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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Dec 14 20:15:22 2020

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