Atomistry » Magnesium » PDB 5egy-5etr » 5eix
Atomistry »
  Magnesium »
    PDB 5egy-5etr »
      5eix »

Magnesium in PDB 5eix: Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae

Enzymatic activity of Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae

All present enzymatic activity of Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae:
5.99.1.3;

Protein crystallography data

The structure of Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae, PDB code: 5eix was solved by D.A.Veselkov, I.Laponogov, X.-S.Pan, J.Selvarajah, A.Branstrom, L.M.Fisher, M.R.Sanderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.01 / 3.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.070, 161.530, 138.600, 90.00, 94.22, 90.00
R / Rfree (%) 22.4 / 25.9

Other elements in 5eix:

The structure of Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae (pdb code 5eix). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae, PDB code: 5eix:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5eix

Go back to Magnesium Binding Sites List in 5eix
Magnesium binding site 1 out of 8 in the Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1501

b:26.7
occ:1.00
 OD2 A:ASP493 2.0 26.2 1.0
OD2 A:ASP491 2.0 75.7 1.0
CG A:ASP493 3.1 81.0 1.0
CG A:ASP491 3.1 71.3 1.0
OD1 A:ASP493 3.5 82.7 1.0
OD1 A:ASP491 3.5 71.3 1.0
OE1 A:GLU419 3.8 72.8 1.0
CE1 G:TYR1120 4.3 42.6 1.0
CB A:ASP493 4.4 76.2 1.0
CB A:ASP491 4.4 66.1 1.0
O A:LYS565 4.5 67.1 1.0
OP1 E:DT15 4.6 50.7 1.0
OH G:TYR1120 4.7 54.8 1.0
CA A:GLY566 4.8 53.6 1.0
CD A:GLU419 4.9 76.5 1.0
C5' E:DT15 5.0 30.6 1.0

Magnesium binding site 2 out of 8 in 5eix

Go back to Magnesium Binding Sites List in 5eix
Magnesium binding site 2 out of 8 in the Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1502

b:52.7
occ:1.00
 O F:LFX100 2.0 31.1 1.0
O02 F:LFX100 2.0 72.2 1.0
C15 F:LFX100 3.0 62.4 1.0
C F:LFX100 3.0 58.5 1.0
C17 F:LFX100 3.4 58.0 1.0
N4 F:DC4 4.0 47.8 1.0
O03 F:LFX100 4.2 62.0 1.0
OE2 A:GLU1084 4.3 83.8 1.0
C10 F:LFX100 4.4 60.7 1.0
O6 I:DG1 4.4 70.3 1.0
OE1 A:GLU1084 4.7 88.0 1.0
C12 F:LFX100 4.7 57.6 1.0
O4 E:DT15 4.8 52.9 1.0
CD A:GLU1084 4.8 82.7 1.0
C13 F:LFX100 4.9 55.9 1.0
N6 F:DA5 4.9 63.7 1.0

Magnesium binding site 3 out of 8 in 5eix

Go back to Magnesium Binding Sites List in 5eix
Magnesium binding site 3 out of 8 in the Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1501

b:35.9
occ:1.00
 OD2 B:ASP493 2.0 44.8 1.0
OD2 B:ASP491 2.0 74.9 1.0
CG B:ASP493 3.1 55.9 1.0
CG B:ASP491 3.1 73.1 1.0
OD1 B:ASP493 3.5 66.8 1.0
OD1 B:ASP491 3.5 77.7 1.0
OE1 B:GLU419 3.8 73.4 1.0
CB B:ASP493 4.4 54.0 1.0
CB B:ASP491 4.4 68.2 1.0
OP1 C:DT15 4.6 46.1 1.0
O B:LYS565 4.6 41.0 1.0
CE1 J:TYR1120 4.6 64.0 1.0
CA B:GLY566 4.8 53.6 1.0
CD B:GLU419 4.9 74.8 1.0
C5' C:DT15 4.9 35.6 1.0

Magnesium binding site 4 out of 8 in 5eix

Go back to Magnesium Binding Sites List in 5eix
Magnesium binding site 4 out of 8 in the Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1501

b:54.0
occ:1.00
 OD2 G:ASP493 2.0 37.9 1.0
OD2 G:ASP491 2.0 85.2 1.0
CG G:ASP493 3.1 69.4 1.0
CG G:ASP491 3.1 82.8 1.0
OD1 G:ASP493 3.5 71.6 1.0
OD1 G:ASP491 3.5 86.9 1.0
OE1 G:GLU419 3.9 69.8 1.0
CB G:ASP493 4.4 64.4 1.0
CB G:ASP491 4.4 76.4 1.0
O G:LYS565 4.5 0.1 1.0
CE1 A:TYR1120 4.6 57.4 1.0
CA G:GLY566 4.7 74.8 1.0
OP1 H:DT15 4.7 63.1 1.0
OH A:TYR1120 4.9 68.9 1.0
CD G:GLU419 5.0 71.3 1.0

