Fluorine in PDB 7ve6: N-Terminal Domain of Vrar

The structure of N-Terminal Domain of Vrar, PDB code: 7ve6 was solved by J.V.Kumar, C.Chen, C.H.Hsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.93 / 2.77
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.713, 122.713, 67.522, 90, 90, 120
R / Rfree (%)	17.8 / 21.7

The structure of N-Terminal Domain of Vrar also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the N-Terminal Domain of Vrar (pdb code 7ve6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the N-Terminal Domain of Vrar, PDB code: 7ve6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the N-Terminal Domain of Vrar


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of N-Terminal Domain of Vrar within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:41.9 occ:1.00 F1 A:BEF301 0.0 41.9 1.0 BE A:BEF301 1.5 30.2 1.0 HG1 A:THR83 1.8 38.7 1.0 H A:LEU57 1.9 39.9 1.0 HE2 A:PHE85 2.3 55.8 1.0 F2 A:BEF301 2.4 26.7 1.0 OD1 A:ASP55 2.5 30.7 1.0 F3 A:BEF301 2.5 32.0 1.0 OG1 A:THR83 2.6 32.2 1.0 HB3 A:LEU56 2.6 46.0 1.0 H A:LEU56 2.6 31.4 1.0 HD2 A:PHE85 2.7 63.8 1.0 N A:LEU57 2.8 33.2 1.0 CE2 A:PHE85 3.0 46.5 1.0 HB3 A:LEU57 3.1 55.9 1.0 CD2 A:PHE85 3.2 53.2 1.0 H A:SER84 3.2 40.5 1.0 N A:LEU56 3.3 26.1 1.0 CB A:LEU56 3.3 38.3 1.0 CG A:ASP55 3.5 36.3 1.0 CA A:LEU56 3.5 31.9 1.0 HA A:THR83 3.6 29.0 1.0 HB2 A:LEU56 3.6 46.0 1.0 CB A:THR83 3.6 26.2 1.0 HB2 A:LEU57 3.6 55.9 1.0 C A:LEU56 3.6 28.8 1.0 CB A:LEU57 3.6 46.6 1.0 HB A:THR83 3.7 31.5 1.0 CA A:LEU57 3.7 33.9 1.0 HZ1 A:LYS105 4.0 34.2 1.0 OD2 A:ASP55 4.0 32.5 1.0 N A:SER84 4.0 33.7 1.0 CA A:THR83 4.1 24.1 1.0 O A:LEU57 4.1 36.0 1.0 MG A:MG302 4.2 34.1 1.0 HD22 A:LEU56 4.2 43.7 1.0 CZ A:PHE85 4.2 52.9 1.0 C A:LEU57 4.4 36.6 1.0 C A:ASP55 4.4 23.1 1.0 HA A:LEU57 4.5 40.8 1.0 HA A:LEU56 4.5 38.4 1.0 HA A:ASP55 4.5 28.0 1.0 H A:PHE85 4.5 36.3 1.0 CG A:PHE85 4.5 56.5 1.0 HZ A:PHE85 4.5 63.6 1.0 CG A:LEU56 4.6 35.4 1.0 C A:THR83 4.6 29.3 1.0 OG A:SER84 4.6 53.9 1.0 HB2 A:SER84 4.7 49.9 1.0 HD13 A:LEU56 4.7 47.9 1.0 CB A:ASP55 4.8 27.0 1.0 NZ A:LYS105 4.8 28.5 1.0 O A:LEU56 4.8 35.8 1.0 CA A:ASP55 4.8 23.3 1.0 CG2 A:THR83 4.8 25.7 1.0 CD2 A:LEU56 4.9 36.4 1.0 HZ2 A:LYS105 4.9 34.2 1.0 HB2 A:PHE85 4.9 49.1 1.0 HG23 A:THR83 5.0 30.9 1.0

Fluorine binding site 2 out of 6 in the N-Terminal Domain of Vrar


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of N-Terminal Domain of Vrar within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:26.7 occ:1.00 F2 A:BEF301 0.0 26.7 1.0 BE A:BEF301 1.6 30.2 1.0 HZ1 A:LYS105 1.8 34.2 1.0 H A:SER84 2.4 40.5 1.0 F1 A:BEF301 2.4 41.9 1.0 HA A:THR83 2.5 29.0 1.0 OD1 A:ASP55 2.6 30.7 1.0 NZ A:LYS105 2.6 28.5 1.0 F3 A:BEF301 2.6 32.0 1.0 HZ2 A:LYS105 2.6 34.2 1.0 HG1 A:THR83 2.7 38.7 1.0 HD2 A:LYS105 2.9 31.3 1.0 OG A:SER84 3.0 53.9 1.0 N A:SER84 3.0 33.7 1.0 HZ3 A:LYS105 3.2 34.2 1.0 CA A:THR83 3.3 24.1 1.0 OG1 A:THR83 3.3 32.2 1.0 HE2 A:PHE85 3.5 55.8 1.0 HG A:SER84 3.5 64.7 1.0 CE A:LYS105 3.5 26.4 1.0 C A:THR83 3.5 29.3 1.0 CG A:ASP55 3.6 36.3 1.0 CD A:LYS105 3.6 26.0 1.0 HE3 A:LYS105 3.7 31.7 1.0 H A:LEU56 3.8 31.4 1.0 CB A:SER84 3.8 41.5 1.0 CB A:THR83 3.8 26.2 1.0 HB2 A:SER84 3.9 49.9 1.0 CA A:SER84 4.0 29.0 1.0 CE2 A:PHE85 4.0 46.5 1.0 OD2 A:ASP55 4.1 32.5 1.0 HD2 A:PHE85 4.1 63.8 1.0 HD3 A:LYS105 4.1 31.3 1.0 HB A:THR83 4.1 31.5 1.0 H A:LEU57 4.2 39.9 1.0 O A:LEU82 4.2 22.8 1.0 HE2 A:LYS105 4.3 31.7 1.0 CD2 A:PHE85 4.4 53.2 1.0 HA A:SER84 4.5 34.8 1.0 MG A:MG302 4.5 34.1 1.0 N A:THR83 4.5 17.6 1.0 HA A:ASP55 4.5 28.0 1.0 N A:LEU56 4.6 26.1 1.0 HG3 A:LYS105 4.6 27.9 1.0 O A:THR83 4.7 25.4 1.0 OD2 A:ASP9 4.7 45.2 1.0 HB3 A:SER84 4.7 49.9 1.0 H A:PHE85 4.7 36.3 1.0 HB3 A:LEU57 4.7 55.9 1.0 CB A:ASP55 4.7 27.0 1.0 HB3 A:LEU56 4.8 46.0 1.0 CG A:LYS105 4.8 23.2 1.0 C A:LEU82 4.8 21.6 1.0 HB2 A:ASP55 4.8 32.5 1.0 OD1 A:ASP9 4.9 39.6 1.0 CZ A:PHE85 4.9 52.9 1.0 N A:LEU57 5.0 33.2 1.0

