45.6 1.0 H5' F:DT10 5.0 77.5 0.5 H5' H:DT10 5.0 35.1 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:Mg102 b:35.4 occ:1.00 O03 E:LFX101 2.0 36.0 1.0 O02 E:LFX101 2.1 36.0 1.0 O E:HOH210 2.1 34.6 1.0 O A:HOH626 2.1 33.2 1.0 O E:HOH201 2.1 37.6 1.0 O E:HOH204 2.1 34.7 1.0 C E:LFX101 3.1 36.0 1.0 C15 E:LFX101 3.1 36.8 1.0 C17 E:LFX101 3.5 36.8 1.0 OG A:SER90 3.7 42.0 1.0 O4 E:DT10 3.7 82.6 0.5 O4 G:DT10 4.0 31.3 0.5 O6 E:DG11 4.0 0.2 0.5 N6 G:DA11 4.1 29.9 0.5 O E:HOH206 4.1 0.3 1.0 O E:LFX101 4.2 35.7 1.0 H71 G:DT10 4.2 34.9 0.5 H61 H:DA15 4.2 33.2 0.5 HG A:SER90 4.3 50.4 1.0 HB3 A:SER90 4.3 49.8 1.0 H13 E:LFX101 4.3 45.2 1.0 H61 F:DA15 4.3 79.9 0.5 OD2 A:ASP94 4.4 45.4 1.0 C10 E:LFX101 4.4 37.8 1.0 H71 E:DT10 4.5 97.4 0.5 H62 H:DA15 4.5 33.2 0.5 HB3 A:SER91 4.6 56.7 1.0 CB A:SER90 4.6 41.5 1.0 H62 F:DA15 4.6 95.9 0.5 H42 F:DC14 4.6 0.7 0.5 O A:HOH605 4.7 44.8 1.0 N6 H:DA15 4.7 27.7 0.5 C6 E:DG11 4.8 0.9 0.5 N6 F:DA15 4.8 79.9 0.5 H62 E:DA9 4.8 0.3 0.5 C13 E:LFX101 4.8 37.6 1.0 HA A:SER91 4.8 54.4 1.0 C4 E:DT10 4.9 81.9 0.5 C6 G:DA11 5.0 31.5 0.5 C12 E:LFX101 5.0 38.7 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