Fluorine in PDB 8vc9: Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form

The structure of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form, PDB code: 8vc9 was solved by A.Mechaly, A.Buschiazzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.27 / 2.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	175.074, 102.327, 184.476, 90, 92.49, 90
R / Rfree (%)	21 / 25.4

The structure of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form also contains other interesting chemical elements:

Magnesium

(Mg)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form (pdb code 8vc9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form, PDB code: 8vc9:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:77.8 occ:1.00 F1 A:BEF403 0.0 77.8 1.0 BE A:BEF403 1.6 79.3 1.0 OD1 A:ASP56 2.5 80.5 1.0 F3 A:BEF403 2.6 78.4 1.0 F2 A:BEF403 2.6 75.7 1.0 OG1 A:THR86 2.8 86.5 1.0 N A:SER58 2.8 75.0 1.0 N A:PHE57 2.9 76.3 1.0 CB A:PHE57 3.2 74.1 1.0 CB A:SER84 3.3 76.0 1.0 CA A:PHE57 3.3 76.1 1.0 CG A:ASP56 3.3 79.1 1.0 C A:PHE57 3.4 76.5 1.0 CG2 A:THR86 3.5 74.5 1.0 CB A:SER58 3.7 82.6 1.0 OD2 A:ASP56 3.7 84.5 1.0 CB A:THR86 3.7 80.0 1.0 CA A:SER58 3.8 80.1 1.0 CA A:SER84 3.9 78.9 1.0 C A:ASP56 4.0 76.1 1.0 N A:THR86 4.2 82.3 1.0 CG A:PHE57 4.2 74.8 1.0 N A:GLY85 4.2 74.5 1.0 CD2 A:PHE57 4.2 76.2 1.0 MG A:MG402 4.3 82.5 1.0 CA A:ASP56 4.4 76.1 1.0 CB A:ASP56 4.4 79.9 1.0 C A:SER84 4.5 75.2 1.0 OG A:SER84 4.5 76.9 1.0 CA A:THR86 4.6 72.3 1.0 C A:SER58 4.6 84.3 1.0 O A:PHE57 4.6 77.7 1.0 O A:SER58 4.7 86.9 1.0 O A:HOH502 4.9 82.1 1.0

Fluorine binding site 2 out of 18 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:75.7 occ:1.00 F2 A:BEF403 0.0 75.7 1.0 BE A:BEF403 1.6 79.3 1.0 OD1 A:ASP56 2.4 80.5 1.0 N A:GLY85 2.6 74.5 1.0 F1 A:BEF403 2.6 77.8 1.0 F3 A:BEF403 2.6 78.4 1.0 NZ A:LYS106 2.8 81.3 1.0 CE A:LYS106 3.2 75.7 1.0 CA A:SER84 3.3 78.9 1.0 C A:SER84 3.4 75.2 1.0 CA A:GLY85 3.5 77.1 1.0 CG A:ASP56 3.6 79.1 1.0 O A:HOH502 3.6 82.1 1.0 CB A:SER84 3.7 76.0 1.0 N A:THR86 3.8 82.3 1.0 CD A:LYS106 3.8 75.8 1.0 C A:GLY85 4.1 76.9 1.0 CG2 A:THR86 4.2 74.5 1.0 OD2 A:ASP56 4.2 84.5 1.0 MG A:MG402 4.3 82.5 1.0 OG1 A:THR86 4.3 86.5 1.0 O A:VAL83 4.5 80.5 1.0 O A:SER84 4.6 77.3 1.0 N A:SER84 4.6 78.2 1.0 CG A:LYS106 4.7 77.9 1.0 CB A:THR86 4.7 80.0 1.0 CB A:ASP56 4.7 79.9 1.0 N A:PHE57 4.8 76.3 1.0 CA A:THR86 4.8 72.3 1.0 OD2 A:ASP15 4.9 100.8 1.0