Magnesium binding site 5 out of 8 in 5eix

Go back to Magnesium Binding Sites List in 5eix
Magnesium binding site 5 out of 8 in the Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1502

b:44.1
occ:1.00
 O I:LFX100 2.0 40.7 1.0
O02 I:LFX100 2.0 66.8 1.0
C15 I:LFX100 3.0 65.1 1.0
C I:LFX100 3.0 59.8 1.0
C17 I:LFX100 3.4 62.0 1.0
O6 F:DG1 4.1 66.4 1.0
O03 I:LFX100 4.2 53.1 1.0
N4 I:DC4 4.2 61.3 1.0
OE2 G:GLU1084 4.2 73.0 1.0
C10 I:LFX100 4.4 66.6 1.0
O4 H:DT15 4.7 60.7 1.0
C12 I:LFX100 4.8 59.7 1.0
CB G:SER1080 4.8 58.4 1.0
C13 I:LFX100 4.8 66.6 1.0
CD G:GLU1084 4.9 72.9 1.0
OE1 G:GLU1084 4.9 73.8 1.0
C6 F:DG1 4.9 67.7 1.0

Magnesium binding site 6 out of 8 in 5eix

Go back to Magnesium Binding Sites List in 5eix
Magnesium binding site 6 out of 8 in the Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg1501

b:42.4
occ:1.00
 OD2 J:ASP493 2.0 79.4 1.0
OD2 J:ASP491 2.0 99.8 1.0
CG J:ASP493 3.1 82.9 1.0
CG J:ASP491 3.1 99.7 1.0
OD1 J:ASP493 3.5 87.6 1.0
OD1 J:ASP491 3.5 0.2 1.0
CB J:ASP493 4.4 79.8 1.0
CB J:ASP491 4.4 94.6 1.0
O J:LYS565 4.4 0.6 1.0
CE1 B:TYR1120 4.5 51.6 1.0
CA J:GLY566 4.7 75.5 1.0
OP1 K:DT15 4.7 72.4 1.0
OH B:TYR1120 4.9 64.5 1.0

Magnesium binding site 7 out of 8 in 5eix

Go back to Magnesium Binding Sites List in 5eix
Magnesium binding site 7 out of 8 in the Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg101

b:36.3
occ:1.00
 O03 D:LFX100 2.0 46.2 1.0
O02 D:LFX100 2.0 76.9 1.0
C15 D:LFX100 3.0 69.7 1.0
C D:LFX100 3.0 51.0 1.0
C17 D:LFX100 3.4 60.1 1.0
O6 L:DG1 4.1 73.5 1.0
O D:LFX100 4.2 45.7 1.0
C10 D:LFX100 4.4 70.1 1.0
N4 D:DC4 4.4 58.3 1.0
O4 C:DT15 4.5 53.6 1.0
CB B:SER1080 4.6 51.1 1.0
C12 D:LFX100 4.8 59.8 1.0
C13 D:LFX100 4.9 73.1 1.0
C6 L:DG1 4.9 68.5 1.0

Magnesium binding site 8 out of 8 in 5eix

Go back to Magnesium Binding Sites List in 5eix
Magnesium binding site 8 out of 8 in the Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg102

b:48.9
occ:1.00
 O L:LFX103 2.0 46.1 1.0
O02 L:LFX103 2.0 64.7 1.0
C15 L:LFX103 3.0 63.2 1.0
C L:LFX103 3.0 66.4 1.0
C17 L:LFX103 3.4 59.8 1.0
O03 L:LFX103 4.2 70.2 1.0
N4 L:DC4 4.2 76.5 1.0
C10 L:LFX103 4.4 66.2 1.0
O6 D:DG1 4.4 50.5 1.0
O4 K:DT15 4.6 58.1 1.0
C12 L:LFX103 4.8 56.6 1.0
N6 L:DA5 4.8 75.5 1.0
C13 L:LFX103 4.8 69.5 1.0

Reference:

D.A.Veselkov, I.Laponogov, X.S.Pan, J.Selvarajah, G.B.Skamrova, A.Branstrom, J.Narasimhan, J.V.Prasad, L.M.Fisher, M.R.Sanderson. Structure of A Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae and Comparison with A Related Streptococcus Pneumoniae Complex. Acta Crystallogr D Struct V. 72 488 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 27050128
DOI: 10.1107/S2059798316001212
Page generated: Tue Aug 12 07:46:49 2025

Last articles

Zn in 9MPO
Zn in 9MPP
Zn in 9MRI
Zn in 9MMW
Zn in 9N07
Zn in 9MYR
Zn in 9M59
Zn in 9MWN
Zn in 9MWA
Zn in 9MMP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy