Fluorine in PDB 4s05: Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna

The structure of Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna, PDB code: 4s05 was solved by C.D.Hsiao, T.H.Weng, Y.C.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.83 / 3.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	162.640, 162.640, 131.707, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 22.9

The structure of Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna (pdb code 4s05). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna, PDB code: 4s05:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:57.5 occ:1.00 F1 A:BEF301 0.0 57.5 1.0 BE A:BEF301 1.5 56.7 1.0 F3 A:BEF301 2.5 59.1 1.0 MG A:MG302 2.5 4.6 1.0 F2 A:BEF301 2.5 59.0 1.0 OD2 A:ASP51 3.4 5.0 1.0 OD1 A:ASP51 3.7 29.3 1.0 CA A:GLY53 3.8 54.6 1.0 NZ A:LYS101 3.8 56.5 1.0 CG A:ASP51 4.0 10.4 1.0 CB A:ALA80 4.2 46.4 1.0 N A:GLY53 4.3 10.4 1.0 O A:GLY53 4.3 38.6 1.0 OD1 A:ASP8 4.4 68.3 1.0 C A:GLY53 4.4 56.3 1.0 CE A:LYS101 4.6 64.2 1.0 N A:ALA80 4.8 10.2 1.0 OG1 A:THR79 4.9 45.3 1.0 OE2 A:GLU7 4.9 56.0 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:59.0 occ:1.00 F2 A:BEF301 0.0 59.0 1.0 BE A:BEF301 1.6 56.7 1.0 F3 A:BEF301 2.5 59.1 1.0 F1 A:BEF301 2.5 57.5 1.0 OG1 A:THR79 2.5 45.3 1.0 N A:GLY53 3.0 10.4 1.0 OD1 A:ASP51 3.2 29.3 1.0 OD2 A:ASP51 3.2 5.0 1.0 CA A:GLY53 3.2 54.6 1.0 CG A:ASP51 3.5 10.4 1.0 N A:ALA80 3.6 10.2 1.0 N A:LEU52 3.8 5.6 1.0 CB A:THR79 3.8 4.1 1.0 MG A:MG302 3.8 4.6 1.0 C A:LEU52 3.9 27.1 1.0 CB A:ALA80 4.2 46.4 1.0 CA A:THR79 4.2 26.2 1.0 CA A:LEU52 4.3 10.0 1.0 CG A:ARG81 4.3 61.5 1.0 CD A:ARG81 4.4 24.8 1.0 CA A:ALA80 4.4 3.9 1.0 C A:THR79 4.4 25.2 1.0 CB A:LEU52 4.5 69.3 1.0 C A:GLY53 4.5 56.3 1.0 N A:ARG81 4.7 33.0 1.0 C A:ASP51 4.7 17.2 1.0 CB A:ASP51 4.8 5.0 1.0 NZ A:LYS101 4.8 56.5 1.0 CE A:LYS101 4.9 64.2 1.0 CG2 A:THR79 4.9 3.8 1.0 C A:ALA80 4.9 36.6 1.0 O A:LEU52 4.9 51.0 1.0 CA A:ASP51 5.0 9.9 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:59.1 occ:1.00 F3 A:BEF301 0.0 59.1 1.0 BE A:BEF301 1.5 56.7 1.0 OD1 A:ASP51 2.2 29.3 1.0 NZ A:LYS101 2.4 56.5 1.0 F1 A:BEF301 2.5 57.5 1.0 F2 A:BEF301 2.5 59.0 1.0 CE A:LYS101 2.5 64.2 1.0 CG A:ASP51 3.2 10.4 1.0 N A:ALA80 3.2 10.2 1.0 OD2 A:ASP51 3.5 5.0 1.0 CB A:ALA80 3.5 46.4 1.0 OG1 A:THR79 3.7 45.3 1.0 OE2 A:GLU7 3.7 56.0 1.0 CA A:THR79 3.8 26.2 1.0 C A:THR79 3.9 25.2 1.0 