Magnesium in PDB 4s04: 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: 4s04 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)	24.19 / 3.20
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	194.327, 250.761, 108.944, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 23.2

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

Fluorine

(F)

12 atoms

The binding sites of Magnesium atom in the Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna (pdb code 4s04). 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 Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna, PDB code: 4s04:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna


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 Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:29.4 occ:1.00 OD2 A:ASP51 1.9 53.7 1.0 OD1 A:ASP8 2.0 0.6 1.0 O A:GLY53 2.1 45.9 1.0 F1 A:BEF301 2.2 61.4 1.0 OD2 A:ASP8 2.2 58.1 1.0 CG A:ASP8 2.3 1.0 1.0 CG A:ASP51 2.9 38.6 1.0 BE A:BEF301 3.1 60.9 1.0 C A:GLY53 3.1 66.3 1.0 OD1 A:ASP51 3.3 18.2 1.0 CA A:GLY53 3.6 62.1 1.0 CB A:ASP8 3.7 16.6 1.0 F3 A:BEF301 3.8 60.4 1.0 N A:GLY53 3.8 22.9 1.0 OE2 A:GLU7 4.1 43.1 1.0 CB A:ASP51 4.3 33.2 1.0 N A:LEU54 4.3 48.9 1.0 N A:ASP8 4.3 53.4 1.0 CD2 A:LEU54 4.4 36.2 1.0 F2 A:BEF301 4.5 61.1 1.0 CA A:ASP8 4.6 37.5 1.0 CD A:GLU7 4.7 83.8 1.0 N A:ASP9 4.7 30.5 1.0 NZ A:LYS101 4.8 35.7 1.0 OE1 A:GLU7 4.8 77.1 1.0 C A:LEU52 4.8 94.2 1.0 CA A:LEU54 4.8 23.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna


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 Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:40.6 occ:1.00 OD2 B:ASP51 1.8 73.1 1.0 OD1 B:ASP8 2.0 83.1 1.0 OD2 B:ASP8 2.1 0.0 1.0 O B:GLY53 2.1 82.5 1.0 F2 B:BEF301 2.3 57.2 1.0 CG B:ASP8 2.3 86.3 1.0 CG B:ASP51 3.0 33.1 1.0 C B:GLY53 3.2 61.3 1.0 BE B:BEF301 3.3 56.4 1.0 OE1 B:GLU7 3.5 66.0 1.0 OD1 B:ASP51 3.6 32.1 1.0 CA B:GLY53 3.7 66.9 1.0 CB B:ASP8 3.8 28.7 1.0 F3 B:BEF301 4.0 55.8 1.0 N B:GLY53 4.1 24.1 1.0 CB B:ASP51 4.1 28.9 1.0 N B:ASP8 4.3 83.1 1.0 N B:LEU54 4.4 60.0 1.0 F1 B:BEF301 4.6 56.7 1.0 CA B:ASP8 4.6 29.3 1.0 CD B:GLU7 4.6 45.7 1.0 N B:ASP9 4.8 56.7 1.0 CA B:LEU54 4.9 32.0 1.0 NZ B:LYS101 5.0 51.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna


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 Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg302 b:12.7 occ:1.00 OD2 E:ASP51 1.9 26.6 1.0 OD1 E:ASP8 1.9 61.3 1.0 O E:GLY53 2.1 0.1 1.0 OD2 E:ASP8 2.2 22.6 1.0 CG E:ASP8 2.3 68.3 1.0 F1 E:BEF301 2.3 52.8 1.0 C E:GLY53 3.0 21.6 1.0 CG E:ASP51 3.1 96.0 1.0 CA E:GLY53 3.2 29.5 1.0 BE E:BEF301 3.2 52.7 1.0 OD1 E:ASP51 3.6 20.6 1.0 OE1 E:GLU7 3.7 46.7 1.0 CB E:ASP8 3.8 12.9 1.0 N E:GLY53 3.9 11.7 1.0 N E:LEU54 4.2 13.6 1.0 CB E:ASP51 4.3 37.2 1.0 F3 E:BEF301 4.3 53.0 1.0 F2 E:BEF301 4.3 52.3 1.0 N E:ASP8 4.4 41.7 1.0 CA E:ASP8 4.6 13.1 1.0 CD E:GLU7 4.7 46.4 1.0 N E:ASP9 4.8 30.9 1.0 NZ E:LYS101 4.9 26.9 1.0 CA E:LEU54 4.9 19.2 1.0 C E:ASP8 5.0 45.4 1.0

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


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 Klebsiella Pneumoniae Pmra in Complex with Pmra Box Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg302 b:33.4 occ:1.00 OD2 F:ASP51 1.8 47.4 1.0 OD1 F:ASP8 2.1 89.7 1.0 F2 F:BEF301 2.2 59.2 1.0 O F:GLY53 2.4 79.5 1.0 OD2 F:ASP8 2.4 60.0 1.0 CG F:ASP8 2.6 50.0 1.0 CG F:ASP51 3.1 93.7 1.0 BE F:BEF301 3.2 58.8 1.0 OE1 F:GLU7 3.2 41.4 1.0 C F:GLY53 3.4 69.9 1.0 OD1 F:ASP51 3.7 46.0 1.0 CA F:GLY53 3.9 56.3 1.0 CB F:ASP8 4.0 24.1 1.0 F3 F:BEF301 4.1 58.6 1.0 CB F:ASP51 4.2 20.3 1.0 CD F:GLU7 4.3 87.8 1.0 N F:GLY53 4.3 52.8 1.0 N F:ASP8 4.4 45.5 1.0 F1 F:BEF301 4.4 58.6 1.0 N F:LEU54 4.5 81.2 1.0 CD2 F:LEU54 4.6 0.2 1.0 CA F:ASP8 4.7 48.4 1.0 NZ F:LYS101 4.7 19.3 1.0 OE2 F:GLU7 4.8 46.9 1.0 N F:ASP9 4.8 66.7 1.0 CA F:LEU54 5.0 60.1 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