Fluorine in PDB 4zmr: Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region

The structure of Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region, PDB code: 4zmr was solved by Y.M.Chi, A.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.71 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.233, 114.491, 50.148, 90.00, 92.12, 90.00
R / Rfree (%)	18 / 22.7

The structure of Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region (pdb code 4zmr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region, PDB code: 4zmr:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:16.4 occ:1.00 F1 A:BEF202 0.0 16.4 1.0 BE A:BEF202 1.6 26.6 1.0 MG A:MG201 2.0 17.9 1.0 HB2 A:GLU55 2.6 31.2 1.0 F2 A:BEF202 2.6 31.5 1.0 F3 A:BEF202 2.7 21.3 1.0 O A:HOH409 2.8 17.8 1.0 OD1 A:ASP53 2.8 13.6 1.0 H A:GLU55 2.8 18.2 1.0 O A:HOH322 2.8 18.9 1.0 O A:GLU55 2.8 13.8 1.0 OD2 A:ASP53 2.8 19.3 1.0 O A:HOH393 2.9 21.2 1.0 CG A:ASP53 3.2 18.8 1.0 HE2 A:PHE83 3.3 34.7 1.0 CB A:GLU55 3.4 26.0 1.0 N A:GLU55 3.4 15.2 1.0 C A:GLU55 3.6 18.3 1.0 CA A:GLU55 3.6 20.5 1.0 HB3 A:GLU55 3.7 31.2 1.0 HZ2 A:LYS103 3.8 32.4 1.0 OD1 A:ASP8 4.0 18.2 1.0 CE2 A:PHE83 4.1 28.9 1.0 O A:HOH302 4.1 28.6 1.0 HZ1 A:LYS103 4.2 32.4 1.0 HG1 A:THR81 4.4 21.6 1.0 O A:HOH429 4.4 49.8 1.0 NZ A:LYS103 4.4 27.0 1.0 H A:VAL54 4.5 18.1 1.0 HG3 A:GLU55 4.5 43.6 1.0 CG A:GLU55 4.6 36.3 1.0 C A:VAL54 4.6 20.8 1.0 HA A:GLU55 4.6 24.6 1.0 H A:THR82 4.6 18.3 1.0 HG23 A:THR82 4.6 21.5 1.0 CB A:ASP53 4.7 15.3 1.0 HD2 A:PHE83 4.7 34.6 1.0 HZ A:PHE83 4.8 38.3 1.0 N A:VAL54 4.8 15.1 1.0 CD2 A:PHE83 4.8 28.9 1.0 HB A:VAL54 4.8 13.1 1.0 CZ A:PHE83 4.9 31.9 1.0 CG A:ASP8 4.9 18.0 1.0 N A:MET56 4.9 14.2 1.0 O A:HOH416 4.9 35.6 1.0 HZ3 A:LYS103 4.9 32.4 1.0 HA A:THR81 4.9 15.4 1.0 HG3 A:MET56 4.9 20.5 1.0 OE1 A:GLU7 5.0 16.2 1.0 HB3 A:ASP53 5.0 18.3 1.0 HG1 A:THR82 5.0 23.8 1.0

Fluorine binding site 2 out of 6 in the Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:31.5 occ:1.00 F2 A:BEF202 0.0 31.5 1.0 BE A:BEF202 1.6 26.6 1.0 H A:GLU55 1.9 18.2 1.0 HG1 A:THR81 2.1 21.6 1.0 OD1 A:ASP53 2.4 13.6 1.0 H A:VAL54 2.4 18.1 1.0 HB A:VAL54 2.5 13.1 1.0 F3 A:BEF202 2.6 21.3 1.0 F1 A:BEF202 2.6 16.4 1.0 N A:GLU55 2.8 15.2 1.0 OG1 A:THR81 2.9 18.0 1.0 HD2 A:PHE83 3.0 34.6 1.0 N A:VAL54 3.0 15.1 1.0 HE2 A:PHE83 3.1 34.7 1.0 HB2 A:GLU55 3.2 31.2 1.0 CB A:VAL54 3.3 10.9 1.0 HA A:THR81 3.3 15.4 1.0 CA A:VAL54 3.4 17.5 1.0 CG A:ASP53 3.4 18.8 1.0 HB A:THR81 3.5 20.2 1.0 C A:VAL54 3.5 20.8 1.0 CD2 A:PHE83 3.6 28.9 1.0 H A:THR82 3.6 18.3 1.0 CB A:THR81 3.6 16.9 1.0 CE2 A:PHE83 3.6 28.9 1.0 CA A:GLU55 3.8 20.5 1.0 HG3 A:GLU55 3.9 43.6 1.0 HG23 A:VAL54 3.9 21.1 1.0 CB A:GLU55 3.9 26.0 1.0 CA A:THR81 4.0 12.8 1.0 OD2 A:ASP53 4.0 19.3 1.0 C A:ASP53 4.1 15.1 1.0 CG2 A:VAL54 4.1 17.6 1.0 HA A:ASP53 4.2 12.9 1.0 O A:HOH409 4.2 17.8 1.0 HG12 A:VAL54 4.3 24.8 1.0 N A:THR82 4.3 15.2 1.0 MG A:MG201 4.3 17.9 1.0 HA A:VAL54 4.3 21.0 1.0 H A:PHE83 4.3 21.1 1.0 CG1 A:VAL54 4.4 20.7 1.0 O A:GLU55 4.4 13.8 1.0 CG A:GLU55 4.4 36.3 1.0 HG21 A:VAL54 4.5 21.1 1.0 CA A:ASP53 4.5 10.7 1.0 HZ2 A:LYS103 4.5 32.4 1.0 CB A:ASP53 4.6 15.3 1.0 C A:GLU55 4.6 18.3 1.0 HA A:GLU55 4.6 24.6 1.0 C A:THR81 4.7 14.5 1.0 HG11 A:VAL54 4.7 24.8 1.0 O A:VAL80 4.7 12.3 1.0 O A:VAL54 4.7 14.5 1.0 HB3 A:GLU55 4.7 31.2 1.0 HE3 A:LYS103 4.8 25.1 1.0 CG A:PHE83 4.8 30.1 1.0 OG1 A:THR82 4.8 19.9 1.0 HZ1 A:LYS103 4.8 32.4 1.0 HB2 A:PHE83 4.9 33.3 1.0 HG23 A:THR82 4.9 21.5 1.0 CZ A:PHE83 4.9 31.9 1.0 HG22 A:VAL54 4.9 21.1 1.0

Fluorine binding site 3 out of 6 in the Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:21.3 occ:1.00 F3 A:BEF202 0.0 21.3 1.0 BE A:BEF202 1.6 26.6 1.0 HZ2 A:LYS103 2.1 32.4 1.0 H A:THR82 2.3 18.3 1.0 OD1 A:ASP53 2.5 13.6 1.0 F2 A:BEF202 2.6 31.5 1.0 HG23 A:THR82 2.6 21.5 1.0 HA A:THR81 2.7 15.4 1.0 F1 A:BEF202 2.7 16.4 1.0 O A:HOH409 2.8 17.8 1.0 NZ A:LYS103 2.8 27.0 1.0 HE3 A:LYS103 2.9 25.1 1.0 HZ1 A:LYS103 3.0 32.4 1.0 N A:THR82 3.1 15.2 1.0 HG1 A:THR81 3.1 21.6 1.0 CE A:LYS103 3.3 20.9 1.0 HD2 A:LYS103 3.4 24.1 1.0 CA A:THR81 3.5 