Fluorine in PDB 4zms: Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C

The structure of Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C, PDB code: 4zms 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)	37.82 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.980, 115.526, 50.073, 90.00, 92.41, 90.00
R / Rfree (%)	16.5 / 21.5

The structure of Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Bromine	(Br)	3 atoms

The binding sites of Fluorine atom in the Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C (pdb code 4zms). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C, PDB code: 4zms:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:10.3 occ:1.00 F1 A:BEF202 0.0 10.3 1.0 BE A:BEF202 1.5 20.8 1.0 MG A:MG201 1.9 12.1 1.0 HB2 A:GLU55 2.4 15.1 1.0 F2 A:BEF202 2.6 13.1 1.0 F3 A:BEF202 2.6 9.8 1.0 OD1 A:ASP53 2.6 9.8 1.0 O A:HOH433 2.7 12.0 1.0 O A:HOH366 2.8 11.7 1.0 HE2 A:PHE83 2.8 22.1 1.0 O A:HOH460 2.9 17.5 1.0 OD2 A:ASP53 3.0 8.6 1.0 H A:GLU55 3.0 13.6 1.0 O A:GLU55 3.0 11.5 1.0 CG A:ASP53 3.1 10.4 1.0 CB A:GLU55 3.3 12.6 1.0 N A:GLU55 3.6 11.3 1.0 HZ2 A:LYS103 3.6 16.9 1.0 CA A:GLU55 3.7 11.7 1.0 CE2 A:PHE83 3.7 18.4 1.0 C A:GLU55 3.7 13.1 1.0 HB3 A:GLU55 3.8 15.1 1.0 OD1 A:ASP8 4.0 11.9 1.0 HZ1 A:LYS103 4.1 16.9 1.0 O A:HOH320 4.2 17.3 1.0 HG1 A:THR81 4.2 14.0 1.0 HG3 A:GLU55 4.2 25.6 1.0 NZ A:LYS103 4.2 14.1 1.0 HD2 A:PHE83 4.3 20.3 1.0 CG A:GLU55 4.4 21.4 1.0 H A:VAL54 4.4 11.0 1.0 HG23 A:THR82 4.5 8.7 1.0 HZ A:PHE83 4.5 20.5 1.0 H A:THR82 4.5 14.4 1.0 CD2 A:PHE83 4.5 16.9 1.0 HZ3 A:LYS103 4.6 16.9 1.0 CZ A:PHE83 4.6 17.1 1.0 O A:HOH486 4.6 37.2 1.0 C A:VAL54 4.6 12.3 1.0 HA A:GLU55 4.7 14.1 1.0 CB A:ASP53 4.7 9.2 1.0 HB A:VAL54 4.7 8.4 1.0 N A:VAL54 4.8 9.2 1.0 HG1 A:THR82 4.8 32.1 1.0 OG1 A:THR82 4.8 26.8 1.0 HA A:THR81 4.9 14.1 1.0 HG3 A:MET56 5.0 12.2 1.0 OE1 A:GLU55 5.0 20.9 1.0

Fluorine binding site 2 out of 6 in the Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:13.1 occ:1.00 F2 A:BEF202 0.0 13.1 1.0 BE A:BEF202 1.6 20.8 1.0 HG1 A:THR81 2.0 14.0 1.0 H A:GLU55 2.0 13.6 1.0 OD1 A:ASP53 2.4 9.8 1.0 HB A:VAL54 2.4 8.4 1.0 H A:VAL54 2.5 11.0 1.0 F3 A:BEF202 2.5 9.8 1.0 F1 A:BEF202 2.6 10.3 1.0 OG1 A:THR81 2.8 11.7 1.0 HD2 A:PHE83 2.8 20.3 1.0 N A:GLU55 2.8 11.3 1.0 HE2 A:PHE83 3.0 22.1 1.0 N A:VAL54 3.0 9.2 1.0 HB2 A:GLU55 3.2 15.1 1.0 CB A:VAL54 3.2 7.0 1.0 CA A:VAL54 3.4 12.4 1.0 CG A:ASP53 3.4 10.4 1.0 HA A:THR81 3.4 14.1 1.0 CD2 A:PHE83 3.5 16.9 1.0 HB A:THR81 3.5 13.3 1.0 HG3 A:GLU55 3.5 25.6 1.0 CE2 A:PHE83 3.5 18.4 1.0 C A:VAL54 3.6 12.3 1.0 H A:THR82 3.6 14.4 1.0 CB A:THR81 3.6 11.1 1.0 CB A:GLU55 3.8 12.6 1.0 CA A:GLU55 3.8 11.7 1.0 HG23 A:VAL54 3.9 15.9 1.0 CA A:THR81 4.0 11.8 1.0 OD2 A:ASP53 4.1 8.6 1.0 C A:ASP53 4.1 8.1 1.0 CG A:GLU55 4.1 21.4 1.0 CG2 A:VAL54 4.1 13.2 1.0 MG A:MG201 4.2 12.1 1.0 HA A:ASP53 4.2 8.5 1.0 HG12 A:VAL54 4.2 11.7 1.0 HZ2 A:LYS103 4.3 16.9 1.0 N A:THR82 4.3 12.0 1.0 CG1 A:VAL54 4.3 9.8 1.0 HA A:VAL54 4.3 14.9 1.0 H A:PHE83 4.4 19.1 1.0 O A:GLU55 4.4 11.5 1.0 HG21 A:VAL54 4.5 15.9 1.0 CA A:ASP53 4.5 7.1 1.0 CB A:ASP53 4.5 9.2 1.0 O A:HOH460 4.5 17.5 1.0 C A:GLU55 4.6 13.1 1.0 HG11 A:VAL54 4.6 11.7 1.0 HA A:GLU55 4.6 14.1 1.0 HB3 A:GLU55 4.7 15.1 1.0 O A:VAL80 4.7 9.7 1.0 C A:THR81 4.7 11.3 1.0 O A:VAL54 4.7 8.0 1.0 OG1 A:THR82 4.8 26.8 1.0 CG A:PHE83 4.8 25.6 1.0 HG2 A:GLU55 4.8 25.6 1.0 HG23 A:THR82 4.8 8.7 1.0 HZ1 A:LYS103 4.9 16.9 1.0 HB2 A:PHE83 4.9 21.5 1.0 CZ A:PHE83 4.9 17.1 1.0 CG2 A:THR81 4.9 11.4 1.0 HG22 A:VAL54 5.0 15.9 1.0 NZ A:LYS103 5.0 14.1 1.0 O A:HOH366 5.0 11.7 1.0

Fluorine binding site 3 out of 6 in the Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:9.8 occ:1.00 F3 A:BEF202 0.0 9.8 1.0 BE A:BEF202 1.6 20.8 1.0 HZ2 A:LYS103 2.0 16.9 1.0 H A:THR82 2.1 14.4 1.0 HG23 A:THR82 2.5 8.7 1.0 F2 A:BEF202 2.5 13.1 1.0 OD1 A:ASP53 2.6 9.8 1.0 F1 A:BEF202 2.6 10.3 1.0 HA A:THR81 2.8 14.1 1.0 HG1 A:THR81 2.9 14.0 1.0 NZ A:LYS103 2.9 14.1 1.0 O A:HOH460 2.9 17.5 1.0 N A:THR82 2.9 12.0 1.0 HZ1 A:LYS103 3.1 16.9 1.0 HD2 A:LYS103 3.3 15.2 1.0 HE3 A:LYS103 3.4 10.1 1.0 CG2 A:THR82 3.4 7.2 1.0 HZ3 A:LYS103 3.4 16.9 1.0 OG1 A:THR82 3.5 26.8 1.0 OG1 A:THR81 3.5 11.7 1.0 CE A:LYS103 3.5 8.4 1.0 CA A:THR81 3.6 11.8 1.0 HE2 A:PHE83 3.6 22.1 1.0 CG A:ASP53 3.7 10.4 1.0 C A:THR81 3.7 11.3 1.0 O A:HOH366 3.7 11.7 1.0 HG1 A:THR82 3.8 32.1 1.0 CB A:THR82 3.8 10.1 1.0 HG21 A:THR82 3.8 8.7 1.0 CA A:THR82 3.9 12.8 1.0 CD A:LYS103 3.9 12.7 1.0 HD2 A:PHE83 4.0 20.3 1.0 CE2 A:PHE83 4.0 18.4 1.0 HG22 A:THR82 4.0 8.7 1.0 CB A:THR81 4.1 11.1 1.0 MG A:MG201 4.1 12.1 1.0 CD2 A:PHE83 4.2 16.9 1.0 OD2 A:ASP53 4.2 8.6 1.0 H A:VAL54 4.2 11.0 1.0 H A:PHE83 4.3 19.1 1.0 H A:GLU55 4.3 13.6 1.0 HB A:THR81 4.4 13.3 1.0 O A:VAL80 4.4 9.7 1.0 HE2 A:LYS103 4.4 10.1 1.0 HB2 A:GLU55 4.5 15.1 1.0 HA A:THR82 4.5 15.3 1.0 HD3 A:LYS103 4.5 15.2 1.0 HB A:THR82 4.7 12.2 1.0 O B:HOH452 4.7 11.8 1.0 N A:THR81 4.7 11.1 1.0 HG3 A:LYS103 4.7 12.4 1.0 OE2 A:GLU7 4.7 10.4 1.0 HA A:ASP53 4.8 8.5 1.0 N A:PHE83 4.8 15.9 1.0 HB A:VAL54 4.8 8.4 1.0 O A:THR81 4.9 9.2 1.0 CZ A:PHE83 4.9 17.1 1.0 C A:THR82 4.9 15.8 1.0 N A:VAL54 4.9 9.2 1.0 CB A:ASP53 5.0 9.2 1.0 CG A:LYS103 5.0 10.3 1.0 O A:HOH433 5.0 12.0 1.0

Fluorine binding site 4 out of 6 in the Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:10.5 occ:1.00 F1 B:BEF202 0.0 10.5 1.0 BE B:BEF202 1.5 16.1 1.0 HZ2 B:LYS103 1.9 12.8 1.0 H B:THR82 1.9 13.9 1.0 HG23 B:THR82 2.4 12.8 1.0 OD2 B:ASP53 2.6 10.8 1.0 F3 B:BEF202 2.6 13.9 1.0 HA B:THR81 2.7 15.2 1.0 F2 B:BEF202 2.7 12.8 1.0 NZ B:LYS103 2.7 10.7 1.0 N B:THR82 2.8 11.6 1.0 O B:HOH478 2.9 19.4 1.0 HG1 B:THR81 2.9 12.0 1.0 HZ1 B:LYS103 3.0 12.8 1.0 HZ3 B:LYS103 3.2 12.8 1.0 HD2 B:LYS103 3.3 16.1 1.0 CG2 B:THR82 3.3 10.6 1.0 CA B:THR81 3.4 12.7 1.0 HE3 B:LYS103 3.5 10.2 1.0 OG1 B:THR82 3.5 27.2 1.0 HE2 B:PHE83 3.5 29.9 1.0 C B:THR81 3.5 14.1 1.0 OG1 B:THR81 3.6 10.0 1.0 CE B:LYS103 3.6 8.5 1.0 O B:HOH394 3.6 13.2 1.0 CG B:ASP53 3.7 14.2 1.0 HG21 B:THR82 3.7 12.8 1.0 CB B:THR82 3.7 20.7 1.0 CA B:THR82 