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Fluorine 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:

Magnesium (Mg) 8 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae, PDB code: 5eix:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5eix

Go back to Fluorine Binding Sites List in 5eix
Fluorine binding site 1 out of 4 in the Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
F:F100

b:51.5
occ:1.00
 F F:LFX100 0.0 51.5 1.0
C11 F:LFX100 1.4 51.3 1.0
C13 F:LFX100 2.3 55.9 1.0
C04 F:LFX100 2.4 50.0 1.0
N01 F:LFX100 2.8 45.0 1.0
C01 F:LFX100 3.1 45.1 1.0
N1 F:DC4 3.2 57.4 1.0
C5 F:DA5 3.3 50.0 1.0
C6 F:DC4 3.3 59.3 1.0
N7 F:DA5 3.4 46.1 1.0
C2 F:DC4 3.4 59.3 1.0
C4 F:DA5 3.5 47.5 1.0
C07 F:LFX100 3.6 43.0 1.0
C06 F:LFX100 3.6 53.0 1.0
C10 F:LFX100 3.6 60.7 1.0
C8 F:DA5 3.6 47.1 1.0
C2' F:DC4 3.7 53.6 1.0
C1' F:DC4 3.7 57.0 1.0
C5 F:DC4 3.7 59.9 1.0
N9 F:DA5 3.7 45.5 1.0
C6 F:DA5 3.8 57.6 1.0
N3 F:DC4 3.8 57.2 1.0
C02 F:LFX100 3.8 45.1 1.0
C4 F:DC4 3.9 54.0 1.0
O2 F:DC4 4.0 62.0 1.0
C05 F:LFX100 4.1 56.8 1.0
N3 F:DA5 4.2 46.8 1.0
C08 F:LFX100 4.2 47.2 1.0
N6 F:DA5 4.3 63.7 1.0
N1 F:DA5 4.3 51.5 1.0
O4' F:DA5 4.3 36.3 1.0
N2 I:DG1 4.4 70.3 1.0
C2 F:DA5 4.4 46.0 1.0
N F:LFX100 4.5 46.4 1.0
C1' F:DA5 4.6 40.5 1.0
O01 F:LFX100 4.7 45.1 1.0
N4 F:DC4 4.8 47.8 1.0
C15 F:LFX100 4.9 62.4 1.0
N1 I:DG1 4.9 65.5 1.0

Fluorine binding site 2 out of 4 in 5eix

Go back to Fluorine Binding Sites List in 5eix
Fluorine binding site 2 out of 4 in the Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
D:F100

b:78.1
occ:1.00
 F D:LFX100 0.0 78.1 1.0
C11 D:LFX100 1.4 74.0 1.0
C13 D:LFX100 2.3 73.1 1.0
C04 D:LFX100 2.4 71.0 1.0
N01 D:LFX100 2.8 70.7 1.0
N1 D:DC4 2.9 61.3 1.0
C2 D:DC4 3.0 61.4 1.0
C01 D:LFX100 3.2 72.6 1.0
C6 D:DC4 3.3 64.1 1.0
N7 D:DA5 3.3 53.8 1.0
C2' D:DC4 3.3 57.6 1.0
N3 D:DC4 3.4 59.1 1.0
O2 D:DC4 3.5 62.7 1.0
C1' D:DC4 3.5 55.6 1.0
C8 D:DA5 3.5 56.6 1.0
C5 D:DA5 3.5 52.7 1.0
C06 D:LFX100 3.6 67.5 1.0
C10 D:LFX100 3.6 70.1 1.0
C5 D:DC4 3.6 63.2 1.0
C02 D:LFX100 3.7 69.9 1.0
C4 D:DC4 3.7 59.6 1.0
N9 D:DA5 3.9 55.1 1.0
C4 D:DA5 3.9 56.4 1.0
C05 D:LFX100 4.1 67.0 1.0
C6 D:DA5 4.1 50.9 1.0
O4' D:DA5 4.4 45.5 1.0
N6 D:DA5 4.5 50.9 1.0
N2 L:DG1 4.5 55.9 1.0
N4 D:DC4 4.6 58.3 1.0
C07 D:LFX100 4.7 73.7 1.0
C3' D:DC4 4.7 65.0 1.0
O01 D:LFX100 4.7 63.5 1.0
N3 D:DA5 4.8 57.9 1.0
C1' D:DA5 4.8 56.9 1.0
O4' D:DC4 4.8 55.6 1.0
C15 D:LFX100 4.9 69.7 1.0
N1 D:DA5 4.9 51.2 1.0
N1 L:DG1 4.9 65.5 1.0
C08 D:LFX100 5.0 70.3 1.0

Fluorine binding site 3 out of 4 in 5eix

Go back to Fluorine Binding Sites List in 5eix
Fluorine binding site 3 out of 4 in the Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
I:F100

b:66.5
occ:1.00
 F I:LFX100 0.0 66.5 1.0
C11 I:LFX100 1.4 65.2 1.0
C13 I:LFX100 2.3 66.6 1.0
C04 I:LFX100 2.4 60.6 1.0
N01 I:LFX100 2.8 56.1 1.0
N1 I:DC4 2.9 61.7 1.0
C2 I:DC4 3.1 56.9 1.0
C01 I:LFX100 3.2 59.4 1.0
C6 I:DC4 3.2 61.9 1.0
N7 I:DA5 3.3 60.6 1.0
C5 I:DA5 3.4 59.5 1.0
N3 I:DC4 3.5 56.0 1.0
C1' I:DC4 3.5 64.7 1.0
C2' I:DC4 3.5 60.9 1.0
O2 I:DC4 3.6 55.1 1.0
C5 I:DC4 3.6 60.5 1.0
C8 I:DA5 3.6 67.2 1.0
C06 I:LFX100 3.6 61.2 1.0
C07 I:LFX100 3.6 63.5 1.0
C10 I:LFX100 3.6 66.6 1.0
C4 I:DC4 3.7 59.0 1.0
C02 I:LFX100 3.8 54.0 1.0
C4 I:DA5 3.8 63.8 1.0
N9 I:DA5 3.9 66.0 1.0
C6 I:DA5 4.0 58.8 1.0
C05 I:LFX100 4.1 62.8 1.0
C08 I:LFX100 4.2 62.1 1.0
N6 I:DA5 4.4 56.0 1.0
N2 F:DG1 4.5 65.3 1.0
O4' I:DA5 4.5 53.9 1.0
N I:LFX100 4.5 65.7 1.0
N3 I:DA5 4.6 63.5 1.0
N4 I:DC4 4.6 61.3 1.0
N1 F:DG1 4.6 68.6 1.0
N1 I:DA5 4.7 61.1 1.0
O01 I:LFX100 4.7 56.5 1.0
C1' I:DA5 4.8 65.4 1.0
O4' I:DC4 4.9 68.5 1.0
C15 I:LFX100 4.9 65.1 1.0
C2 I:DA5 4.9 62.6 1.0
C2 F:DG1 4.9 66.8 1.0
C3' I:DC4 4.9 59.2 1.0

Fluorine binding site 4 out of 4 in 5eix

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


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
L:F103

b:73.2
occ:1.00
 F L:LFX103 0.0 73.2 1.0
C11 L:LFX103 1.4 69.8 1.0
C13 L:LFX103 2.3 69.5 1.0
C04 L:LFX103 2.4 63.9 1.0
N01 L:LFX103 2.8 61.5 1.0
N1 L:DC4 3.1 67.6 1.0
C01 L:LFX103 3.2 60.4 1.0
C2 L:DC4 3.2 66.4 1.0
C6 L:DC4 3.4 68.3 1.0
C5 L:DA5 3.4 71.6 1.0
N7 L:DA5 3.5 72.3 1.0
C2' L:DC4 3.6 70.1 1.0
N3 L:DC4 3.6 72.8 1.0
C06 L:LFX103 3.6 58.6 1.0
C07 L:LFX103 3.6 59.1 1.0
C4 L:DA5 3.6 71.8 1.0
C10 L:LFX103 3.6 66.2 1.0
C1' L:DC4 3.6 70.5 1.0
C8 L:DA5 3.6 74.1 1.0
C5 L:DC4 3.7 70.1 1.0
O2 L:DC4 3.7 60.2 1.0
N9 L:DA5 3.8 74.9 1.0
C4 L:DC4 3.8 74.4 1.0
C02 L:LFX103 3.8 60.3 1.0
C6 L:DA5 3.9 73.9 1.0
C05 L:LFX103 4.1 61.1 1.0
C08 L:LFX103 4.2 60.0 1.0
O4' L:DA5 4.3 75.2 1.0
N3 L:DA5 4.3 72.7 1.0
N2 D:DG1 4.4 47.3 1.0
N6 L:DA5 4.5 75.5 1.0
N L:LFX103 4.5 57.7 1.0
N1 L:DA5 4.5 74.4 1.0
C2 L:DA5 4.6 75.2 1.0
C1' L:DA5 4.6 77.9 1.0
N4 L:DC4 4.7 76.5 1.0
O01 L:LFX103 4.7 53.8 1.0
N1 D:DG1 4.9 53.4 1.0
C15 L:LFX103 4.9 63.2 1.0
C3' L:DC4 4.9 72.4 1.0
C2 D:DG1 5.0 45.6 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: Sun Dec 13 12:21:37 2020

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