12.8 1.0 CG A:ASP53 3.6 18.8 1.0 O A:HOH322 3.6 18.9 1.0 HZ3 A:LYS103 3.6 32.4 1.0 CG2 A:THR82 3.6 17.9 1.0 C A:THR81 3.7 14.5 1.0 OG1 A:THR81 3.8 18.0 1.0 OG1 A:THR82 3.8 19.9 1.0 CD A:LYS103 3.9 20.1 1.0 HG21 A:THR82 4.0 21.5 1.0 OD2 A:ASP53 4.0 19.3 1.0 CB A:THR82 4.0 19.6 1.0 HG1 A:THR82 4.1 23.8 1.0 CA A:THR82 4.1 15.9 1.0 CB A:THR81 4.1 16.9 1.0 HG22 A:THR82 4.1 21.5 1.0 HE2 A:LYS103 4.2 25.1 1.0 H A:VAL54 4.2 18.1 1.0 H A:GLU55 4.2 18.2 1.0 MG A:MG201 4.2 17.9 1.0 O A:HOH429 4.3 49.8 1.0 HE2 A:PHE83 4.3 34.7 1.0 O A:VAL80 4.3 12.3 1.0 HB A:THR81 4.4 20.2 1.0 HD3 A:LYS103 4.4 24.1 1.0 H A:PHE83 4.5 21.1 1.0 HD2 A:PHE83 4.5 34.6 1.0 O A:HOH356 4.5 24.0 1.0 OE2 A:GLU7 4.6 13.2 1.0 CE2 A:PHE83 4.6 28.9 1.0 N A:THR81 4.6 13.7 1.0 HA A:ASP53 4.7 12.9 1.0 HB2 A:GLU55 4.7 31.2 1.0 HA A:THR82 4.7 19.1 1.0 CD2 A:PHE83 4.7 28.9 1.0 CB A:ASP53 4.8 15.3 1.0 HG3 A:LYS103 4.8 19.8 1.0 N A:VAL54 4.9 15.1 1.0 O A:THR81 4.9 14.0 1.0 C A:VAL80 4.9 18.1 1.0 HB A:VAL54 5.0 13.1 1.0 HB2 A:ASP53 5.0 18.3 1.0 HB A:THR82 5.0 23.6 1.0 N A:GLU55 5.0 15.2 1.0

Fluorine binding site 4 out of 6 in the Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:24.1 occ:1.00 F1 B:BEF202 0.0 24.1 1.0 BE B:BEF202 1.5 24.8 1.0 H B:THR82 2.0 17.3 1.0 HZ2 B:LYS103 2.1 22.8 1.0 HG23 B:THR82 2.4 16.2 1.0 F3 B:BEF202 2.5 27.8 1.0 HG1 B:THR81 2.5 19.6 1.0 HA B:THR81 2.6 25.4 1.0 OD2 B:ASP53 2.6 11.7 1.0 F2 B:BEF202 2.6 17.7 1.0 N B:THR82 2.8 14.4 1.0 NZ B:LYS103 2.9 19.0 1.0 HZ1 B:LYS103 2.9 22.8 1.0 O B:HOH413 3.1 29.7 1.0 HE3 B:LYS103 3.1 19.3 1.0 OG1 B:THR81 3.3 16.3 1.0 CA B:THR81 3.3 21.2 1.0 CG2 B:THR82 3.4 13.5 1.0 CE B:LYS103 3.5 16.1 1.0 HZ3 B:LYS103 3.6 22.8 1.0 C B:THR81 3.6 16.6 1.0 OG1 B:THR82 3.6 27.1 1.0 HD2 B:LYS103 3.6 20.4 1.0 CG B:ASP53 3.7 20.8 1.0 O B:HOH325 3.8 13.8 1.0 CB B:THR81 3.8 13.3 1.0 HE2 B:PHE83 3.8 43.8 1.0 CB B:THR82 3.8 17.4 1.0 HG21 B:THR82 3.8 16.2 1.0 CA B:THR82 3.9 17.6 1.0 HG22 B:THR82 3.9 16.2 1.0 HG1 B:THR82 4.0 32.5 1.0 HD2 B:PHE83 4.0 30.2 1.0 H B:VAL54 4.0 18.1 1.0 HB B:THR81 4.0 15.9 1.0 H B:PHE83 4.1 23.3 1.0 CE2 B:PHE83 4.1 36.5 1.0 CD B:LYS103 4.1 17.0 1.0 OD1 B:ASP53 4.2 16.9 1.0 CD2 B:PHE83 4.2 25.2 1.0 H B:GLU55 4.2 20.6 1.0 MG B:MG201 4.2 18.2 1.0 O B:VAL80 4.3 16.9 1.0 HE2 B:LYS103 4.3 19.3 1.0 HG3 B:LYS103 4.5 12.5 1.0 HA B:THR82 4.5 21.1 1.0 N B:THR81 4.6 14.8 1.0 O B:HOH369 4.6 23.1 1.0 HA B:ASP53 4.6 19.8 1.0 N B:PHE83 4.7 19.4 1.0 N B:VAL54 4.7 15.1 1.0 HB B:VAL54 4.8 16.5 1.0 O B:THR81 4.8 13.7 1.0 HB B:THR82 4.8 20.9 1.0 OE2 B:GLU7 4.8 16.5 1.0 C B:THR82 4.8 20.5 1.0 HD3 B:LYS103 4.9 20.4 1.0 C B:VAL80 4.9 17.9 1.0 CB B:ASP53 4.9 18.3 1.0 CG B:LYS103 4.9 10.4 1.0 HB2 B:GLU55 4.9 19.8 1.0 CZ B:PHE83 5.0 29.7 1.0

Fluorine binding site 5 out of 6 in the Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:17.7 occ:1.00 F2 B:BEF202 0.0 17.7 1.0 BE B:BEF202 1.6 24.8 1.0 MG B:MG201 1.9 18.2 1.0 F3 B:BEF202 2.6 27.8 1.0 OD2 B:ASP53 2.6 11.7 1.0 F1 B:BEF202 2.6 24.1 1.0 O B:HOH325 2.7 13.8 1.0 OD1 B:ASP53 2.8 16.9 1.0 O B:HOH389 2.8 18.4 1.0 HB2 B:GLU55 2.8 19.8 1.0 H B:GLU55 2.9 20.6 1.0 O B:HOH413 3.0 29.7 1.0 HE2 B:PHE83 3.0 43.8 1.0 O B:GLU55 3.0 14.2 1.0 CG B:ASP53 3.1 20.8 1.0 N B:GLU55 3.5 17.1 1.0 HZ2 B:LYS103 3.6 22.8 1.0 CB B:GLU55 3.7 16.5 1.0 CE2 B:PHE83 3.8 36.5 1.0 C B:GLU55 3.8 16.5 1.0 CA B:GLU55 3.8 13.8 1.0 HZ1 B:LYS103 3.9 22.8 1.0 OD1 B:ASP8 3.9 15.9 1.0 HG1 B:THR81 4.1 19.6 1.0 O B:HOH309 4.1 27.4 1.0 NZ B:LYS103 4.2 19.0 1.0 H B:VAL54 4.3 18.1 1.0 HB3 B:GLU55 4.3 19.8 1.0 HG23 B:THR82 4.3 16.2 1.0 HG3 B:GLU55 4.3 27.0 1.0 HD2 B:PHE83 4.4 30.2 1.0 H B:THR82 4.5 17.3 1.0 CD2 B:PHE83 4.5 25.2 1.0 HZ B:PHE83 4.5 35.6 1.0 CB B:ASP53 4.5 18.3 1.0 C B:VAL54 4.6 17.7 1.0 CG B:GLU55 4.6 22.5 1.0 HZ3 B:LYS103 4.6 22.8 1.0 CZ B:PHE83 4.6 29.7 1.0 N B:VAL54 4.6 15.1 1.0 HB B:VAL54 4.8 16.5 1.0 HA B:GLU55 4.8 16.6 1.0 O B:HOH408 4.9 29.6 1.0 HA B:THR81 4.9 25.4 1.0 CG B:ASP8 4.9 21.0 1.0 HB3 B:ASP53 4.9 22.0 1.0 OG1 B:THR81 4.9 16.3 1.0 HG1 B:THR82 5.0 32.5 1.0 OG1 B:THR82 5.0 27.1 1.0 HG2 B:MET56 5.0 25.4 1.0