3.8 16.2 1.0 HG22 B:THR82 3.9 12.8 1.0 HG1 B:THR82 3.9 32.7 1.0 CE2 B:PHE83 3.9 24.9 1.0 CD B:LYS103 3.9 13.4 1.0 HD2 B:PHE83 3.9 22.6 1.0 CB B:THR81 4.1 11.6 1.0 CD2 B:PHE83 4.1 18.8 1.0 H B:PHE83 4.2 18.4 1.0 H B:VAL54 4.2 12.9 1.0 OD1 B:ASP53 4.2 9.8 1.0 MG B:MG201 4.3 13.2 1.0 H B:GLU55 4.4 19.1 1.0 O B:VAL80 4.4 12.1 1.0 HB B:THR81 4.4 13.9 1.0 HA B:THR82 4.5 19.5 1.0 HE2 B:LYS103 4.5 10.2 1.0 HD3 B:LYS103 4.5 16.1 1.0 O B:HOH448 4.6 11.0 1.0 HB2 B:GLU55 4.6 17.9 1.0 N B:THR81 4.6 10.7 1.0 HG3 B:LYS103 4.7 10.8 1.0 HB B:THR82 4.7 24.8 1.0 O B:THR81 4.7 13.8 1.0 N B:PHE83 4.7 15.4 1.0 HA B:ASP53 4.8 13.8 1.0 CZ B:PHE83 4.8 23.1 1.0 OE2 B:GLU7 4.8 8.9 1.0 C B:THR82 4.8 15.4 1.0 HB B:VAL54 4.9 13.5 1.0 N B:VAL54 4.9 10.8 1.0 CB B:ASP53 4.9 10.6 1.0 CG B:LYS103 4.9 9.0 1.0 C B:VAL80 5.0 13.3 1.0

Fluorine binding site 5 out of 6 in the Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:12.8 occ:1.00 F2 B:BEF202 0.0 12.8 1.0 BE B:BEF202 1.6 16.1 1.0 MG B:MG201 2.0 13.2 1.0 HB2 B:GLU55 2.5 17.9 1.0 OD2 B:ASP53 2.6 10.8 1.0 F3 B:BEF202 2.6 13.9 1.0 O B:HOH394 2.7 13.2 1.0 F1 B:BEF202 2.7 10.5 1.0 OD1 B:ASP53 2.7 9.8 1.0 HE2 B:PHE83 2.8 29.9 1.0 O B:GLU55 2.9 15.4 1.0 O B:HOH451 2.9 15.9 1.0 O B:HOH478 3.0 19.4 1.0 H B:GLU55 3.0 19.1 1.0 CG B:ASP53 3.0 14.2 1.0 CB B:GLU55 3.4 14.9 1.0 N B:GLU55 3.5 15.9 1.0 HZ2 B:LYS103 3.6 12.8 1.0 C B:GLU55 3.6 15.2 1.0 CE2 B:PHE83 3.6 24.9 1.0 CA B:GLU55 3.7 13.7 1.0 HB3 B:GLU55 3.9 17.9 1.0 HZ1 B:LYS103 3.9 12.8 1.0 OD1 B:ASP8 4.0 15.6 1.0 NZ B:LYS103 4.2 10.7 1.0 O B:HOH311 4.2 19.4 1.0 H B:VAL54 4.2 12.9 1.0 HG1 B:THR81 4.3 12.0 1.0 HZ B:PHE83 4.4 27.8 1.0 HD2 B:PHE83 4.4 22.6 1.0 HG3 B:GLU55 4.4 26.2 1.0 HZ3 B:LYS103 4.4 12.8 1.0 HG23 B:THR82 4.5 12.8 1.0 CZ B:PHE83 4.5 23.1 1.0 CG B:GLU55 4.5 21.8 1.0 CD2 B:PHE83 4.5 18.8 1.0 H B:THR82 4.5 13.9 1.0 CB B:ASP53 4.5 10.6 1.0 C B:VAL54 4.6 11.6 1.0 N B:VAL54 4.6 10.8 1.0 HA B:GLU55 4.6 16.4 1.0 O B:HOH506 4.7 21.6 1.0 HB B:VAL54 4.8 13.5 1.0 HB3 B:ASP53 4.8 12.7 1.0 HA B:THR81 4.9 15.2 1.0 N B:MET56 4.9 13.0 1.0 HG2 B:MET56 4.9 20.6 1.0 HB2 B:ASP53 5.0 12.7 1.0 CG B:ASP8 5.0 15.6 1.0 OE1 B:GLU55 5.0 26.2 1.0