Fluorine binding site 3 out of 18 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:78.4 occ:1.00 F3 A:BEF403 0.0 78.4 1.0 BE A:BEF403 1.6 79.3 1.0 MG A:MG402 2.1 82.5 1.0 OD1 A:ASP56 2.6 80.5 1.0 F1 A:BEF403 2.6 77.8 1.0 F2 A:BEF403 2.6 75.7 1.0 O A:HOH502 2.8 82.1 1.0 OD2 A:ASP56 2.8 84.5 1.0 CG A:ASP56 3.1 79.1 1.0 O A:HOH505 3.1 89.2 1.0 O A:SER58 3.1 86.9 1.0 CB A:SER58 3.4 82.6 1.0 N A:SER58 3.6 75.0 1.0 CA A:SER58 3.7 80.1 1.0 CG2 A:THR86 3.7 74.5 1.0 C A:SER58 3.8 84.3 1.0 OD1 A:ASP11 4.1 84.5 1.0 OG A:SER58 4.2 88.0 1.0 NZ A:LYS106 4.2 81.3 1.0 CB A:ASP56 4.6 79.9 1.0 OG1 A:THR86 4.6 86.5 1.0 N A:PHE57 4.8 76.3 1.0 C A:PHE57 4.8 76.5 1.0 CB A:THR86 4.8 80.0 1.0 N A:LEU59 5.0 83.1 1.0

Fluorine binding site 4 out of 18 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ B:F403 b:55.9 occ:1.00 F1 B:BEF403 0.0 55.9 1.0 BE B:BEF403 1.6 58.1 1.0 OD1 B:ASP56 2.5 56.6 1.0 F2 B:BEF403 2.6 58.3 1.0 F3 B:BEF403 2.7 56.6 1.0 OG1 B:THR86 2.8 69.8 1.0 N B:SER58 3.1 55.4 1.0 N B:PHE57 3.2 60.3 1.0 CB B:SER84 3.2 57.8 1.0 CB B:PHE57 3.3 46.9 1.0 CG2 B:THR86 3.4 51.9 1.0 CG B:ASP56 3.5 58.3 1.0 CA B:PHE57 3.6 54.0 1.0 CB B:THR86 3.6 59.1 1.0 C B:PHE57 3.8 55.3 1.0 N B:THR86 3.8 68.1 1.0 CB B:SER58 3.8 63.3 1.0 CA B:SER84 3.9 61.2 1.0 N B:GLY85 3.9 65.1 1.0 CA B:SER58 4.0 58.1 1.0 OD2 B:ASP56 4.0 62.7 1.0 C B:SER84 4.3 61.2 1.0 C B:ASP56 4.3 59.3 1.0 CA B:THR86 4.3 57.7 1.0 CG B:PHE57 4.4 59.9 1.0 CD2 B:PHE57 4.4 65.3 1.0 OG B:SER84 4.4 62.5 1.0 MG B:MG402 4.5 61.2 1.0 CA B:ASP56 4.7 58.0 1.0 CB B:ASP56 4.7 56.2 1.0 C B:GLY85 4.7 59.8 1.0 CA B:GLY85 4.8 65.5 1.0 O B:SER58 4.8 62.2 1.0 C B:SER58 4.9 53.1 1.0 O B:PHE57 4.9 54.4 1.0

Fluorine binding site 5 out of 18 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ B:F403 b:58.3 occ:1.00 F2 B:BEF403 0.0 58.3 1.0 BE B:BEF403 1.5 58.1 1.0 OD1 B:ASP56 2.4 56.6 1.0 F1 B:BEF403 2.6 55.9 1.0 F3 B:BEF403 2.6 56.6 1.0 N B:GLY85 2.8 65.1 1.0 NZ B:LYS106 2.9 53.8 1.0 CE B:LYS106 3.3 59.2 1.0 O B:HOH504 3.5 56.7 1.0 CG B:ASP56 3.5 58.3 1.0 CA B:SER84 3.6 61.2 1.0 CA B:GLY85 3.6 65.5 1.0 C B:SER84 3.6 61.2 1.0 CD B:LYS106 3.7 55.7 1.0 CB B:SER84 4.0 57.8 1.0 N B:THR86 4.0 68.1 1.0 OD2 B:ASP56 4.1 62.7 1.0 MG B:MG402 4.2 61.2 1.0 C B:GLY85 4.2 59.8 1.0 CG2 B:THR86 4.3 51.9 1.0 OD2 B:ASP15 4.4 61.3 1.0 CG B:LYS106 4.6 61.6 1.0 O B:VAL83 4.6 64.8 1.0 OG1 B:THR86 4.7 69.8 1.0 CB B:ASP56 4.7 56.2 1.0 O B:SER84 4.8 61.6 1.0 N B:SER84 4.9 64.2 1.0 N B:PHE57 4.9 60.3 1.0 CB B:THR86 4.9 59.1 1.0 OE1 B:GLU10 5.0 65.1 1.0

