Atomistry » Magnesium » PDB 5bjo-5btl » 5bs8
Atomistry »
  Magnesium »
    PDB 5bjo-5btl »
      5bs8 »

Magnesium in PDB 5bs8: Crystal Structure of A Topoisomerase II Complex

Enzymatic activity of Crystal Structure of A Topoisomerase II Complex

All present enzymatic activity of Crystal Structure of A Topoisomerase II Complex:
5.99.1.3;

Protein crystallography data

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

Other elements in 5bs8:

The structure of Crystal Structure of A Topoisomerase II Complex also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Magnesium Binding Sites:

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 5bs8

Go back to Magnesium Binding Sites List in 5bs8
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 5bs8

Go back to Magnesium Binding Sites List in 5bs8
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 5bs8

Go back to Magnesium Binding Sites List in 5bs8
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 5bs8

Go back to Magnesium Binding Sites List in 5bs8
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

Reference:

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
Page generated: Mon Dec 14 20:03:12 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy