Magnesium in PDB 5bta: 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: 5bta 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)	49.46 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.340, 83.205, 129.757, 90.00, 108.55, 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 5bta). 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: 5bta:
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:63.7 occ:1.00 O H:HOH202 2.1 41.4 1.0 O E:HOH102 2.1 0.4 1.0 O H:HOH206 2.1 0.9 1.0 O A:HOH702 2.1 90.0 1.0 O H:MFX101 2.2 57.6 1.0 O02 H:MFX101 2.2 53.5 1.0 C19 H:MFX101 3.2 52.9 1.0 C20 H:MFX101 3.2 55.7 1.0 HG A:SER90 3.4 63.9 1.0 C18 H:MFX101 3.6 54.1 1.0 OG A:SER90 3.8 53.2 1.0 O4 E:DT10 3.8 1.0 0.5 O4 G:DT10 4.0 33.3 0.5 OD2 A:ASP94 4.1 59.4 1.0 H17 H:MFX101 4.3 62.1 1.0 H61 H:DA15 4.3 48.8 0.5 H61 F:DA15 4.3 0.9 0.5 O03 H:MFX101 4.3 54.8 1.0 N6 G:DA11 4.3 39.5 0.5 H61 G:DA11 4.3 47.4 0.5 H71 G:DT10 4.3 36.7 0.5 O6 E:DG11 4.4 0.9 0.5 HB3 A:SER90 4.5 62.2 1.0 C14 H:MFX101 4.5 51.5 1.0 H62 E:DA9 4.5 0.6 0.5 HB3 A:SER91 4.5 67.7 1.0 H62 F:DA15 4.5 0.9 0.5 H71 E:DT10 4.5 0.9 0.5 H62 H:DA15 4.5 48.8 0.5 HA A:SER91 4.7 65.3 1.0 N6 H:DA15 4.7 40.7 0.5 N6 F:DA15 4.8 0.1 0.5 CB A:SER90 4.8 51.9 1.0 H42 F:DC14 4.8 0.1 0.5 C17 H:MFX101 4.8 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 B:Mg701 b:53.8 occ:1.00 O B:HOH803 2.1 43.7 1.0 O B:HOH807 2.1 59.4 1.0 O B:HOH804 2.1 67.0 1.0 O B:HOH806 2.1 95.1 1.0 OD2 B:ASP534 2.1 51.7 1.0 OD2 B:ASP532 2.1 52.0 1.0 CG B:ASP534 3.0 51.3 1.0 CG B:ASP532 3.1 52.2 1.0 OD1 B:ASP534 3.2 49.5 1.0 HB2 B:ASP532 3.2 61.9 1.0 HB3 B:ASP532 3.4 61.9 1.0 CB B:ASP532 3.5 51.6 1.0 H5'' E:DT10 3.6 0.6 0.5 H5'' G:DT10 3.8 32.3 0.5 OE2 B:GLU459 3.8 64.1 1.0 O B:HOH815 4.0 39.9 1.0 HB2 B:ASP536 4.1 65.6 1.0 O B:LYS611 4.2 70.4 1.0 OD1 B:ASP532 4.3 53.6 1.0 HA3 B:GLY612 4.3 71.6 1.0 OP1 E:DT10 4.4 0.9 0.5 CB B:ASP534 4.4 53.1 1.0 OP1 G:DT10 4.4 27.0 0.5 H3' E:DT10 4.5 0.6 0.5 HB3 B:ASP534 4.5 63.7 1.0 C5' E:DT10 4.6 0.5 0.5 HA2 B:GLY612 4.7 71.6 1.0 HB2 B:ASP534 4.7 63.7 1.0 C5' G:DT10 4.7 26.9 0.5 H B:ASP534 