Fluorine binding site 6 out of 18 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ B:F403 b:56.6 occ:1.00 F3 B:BEF403 0.0 56.6 1.0 BE B:BEF403 1.6 58.1 1.0 MG B:MG402 2.1 61.2 1.0 OD1 B:ASP56 2.6 56.6 1.0 F2 B:BEF403 2.6 58.3 1.0 F1 B:BEF403 2.7 55.9 1.0 OD2 B:ASP56 2.7 62.7 1.0 O B:HOH504 2.8 56.7 1.0 CG B:ASP56 3.0 58.3 1.0 O B:SER58 3.0 62.2 1.0 O B:HOH506 3.1 61.9 1.0 CB B:SER58 3.3 63.3 1.0 N B:SER58 3.5 55.4 1.0 CA B:SER58 3.6 58.1 1.0 C B:SER58 3.7 53.1 1.0 CG2 B:THR86 3.9 51.9 1.0 OG B:SER58 4.1 63.3 1.0 OD1 B:ASP11 4.1 58.0 1.0 NZ B:LYS106 4.5 53.8 1.0 CB B:ASP56 4.5 56.2 1.0 N B:PHE57 4.7 60.3 1.0 OG1 B:THR86 4.7 69.8 1.0 C B:PHE57 4.7 55.3 1.0 N B:LEU59 4.8 56.6 1.0 CB B:THR86 5.0 59.1 1.0

Fluorine binding site 7 out of 18 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ C:F403 b:63.9 occ:1.00 F1 C:BEF403 0.0 63.9 1.0 BE C:BEF403 1.6 63.6 1.0 OD1 C:ASP56 2.5 58.7 1.0 F3 C:BEF403 2.6 62.6 1.0 F2 C:BEF403 2.6 56.9 1.0 N C:SER58 2.7 61.9 1.0 OG1 C:THR86 2.7 80.5 1.0 N C:PHE57 2.9 70.0 1.0 CB C:PHE57 3.1 61.8 1.0 CB C:SER84 3.2 59.0 1.0 CA C:PHE57 3.2 62.8 1.0 C C:PHE57 3.3 59.4 1.0 CG C:ASP56 3.3 59.2 1.0 CB C:SER58 3.6 71.5 1.0 CA C:SER58 3.7 63.8 1.0 CG2 C:THR86 3.7 58.3 1.0 CB C:THR86 3.8 71.7 1.0 OD2 C:ASP56 3.8 70.7 1.0 C C:ASP56 4.0 65.9 1.0 CA C:SER84 4.0 58.9 1.0 CG C:PHE57 4.1 67.6 1.0 CD2 C:PHE57 4.2 66.8 1.0 OG C:SER84 4.3 61.4 1.0 N C:THR86 4.3 65.7 1.0 MG C:MG402 4.3 60.6 1.0 CA C:ASP56 4.4 64.7 1.0 CB C:ASP56 4.4 67.7 1.0 N C:GLY85 4.5 55.7 1.0 O C:PHE57 4.5 60.9 1.0 C C:SER58 4.6 60.0 1.0 O C:SER58 4.6 64.2 1.0 CA C:THR86 4.7 65.5 1.0 C C:SER84 4.7 60.5 1.0 OG C:SER58 4.9 72.1 1.0 O C:ASP56 5.0 63.3 1.0

Fluorine binding site 8 out of 18 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ C:F403 b:56.9 occ:1.00 F2 C:BEF403 0.0 56.9 1.0 BE C:BEF403 1.6 63.6 1.0 OD1 C:ASP56 2.5 58.7 1.0 F3 C:BEF403 2.6 62.6 1.0 F1 C:BEF403 2.6 63.9 1.0 N C:GLY85 2.6 55.7 1.0 NZ C:LYS106 3.0 60.5 1.0 CA C:SER84 3.2 58.9 1.0 C C:SER84 3.4 60.5 1.0 CE C:LYS106 3.4 57.8 1.0 CB C:SER84 3.4 59.0 1.0 CA C:GLY85 3.6 55.9 1.0 N C:THR86 3.6 65.7 1.0 CG C:ASP56 3.7 59.2 1.0 CD C:LYS106 3.9 48.4 1.0 O C:HOH501 3.9 61.2 1.0 CG2 C:THR86 4.0 58.3 1.0 OG1 C:THR86 4.0 80.5 1.0 C C:GLY85 4.0 67.0 1.0 OD2 C:ASP56 4.3 70.7 1.0 MG C:MG402 4.3 60.6 1.0 CB C:THR86 4.4 71.7 1.0 O C:VAL83 4.4 66.6 1.0 N C:SER84 4.6 66.6 1.0 O C:SER84 4.6 60.4 1.0 CA C:THR86 4.6 65.5 1.0 N C:PHE57 4.7 70.0 1.0 CG C:LYS106 4.8 48.2 1.0 OG C:SER84 4.8 61.4 1.0 CB C:ASP56 4.8 67.7 1.0 N C:SER58 4.9 61.9 1.0 OD2 C:ASP15 5.0 59.2 1.0 C C:VAL83 5.0 59.9 1.0