Fluorine binding site 3 out of 6 in the N-Terminal Domain of Vrar


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of N-Terminal Domain of Vrar within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:32.0 occ:1.00 F3 A:BEF301 0.0 32.0 1.0 BE A:BEF301 1.6 30.2 1.0 MG A:MG302 1.9 34.1 1.0 OD2 A:ASP55 2.4 32.5 1.0 OD1 A:ASP55 2.4 30.7 1.0 F1 A:BEF301 2.5 41.9 1.0 F2 A:BEF301 2.6 26.7 1.0 CG A:ASP55 2.7 36.3 1.0 O A:LEU57 2.8 36.0 1.0 HB3 A:LEU57 2.9 55.9 1.0 H A:LEU57 3.0 39.9 1.0 HE2 A:PHE85 3.2 55.8 1.0 HZ1 A:LYS105 3.3 34.2 1.0 OD1 A:ASP10 3.4 39.5 1.0 N A:LEU57 3.6 33.2 1.0 C A:LEU57 3.7 36.6 1.0 HZ2 A:LYS105 3.7 34.2 1.0 CB A:LEU57 3.8 46.6 1.0 NZ A:LYS105 3.8 28.5 1.0 CA A:LEU57 3.9 33.9 1.0 HZ3 A:LYS105 3.9 34.2 1.0 H A:LEU56 4.0 31.4 1.0 HG1 A:THR83 4.0 38.7 1.0 CE2 A:PHE85 4.1 46.5 1.0 CB A:ASP55 4.3 27.0 1.0 OD1 A:ASP9 4.3 39.6 1.0 HB2 A:LEU57 4.3 55.9 1.0 N A:LEU56 4.5 26.1 1.0 HG2 A:MET58 4.5 39.8 1.0 CG A:ASP10 4.5 35.3 1.0 HG A:LEU57 4.6 54.4 1.0 H A:SER84 4.6 40.5 1.0 HD23 A:LEU57 4.6 57.7 1.0 HB2 A:ASP55 4.6 32.5 1.0 HZ A:PHE85 4.6 63.6 1.0 C A:LEU56 4.6 28.8 1.0 HB3 A:ASP55 4.7 32.5 1.0 OG A:SER84 4.7 53.9 1.0 CG A:LEU57 4.7 45.3 1.0 HA A:THR83 4.8 29.0 1.0 HD2 A:PHE85 4.8 63.8 1.0 HB3 A:LEU56 4.8 46.0 1.0 CZ A:PHE85 4.8 52.9 1.0 HG A:SER84 4.8 64.7 1.0 HA A:LEU57 4.8 40.8 1.0 OG1 A:THR83 4.9 32.2 1.0 H A:ASP10 4.9 40.4 1.0 OD2 A:ASP10 4.9 36.8 1.0 CD2 A:PHE85 4.9 53.2 1.0 N A:MET58 5.0 43.4 1.0 CG A:ASP9 5.0 38.4 1.0 HA A:ASP55 5.0 28.0 1.0 OD2 A:ASP9 5.0 45.2 1.0