MG A:MG302 3.9 4.6 1.0 CD A:LYS101 4.0 35.9 1.0 CA A:ALA80 4.0 3.9 1.0 CB A:THR79 4.4 4.1 1.0 O A:LEU78 4.5 43.2 1.0 CB A:ASP51 4.6 5.0 1.0 CG A:LYS101 4.8 44.1 1.0 CD A:GLU7 4.8 81.7 1.0 N A:GLY53 4.9 10.4 1.0 O A:THR79 4.9 13.6 1.0 N A:THR79 5.0 4.1 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:59.7 occ:1.00 F1 B:BEF301 0.0 59.7 1.0 BE B:BEF301 1.5 60.5 1.0 OD1 B:ASP51 2.3 22.1 1.0 F3 B:BEF301 2.5 60.2 1.0 F2 B:BEF301 2.5 60.0 1.0 N B:ALA80 2.9 22.8 1.0 CB B:ALA80 3.2 52.0 1.0 CG B:ASP51 3.3 74.5 1.0 OG1 B:THR79 3.3 23.1 1.0 OD2 B:ASP51 3.5 40.2 1.0 CA B:ALA80 3.6 33.6 1.0 N B:GLY53 3.8 54.0 1.0 C B:THR79 3.8 50.4 1.0 CA B:THR79 3.8 33.3 1.0 CB B:THR79 3.9 24.6 1.0 CA B:GLY53 4.1 63.9 1.0 MG B:MG302 4.1 16.2 1.0 N B:LEU52 4.3 80.7 1.0 CD B:LYS101 4.5 17.6 1.0 N B:ARG81 4.5 25.3 1.0 C B:ALA80 4.5 27.8 1.0 CB B:ASP51 4.7 52.6 1.0 C B:LEU52 4.7 90.6 1.0 NZ B:LYS101 4.9 88.1 1.0 O B:LEU78 4.9 44.8 1.0 CA B:LEU52 5.0 82.6 1.0 O B:THR79 5.0 26.8 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:60.0 occ:1.00 F2 B:BEF301 0.0 60.0 1.0 BE B:BEF301 1.6 60.5 1.0 F3 B:BEF301 2.5 60.2 1.0 MG B:MG302 2.5 16.2 1.0 F1 B:BEF301 2.5 59.7 1.0 OD2 B:ASP51 3.4 40.2 1.0 OD1 B:ASP51 3.8 22.1 1.0 CA B:GLY53 3.9 63.9 1.0 CB B:ALA80 3.9 52.0 1.0 CG B:ASP51 4.0 74.5 1.0 OD2 B:ASP8 4.1 0.2 1.0 OD1 B:ASP8 4.2 78.8 1.0 N B:GLY53 4.5 54.0 1.0 O B:GLY53 4.5 85.8 1.0 CG B:ASP8 4.5 0.7 1.0 C B:GLY53 4.6 85.2 1.0 NZ B:LYS101 4.8 88.1 1.0 N B:ALA80 4.9 22.8 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:60.2 occ:1.00 F3 B:BEF301 0.0 60.2 1.0 BE B:BEF301 1.5 60.5 1.0 F2 B:BEF301 2.5 60.0 1.0 F1 B:BEF301 2.5 59.7 1.0 NZ B:LYS101 2.6 88.1 1.0 OD1 B:ASP51 2.9 22.1 1.0 OD2 B:ASP51 3.1 40.2 1.0 CD B:LYS101 3.2 17.6 1.0 CE B:LYS101 3.3 15.6 1.0 CG B:ASP51 3.3 74.5 1.0 MG B:MG302 3.5 16.2 1.0 CB B:ALA80 3.9 52.0 1.0 N B:ALA80 4.0 22.8 1.0 OE2 B:GLU7 4.2 24.9 1.0 OD1 B:ASP8 4.2 78.8 1.0 OE1 B:GLU7 4.3 53.1 1.0 CA B:ALA80 4.5 33.6 1.0 CD B:GLU7 4.6 69.7 1.0 C B:THR79 4.6 50.4 1.0 CB B:ASP51 4.7 52.6 1.0 CA B:THR79 4.7 33.3 1.0 CG B:LYS101 4.7 48.9 1.0 O B:LEU78 4.9 44.8 1.0

Y.C.Lou, T.H.Weng, Y.C.Li, Y.F.Kao, W.F.Lin, H.L.Peng, S.H.Chou, C.D.Hsiao, C.Chen. Structure and Dynamics of Polymyxin-Resistance-Associated Response Regulator Pmra in Complex with Promoter Dna. Nat Commun V. 6 8838 2015.
ISSN: ESSN 2041-1723
PubMed: 26564787
DOI: 10.1038/NCOMMS9838