4.8 67.2 1.0 CD B:GLU459 4.8 63.3 1.0 O3' G:DT10 4.9 50.4 0.5 H B:GLY537 4.9 58.0 1.0 CA B:GLY612 5.0 59.6 1.0 CA B:ASP532 5.0 50.8 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 C:Mg601 b:52.4 occ:1.00 O G:HOH204 2.1 0.4 1.0 O F:HOH108 2.1 77.4 1.0 O G:HOH201 2.1 65.5 1.0 O C:HOH708 2.1 68.2 1.0 O03 G:MFX101 2.2 53.2 1.0 O02 G:MFX101 2.2 50.7 1.0 C19 G:MFX101 3.2 49.0 1.0 C20 G:MFX101 3.2 52.2 1.0 HG C:SER90 3.4 71.6 1.0 O E:HOH103 3.6 0.3 1.0 C18 G:MFX101 3.7 50.0 1.0 OG C:SER90 3.8 59.6 1.0 O4 F:DT10 3.8 83.0 0.5 H61 E:DA15 3.9 0.9 0.5 H62 F:DA11 3.9 0.8 0.5 O4 H:DT10 4.0 46.0 0.5 H71 H:DT10 4.2 52.1 0.5 H17 G:MFX101 4.3 58.5 1.0 OD2 C:ASP94 4.3 58.7 1.0 N6 F:DA11 4.3 0.7 0.5 H62 E:DA15 4.3 0.9 0.5 O G:MFX101 4.3 52.8 1.0 HB3 C:SER90 4.4 70.2 1.0 H61 F:DA11 4.4 0.8 0.5 H73 F:DT10 4.4 98.1 0.5 N6 E:DA15 4.4 0.5 0.5 C14 G:MFX101 4.5 48.1 1.0 HB3 C:SER91 4.5 75.2 1.0 H62 F:DA9 4.5 93.0 0.5 O6 H:DG11 4.5 50.7 0.5 N6 G:DA15 4.6 34.3 0.5 CB C:SER90 4.7 58.5 1.0 HA C:SER91 4.7 72.4 1.0 C17 G:MFX101 4.8 48.7 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:43.0 occ:1.00 OD2 D:ASP534 2.0 50.5 1.0 O F:HOH105 2.1 44.8 1.0 O D:HOH804 2.1 41.8 1.0 O D:HOH808 2.1 34.1 1.0 OD2 D:ASP532 2.1 54.3 1.0 O D:HOH805 2.1 39.4 1.0 CG D:ASP534 3.0 50.0 1.0 CG D:ASP532 3.1 54.2 1.0 HB2 D:ASP532 3.2 64.5 1.0 OD1 D:ASP534 3.3 47.0 1.0 HB3 D:ASP532 3.3 64.5 1.0 CB D:ASP532 3.4 53.8 1.0 H5'' F:DT10 3.6 89.1 0.5 OE2 D:GLU459 3.7 64.5 1.0 H5'' H:DT10 3.7 48.1 0.5 O D:HOH806 3.9 53.2 1.0 HB2 D:ASP536 4.0 62.6 1.0 O D:LYS611 4.1 65.7 1.0 HA3 D:GLY612 4.1 79.0 1.0 OD1 D:ASP532 4.2 55.3 1.0 CB D:ASP534 4.4 53.6 1.0 OP1 F:DT10 4.4 77.5 0.5 HB3 D:ASP534 4.5 64.3 1.0 HA2 D:GLY612 4.5 79.0 1.0 H3' H:DT10 4.6 52.2 0.5 O3' F:DT10 4.6 78.2 0.5 C5' F:DT10 4.6 74.3 0.5 OP1 H:DT10 4.7 39.9 0.5 CD D:GLU459 4.7 63.0 1.0 C5' H:DT10 4.7 40.1 0.5 HB2 D:ASP534 4.7 64.3 1.0 H D:ASP534 4.8 70.3 1.0 CA D:GLY612 4.8 65.8 1.0 CB D:ASP536 4.9 52.2 1.0 HB3 D:ASP536 4.9 62.6 1.0 H D:GLY537 4.9 71.9 1.0 CA D:ASP532 5.0 52.8 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