Fluorine binding site 4 out of 6 in the N-Terminal Domain of Vrar


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of N-Terminal Domain of Vrar within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:27.8 occ:1.00 F1 B:BEF301 0.0 27.8 1.0 BE B:BEF301 1.5 29.4 1.0 H B:LEU57 1.8 33.8 1.0 HG1 B:THR83 2.1 47.3 1.0 H B:LEU56 2.2 31.9 1.0 OD1 B:ASP55 2.3 29.6 1.0 F2 B:BEF301 2.4 21.2 1.0 F3 B:BEF301 2.5 32.4 1.0 HB3 B:LEU56 2.6 35.0 1.0 N B:LEU57 2.7 28.1 1.0 N B:LEU56 2.9 26.5 1.0 HE2 B:PHE85 2.9 55.8 1.0 OG1 B:THR83 3.0 39.4 1.0 CG B:ASP55 3.1 26.3 1.0 HD2 B:PHE85 3.1 59.7 1.0 CB B:LEU56 3.2 29.1 1.0 HB3 B:LEU57 3.2 36.3 1.0 CA B:LEU56 3.3 29.6 1.0 HB2 B:LEU56 3.3 35.0 1.0 C B:LEU56 3.4 28.5 1.0 OD2 B:ASP55 3.5 26.3 1.0 HB2 B:LEU57 3.6 36.3 1.0 CE2 B:PHE85 3.6 46.4 1.0 H B:SER84 3.6 42.5 1.0 HA B:THR83 3.6 30.7 1.0 CA B:LEU57 3.7 26.9 1.0 HZ2 B:LYS105 3.7 33.4 1.0 CB B:LEU57 3.7 30.2 1.0 CD2 B:PHE85 3.7 49.7 1.0 HB B:THR83 3.8 39.0 1.0 CB B:THR83 3.9 32.5 1.0 C B:ASP55 3.9 25.6 1.0 HA B:ASP55 4.0 35.6 1.0 O B:LEU57 4.1 20.7 1.0 MG B:MG302 4.2 30.8 1.0 CA B:THR83 4.2 25.6 1.0 HA B:LEU56 4.2 35.6 1.0 CB B:ASP55 4.2 24.5 1.0 C B:LEU57 4.3 28.5 1.0 CA B:ASP55 4.3 29.6 1.0 HZ1 B:LYS105 4.4 33.4 1.0 NZ B:LYS105 4.4 27.8 1.0 N B:SER84 4.4 35.4 1.0 HA B:LEU57 4.5 32.4 1.0 O B:LEU56 4.6 26.5 1.0 CG B:LEU56 4.6 27.3 1.0 HZ3 B:LYS105 4.7 33.4 1.0 HB3 B:ASP55 4.8 29.4 1.0 HD22 B:LEU56 4.8 39.2 1.0 CZ B:PHE85 4.9 43.5 1.0 HB2 B:ASP55 4.9 29.4 1.0 C B:THR83 4.9 26.8 1.0 H B:PHE85 4.9 43.2 1.0 O B:ASP55 5.0 20.0 1.0

Fluorine binding site 5 out of 6 in the N-Terminal Domain of Vrar


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of N-Terminal Domain of Vrar within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:21.2 occ:1.00 F2 B:BEF301 0.0 21.2 1.0 BE B:BEF301 1.6 29.4 1.0 HZ2 B:LYS105 1.7 33.4 1.0 OD1 B:ASP55 2.3 29.6 1.0 NZ B:LYS105 2.4 27.8 1.0 F1 B:BEF301 2.4 27.8 1.0 HZ3 B:LYS105 2.4 33.4 1.0 F3 B:BEF301 2.6 32.4 1.0 HZ1 B:LYS105 2.7 33.4 1.0 H B:SER84 2.8 42.5 1.0 HA B:THR83 3.0 30.7 1.0 HG1 B:THR83 3.1 47.3 1.0 OG B:SER84 3.2 44.0 1.0 HD2 B:LYS105 3.3 36.5 1.0 CG B:ASP55 3.4 26.3 1.0 HG B:SER84 3.4 52.9 1.0 N B:SER84 3.5 35.4 1.0 CE B:LYS105 3.6 30.4 1.0 HE2 B:PHE85 3.6 55.8 1.0 MG B:MG302 3.7 30.8 1.0 OG1 B:THR83 3.8 39.4 1.0 OD2 B:ASP55 3.8 26.3 1.0 CA B:THR83 3.8 25.6 1.0 HE3 B:LYS105 3.9 36.5 1.0 HB2 B:SER84 3.9 36.0 1.0 CD B:LYS105 3.9 30.4 1.0 H B:LEU56 4.0 31.9 1.0 CB B:SER84 4.0 30.0 1.0 H B:LEU57 4.1 33.8 1.0 C B:THR83 4.1 26.8 1.0 CE2 B:PHE85 4.2 46.4 1.0 HD2 B:PHE85 4.3 59.7 1.0 HE2 B:LYS105 4.3 36.5 1.0 CB B:THR83 4.3 32.5 1.0 HB3 B:LEU57 4.3 36.3 1.0 CA B:SER84 4.4 35.2 1.0 HD3 B:LYS105 4.4 36.5 1.0 CD2 B:PHE85 4.5 49.7 1.0 O B:HOH414 4.6 24.5 1.0 HA B:ASP55 4.6 35.6 1.0 HB B:THR83 4.7 39.0 1.0 CB B:ASP55 4.7 24.5 1.0 N B:LEU56 4.7 26.5 1.0 O B:LEU82 4.8 33.3 1.0 OD2 B:ASP9 4.8 35.5 1.0 HB2 B:ASP55 4.9 29.4 1.0 N B:LEU57 4.9 28.1 1.0 OD1 B:ASP9 4.9 33.0 1.0 HB3 B:SER84 4.9 36.0 1.0 HG3 B:LYS105 4.9 31.3 1.0 HB3 B:LEU56 4.9 35.0 1.0 HA B:SER84 5.0 42.2 1.0