Fluorine binding site 9 out of 18 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ C:F403 b:62.6 occ:1.00 F3 C:BEF403 0.0 62.6 1.0 BE C:BEF403 1.6 63.6 1.0 MG C:MG402 2.1 60.6 1.0 OD1 C:ASP56 2.6 58.7 1.0 F1 C:BEF403 2.6 63.9 1.0 F2 C:BEF403 2.6 56.9 1.0 OD2 C:ASP56 2.8 70.7 1.0 O C:HOH501 2.9 61.2 1.0 O C:HOH505 3.0 72.1 1.0 CG C:ASP56 3.0 59.2 1.0 O C:SER58 3.0 64.2 1.0 CB C:SER58 3.4 71.5 1.0 N C:SER58 3.5 61.9 1.0 CA C:SER58 3.6 63.8 1.0 C C:SER58 3.7 60.0 1.0 CG2 C:THR86 3.8 58.3 1.0 OD1 C:ASP11 4.1 66.5 1.0 OG C:SER58 4.2 72.1 1.0 NZ C:LYS106 4.2 60.5 1.0 OG1 C:THR86 4.4 80.5 1.0 CB C:ASP56 4.5 67.7 1.0 N C:PHE57 4.7 70.0 1.0 C C:PHE57 4.7 59.4 1.0 CB C:THR86 4.8 71.7 1.0 N C:LEU59 4.9 67.2 1.0

Fluorine binding site 10 out of 18 in the Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Hybrid Response Regulator Lvrb From Leptospira / Phosphorylated Rec Form within 5.0Å range: probe atom residue distance (Å) B Occ D:F403 b:72.1 occ:1.00 F1 D:BEF403 0.0 72.1 1.0 BE D:BEF403 1.6 74.2 1.0 OD1 D:ASP56 2.5 74.0 1.0 F2 D:BEF403 2.6 66.5 1.0 F3 D:BEF403 2.6 72.3 1.0 N D:SER58 2.7 75.6 1.0 OG1 D:THR86 2.8 80.8 1.0 N D:PHE57 2.8 73.2 1.0 CB D:PHE57 3.1 70.0 1.0 CB D:SER84 3.2 72.3 1.0 CA D:PHE57 3.2 74.3 1.0 CG D:ASP56 3.3 72.6 1.0 C D:PHE57 3.4 77.5 1.0 CG2 D:THR86 3.4 67.8 1.0 CB D:SER58 3.6 81.3 1.0 CB D:THR86 3.7 80.7 1.0 OD2 D:ASP56 3.7 74.0 1.0 CA D:SER58 3.7 75.9 1.0 C D:ASP56 3.9 73.9 1.0 CA D:SER84 4.1 69.1 1.0 CG D:PHE57 4.1 82.8 1.0 CD2 D:PHE57 4.2 76.5 1.0 N D:THR86 4.2 78.0 1.0 MG D:MG402 4.3 77.5 1.0 CA D:ASP56 4.3 75.5 1.0 OG D:SER84 4.3 71.1 1.0 CB D:ASP56 4.4 79.9 1.0 N D:GLY85 4.5 69.5 1.0 O D:PHE57 4.6 77.4 1.0 C D:SER58 4.6 80.6 1.0 CA D:THR86 4.6 73.7 1.0 O D:SER58 4.6 80.1 1.0 C D:SER84 4.7 68.3 1.0 O D:ASP56 4.9 71.8 1.0 OG D:SER58 4.9 83.7 1.0 O D:HOH501 5.0 79.5 1.0

E.Agustoni, A.Mechaly, J.Dalla Rizza, P.Isaikina, F.Trajtenberg, T.Muntener, E.Wunder, A.I.Ko, T.Schirmer, A.Buschiazzo, S.Hiller. Coiled Coil Formation and Symmetry Breaking Activates the Leptospira Virulence Regulator Lvrb, A Hybrid Response Regulator To Be Published.