Magnesium in PDB 5btc: 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: 5btc 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)	47.70 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.336, 82.976, 129.703, 90.00, 109.06, 90.00
R / Rfree (%)	22.4 / 25

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 5btc). 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: 5btc:
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 A:Mg601 b:58.9 occ:1.00 O G:HOH204 2.1 78.6 1.0 O A:HOH704 2.1 49.2 1.0 O G:HOH202 2.1 82.1 1.0 O2 G:CPF102 2.2 0.4 1.0 O3 G:CPF102 2.2 82.2 1.0 C3 G:CPF102 3.3 91.5 1.0 C4 G:CPF102 3.3 81.1 1.0 HG A:SER90 3.4 44.4 1.0 C2 G:CPF102 3.7 84.5 1.0 O A:HOH748 3.7 99.1 1.0 OG A:SER90 3.9 37.0 1.0 N6 G:DA11 4.1 47.1 0.5 O4 E:DT10 4.2 48.7 0.5 H61 G:DA11 4.2 56.6 0.5 O1 G:CPF102 4.3 89.6 1.0 O4 G:DT10 4.3 44.4 0.5 OD2 A:ASP94 4.4 56.8 1.0 H6 G:CPF102 4.4 90.0 1.0 O6 E:DG11 4.4 0.9 0.5 H61 H:DA15 4.4 36.0 0.5 H62 H:DA15 4.4 36.0 0.5 HB3 A:SER90 4.5 45.1 1.0 H62 F:DA15 4.6 0.2 0.5 C5 G:CPF102 4.6 78.1 1.0 N6 H:DA15 4.7 30.0 0.5 H41 F:DC14 4.8 0.6 0.5 CB A:SER90 4.8 37.5 1.0 H62 E:DA9 4.8 61.6 0.5 N6 F:DA15 4.8 85.2 0.5 O4 H:DT14 4.8 51.6 0.5 H71 G:DT10 4.9 52.6 0.5 N4 F:DC14 4.9 0.5 0.5 C6 G:CPF102 4.9 75.0 1.0 HB3 A:SER91 4.9 67.3 1.0 C6 G:DA11 5.0 47.7 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 B:Mg701 b:39.4 occ:1.00 OD2 B:ASP534 2.1 51.6 1.0 O B:HOH804 2.1 46.3 1.0 O B:HOH812 2.1 38.8 1.0 O B:HOH805 2.1 68.3 1.0 O B:HOH810 2.1 80.0 1.0 OD2 B:ASP532 2.1 51.5 1.0 CG B:ASP534 3.0 51.8 1.0 CG B:ASP532 3.1 51.9 1.0 HB2 B:ASP532 3.3 62.4 1.0 OD1 B:ASP534 3.3 51.0 1.0 HB3 B:ASP532 3.4 62.4 1.0 CB B:ASP532 3.5 52.0 1.0 H5'' E:DT10 3.7 55.9 0.5 O B:HOH820 3.7 31.8 1.0 H5'' G:DT10 3.8 55.1 0.5 OE2 B:GLU459 3.9 59.8 1.0 O B:LYS611 4.0 73.9 1.0 HA3 B:GLY612 4.1 63.6 1.0 HB2 B:ASP536 4.2 53.5 1.0 OD1 B:ASP532 4.2 52.9 1.0 OP1 G:DT10 4.3 44.3 0.5 OP1 E:DT10 4.3 45.8 0.5 CB B:ASP534 4.4 53.7 1.0 HB3 B:ASP534 4.5 64.5 1.0 H3' E:DT10 4.5 56.8 0.5 HA2 B:GLY612 4.6 63.6 1.0 C5' E:DT10 4.7 46.6 0.5 C5' G:DT10 4.7 45.9 0.5 HB2 B:ASP534 4.8 64.5 