Fluorine binding site 6 out of 6 in the N-Terminal Domain of Vrar


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of N-Terminal Domain of Vrar within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:32.4 occ:1.00 F3 B:BEF301 0.0 32.4 1.0 BE B:BEF301 1.6 29.4 1.0 MG B:MG302 1.8 30.8 1.0 OD2 B:ASP55 2.3 26.3 1.0 HB3 B:LEU57 2.5 36.3 1.0 O B:LEU57 2.5 20.7 1.0 F1 B:BEF301 2.5 27.8 1.0 F2 B:BEF301 2.6 21.2 1.0 OD1 B:ASP55 2.7 29.6 1.0 CG B:ASP55 2.8 26.3 1.0 H B:LEU57 2.9 33.8 1.0 CB B:LEU57 3.3 30.2 1.0 C B:LEU57 3.4 28.5 1.0 HE2 B:PHE85 3.4 55.8 1.0 N B:LEU57 3.4 28.1 1.0 OD1 B:ASP10 3.5 39.5 1.0 CA B:LEU57 3.5 26.9 1.0 O B:HOH414 3.6 24.5 1.0 HZ2 B:LYS105 3.7 33.4 1.0 HZ1 B:LYS105 3.8 33.4 1.0 HB2 B:LEU57 3.8 36.3 1.0 HZ3 B:LYS105 3.9 33.4 1.0 NZ B:LYS105 4.0 27.8 1.0 H B:LEU56 4.1 31.9 1.0 HG B:LEU57 4.2 35.4 1.0 CE2 B:PHE85 4.3 46.4 1.0 HG3 B:MET58 4.3 27.0 1.0 CB B:ASP55 4.3 24.5 1.0 CG B:LEU57 4.4 29.4 1.0 HD23 B:LEU57 4.4 43.0 1.0 OD1 B:ASP9 4.4 33.0 1.0 HG1 B:THR83 4.5 47.3 1.0 CG B:ASP10 4.5 26.6 1.0 C B:LEU56 4.5 28.5 1.0 HA B:LEU57 4.5 32.4 1.0 N B:LEU56 4.5 26.5 1.0 HB3 B:ASP55 4.6 29.4 1.0 OD2 B:ASP10 4.6 27.0 1.0 N B:MET58 4.6 28.7 1.0 HB2 B:ASP55 4.8 29.4 1.0 HB3 B:LEU56 4.8 35.0 1.0 H B:ASP10 4.8 35.8 1.0 HZ B:PHE85 4.9 52.2 1.0 CD2 B:LEU57 4.9 35.8 1.0 HE1 B:HIS11 4.9 36.6 1.0 HD2 B:PHE85 4.9 59.7 1.0

J.V.Kumar, T.S.Tseng, Y.C.Lou, S.Y.Wei, T.H.Wu, H.C.Tang, Y.C.Chiu, C.H.Hsu, C.Chen. Structural Insights Into Dna Binding Domain of Vancomycin-Resistance-Associated Response Regulator in Complex with Its Promoter Dna From Staphylococcus Aureus. Protein Sci. V. 31 E4286 2022.
ISSN: ESSN 1469-896X
PubMed: 35481641
DOI: 10.1002/PRO.4286