Fluorine binding site 6 out of 6 in the Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:27.8 occ:1.00 F3 B:BEF202 0.0 27.8 1.0 BE B:BEF202 1.5 24.8 1.0 HG1 B:THR81 2.0 19.6 1.0 H B:GLU55 2.0 20.6 1.0 H B:VAL54 2.3 18.1 1.0 HB B:VAL54 2.4 16.5 1.0 OD2 B:ASP53 2.4 11.7 1.0 F1 B:BEF202 2.5 24.1 1.0 F2 B:BEF202 2.6 17.7 1.0 OG1 B:THR81 2.7 16.3 1.0 N B:GLU55 2.8 17.1 1.0 N B:VAL54 2.9 15.1 1.0 HD2 B:PHE83 2.9 30.2 1.0 HE2 B:PHE83 3.2 43.8 1.0 CB B:VAL54 3.2 13.7 1.0 CA B:VAL54 3.3 17.3 1.0 HB B:THR81 3.3 15.9 1.0 CG B:ASP53 3.4 20.8 1.0 C B:VAL54 3.4 17.7 1.0 CB B:THR81 3.5 13.3 1.0 HA B:THR81 3.5 25.4 1.0 CD2 B:PHE83 3.5 25.2 1.0 HG3 B:GLU55 3.6 27.0 1.0 HB2 B:GLU55 3.6 19.8 1.0 CE2 B:PHE83 3.7 36.5 1.0 H B:THR82 3.7 17.3 1.0 HG23 B:VAL54 3.8 18.2 1.0 CA B:GLU55 3.9 13.8 1.0 C B:ASP53 4.0 18.0 1.0 OD1 B:ASP53 4.0 16.9 1.0 CA B:THR81 4.0 21.2 1.0 CG2 B:VAL54 4.1 15.2 1.0 HA B:ASP53 4.1 19.8 1.0 CB B:GLU55 4.1 16.5 1.0 HG12 B:VAL54 4.2 19.4 1.0 MG B:MG201 4.2 18.2 1.0 HA B:VAL54 4.2 20.7 1.0 CG1 B:VAL54 4.3 16.2 1.0 CG B:GLU55 4.3 22.5 1.0 H B:PHE83 4.3 23.3 1.0 CA B:ASP53 4.4 16.5 1.0 N B:THR82 4.4 14.4 1.0 HZ2 B:LYS103 4.4 22.8 1.0 O B:GLU55 4.4 14.2 1.0 HG21 B:VAL54 4.4 18.2 1.0 CB B:ASP53 4.5 18.3 1.0 C B:GLU55 4.6 16.5 1.0 HZ1 B:LYS103 4.6 22.8 1.0 HG11 B:VAL54 4.6 19.4 1.0 O B:VAL54 4.6 17.8 1.0 HA B:GLU55 4.7 16.6 1.0 O B:VAL80 4.7 16.9 1.0 O B:HOH413 4.7 29.7 1.0 C B:THR81 4.8 16.6 1.0 CG B:PHE83 4.8 30.5 1.0 HG23 B:THR82 4.8 16.2 1.0 HB2 B:PHE83 4.8 27.0 1.0 CG2 B:THR81 4.8 19.0 1.0 HG22 B:VAL54 4.9 18.2 1.0 O B:HOH325 4.9 13.8 1.0 HG21 B:THR81 4.9 22.8 1.0 NZ B:LYS103 4.9 19.0 1.0 HE3 B:LYS103 4.9 19.3 1.0 HG2 B:GLU55 4.9 27.0 1.0 O B:ASP53 5.0 15.1 1.0 CZ B:PHE83 5.0 29.7 1.0

A.K.Park, J.H.Lee, Y.M.Chi, H.Park. Structural Characterization of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue Reveals A Novel Conformational Plasticity of the Linker Region Biochem.Biophys.Res.Commun. V. 473 625 2016.
ISSN: ESSN 1090-2104
PubMed: 27038544
DOI: 10.1016/J.BBRC.2016.03.144