1.0 H B:ASP534 4.8 69.5 1.0 CA B:GLY612 4.8 53.0 1.0 CD B:GLU459 4.9 58.3 1.0 O3' G:DT10 5.0 48.4 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 C:Mg601 b:42.5 occ:1.00 O G:HOH207 2.1 41.4 1.0 O G:HOH206 2.1 55.3 1.0 O G:HOH203 2.1 53.6 1.0 O1 G:CPF101 2.2 60.2 1.0 O3 G:CPF101 2.3 51.2 1.0 C3 G:CPF101 3.3 56.6 1.0 C4 G:CPF101 3.4 51.8 1.0 HG C:SER90 3.5 50.5 1.0 C2 G:CPF101 3.8 53.6 1.0 OG C:SER90 3.9 42.1 1.0 H62 F:DA11 4.0 0.7 0.5 H61 E:DA15 4.1 0.2 0.5 O4 F:DT10 4.2 83.6 0.5 OD2 C:ASP94 4.2 53.8 1.0 H61 G:DA15 4.3 25.2 0.5 N6 F:DA11 4.3 0.2 0.5 O4 H:DT10 4.3 32.9 0.5 H61 F:DA11 4.3 0.7 0.5 O2 G:CPF101 4.4 56.4 1.0 H62 E:DA15 4.4 0.2 0.5 H6 G:CPF101 4.5 64.0 1.0 O6 H:DG11 4.5 50.9 0.5 N6 G:DA15 4.6 21.0 0.5 H42 G:DC14 4.6 39.8 0.5 HB3 C:SER90 4.6 49.4 1.0 N6 E:DA15 4.6 83.5 0.5 C5 G:CPF101 4.7 52.3 1.0 H71 H:DT10 4.7 37.4 0.5 H62 F:DA9 4.8 96.8 0.5 HB3 C:SER91 4.9 64.9 1.0 HA C:SER91 4.9 59.6 1.0 CB C:SER90 4.9 41.1 1.0 N4 G:DC14 4.9 33.2 0.5 O4 E:DT14 4.9 0.3 0.5 H73 F:DT10 5.0 0.0 0.5 C6 G:CPF101 5.0 53.3 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 D:Mg701 b:47.5 occ:1.00 O D:HOH801 2.1 46.4 1.0 O D:HOH810 2.1 0.2 1.0 O D:HOH806 2.1 0.7 1.0 O D:HOH803 2.1 51.6 1.0 OD2 D:ASP532 2.1 50.1 1.0 OD2 D:ASP534 2.1 53.8 1.0 CG D:ASP534 3.0 51.7 1.0 CG D:ASP532 3.2 49.3 1.0 OD1 D:ASP534 3.3 49.5 1.0 HB2 D:ASP532 3.3 58.0 1.0 H5'' F:DT10 3.5 0.2 0.5 HB3 D:ASP532 3.5 58.0 1.0 CB D:ASP532 3.6 48.4 1.0 H5'' H:DT10 3.6 31.2 0.5 OE2 D:GLU459 3.7 56.5 1.0 HB2 D:ASP536 3.8 59.9 1.0 O D:LYS611 4.2 54.8 1.0 HA3 D:GLY612 4.2 55.0 1.0 OP1 F:DT10 4.2 87.8 0.5 OD1 D:ASP532 4.3 50.0 1.0 OP1 H:DT10 4.4 22.4 0.5 CB D:ASP534 4.4 52.2 1.0 C5' F:DT10 4.4 86.0 0.5 H3' H:DT10 4.5 33.0 0.5 C5' H:DT10 4.5 26.0 0.5 HB3 D:ASP534 4.5 62.7 1.0 O3' F:DT10 4.6 91.4 0.5 HA2 D:GLY612 4.7 55.0 1.0 CB D:ASP536 4.7 49.9 1.0 HB2 D:ASP534 4.7 62.7 1.0 CD D:GLU459 4.7 56.2 1.0 H5' F:DT10 4.9 0.2 0.5 HB3 D:ASP536 4.9 59.9 1.0 CA D:GLY612 4.9 45.8 1.0 H5' H:DT10 4.9 31.2 0.5 H D:GLY537 5.0 54.1 1.0 H D:ASP534 5.0 64.3 1.0 H3' F:DT10 5.0 0.4 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