Fluorine binding site 6 out of 6 in the Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of the Full-Length Response Regulator SPR1814 in Complex with A Phosphate Analogue and B3C within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:13.9 occ:1.00 F3 B:BEF202 0.0 13.9 1.0 BE B:BEF202 1.5 16.1 1.0 HG1 B:THR81 1.9 12.0 1.0 H B:GLU55 2.0 19.1 1.0 H B:VAL54 2.3 12.9 1.0 OD2 B:ASP53 2.4 10.8 1.0 HB B:VAL54 2.4 13.5 1.0 F1 B:BEF202 2.6 10.5 1.0 F2 B:BEF202 2.6 12.8 1.0 HD2 B:PHE83 2.8 22.6 1.0 OG1 B:THR81 2.8 10.0 1.0 N B:GLU55 2.8 15.9 1.0 HE2 B:PHE83 2.9 29.9 1.0 N B:VAL54 2.9 10.8 1.0 CB B:VAL54 3.2 11.2 1.0 HB2 B:GLU55 3.3 17.9 1.0 HA B:THR81 3.3 15.2 1.0 CA B:VAL54 3.3 12.7 1.0 CG B:ASP53 3.4 14.2 1.0 CD2 B:PHE83 3.4 18.8 1.0 CE2 B:PHE83 3.4 24.9 1.0 HB B:THR81 3.5 13.9 1.0 C B:VAL54 3.5 11.6 1.0 CB B:THR81 3.6 11.6 1.0 H B:THR82 3.7 13.9 1.0 HG3 B:GLU55 3.7 26.2 1.0 HG23 B:VAL54 3.8 11.1 1.0 CA B:GLU55 3.9 13.7 1.0 OD1 B:ASP53 3.9 9.8 1.0 CA B:THR81 3.9 12.7 1.0 CB B:GLU55 3.9 14.9 1.0 C B:ASP53 4.0 12.1 1.0 CG2 B:VAL54 4.1 9.3 1.0 HZ2 B:LYS103 4.1 12.8 1.0 HA B:ASP53 4.1 13.8 1.0 HG12 B:VAL54 4.3 15.6 1.0 N B:THR82 4.3 11.6 1.0 HA B:VAL54 4.3 15.2 1.0 MG B:MG201 4.3 13.2 1.0 CG B:GLU55 4.3 21.8 1.0 H B:PHE83 4.3 18.4 1.0 CG1 B:VAL54 4.4 13.0 1.0 O B:GLU55 4.4 15.4 1.0 CA B:ASP53 4.4 11.5 1.0 HG21 B:VAL54 4.4 11.1 1.0 CB B:ASP53 4.5 10.6 1.0 O B:HOH478 4.5 19.4 1.0 C B:GLU55 4.6 15.2 1.0 C B:THR81 4.6 14.1 1.0 HA B:GLU55 4.7 16.4 1.0 HG11 B:VAL54 4.7 15.6 1.0 O B:VAL80 4.7 12.1 1.0 CG B:PHE83 4.7 18.8 1.0 HZ1 B:LYS103 4.7 12.8 1.0 O B:VAL54 4.7 12.5 1.0 CZ B:PHE83 4.8 23.1 1.0 HG23 B:THR82 4.8 12.8 1.0 HB3 B:GLU55 4.8 17.9 1.0 NZ B:LYS103 4.8 10.7 1.0 HB2 B:PHE83 4.8 25.7 1.0 O B:HOH394 4.9 13.2 1.0 HG22 B:VAL54 4.9 11.1 1.0 OG1 B:THR82 4.9 27.2 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