Fluorine in PDB 4d6y: Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium

The structure of Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium, PDB code: 4d6y was solved by L.H.Otero, I.Fernandez, M.C.Carrica, S.Klinke, F.A.Goldbaum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	30.395, 39.343, 52.961, 97.30, 96.97, 89.97
R / Rfree (%)	18.36 / 20.41

The structure of Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium (pdb code 4d6y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium, PDB code: 4d6y:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:F1125 b:16.1 occ:1.00 F1 A:BEF1125 0.0 16.1 1.0 BE A:BEF1125 1.7 19.3 1.0 OD1 A:ASP53 2.7 12.8 1.0 N A:GLY84 2.8 15.6 1.0 NZ A:LYS105 2.8 21.0 1.0 F3 A:BEF1125 2.8 17.0 1.0 F2 A:BEF1125 2.9 18.7 1.0 CE A:LYS105 3.3 21.4 1.0 CA A:SER83 3.3 12.4 1.0 CD A:LYS105 3.5 21.9 1.0 C A:SER83 3.5 17.4 1.0 OG A:SER83 3.6 16.3 1.0 CA A:GLY84 3.8 15.8 1.0 CD2 A:HIS85 3.8 21.8 1.0 CG A:ASP53 3.8 15.4 1.0 O A:HOH2001 3.9 20.0 1.0 CB A:SER83 3.9 15.2 1.0 O A:ILE82 4.2 15.8 1.0 N A:HIS85 4.3 17.6 1.0 O A:HOH2005 4.3 24.7 1.0 OD2 A:ASP53 4.3 18.8 1.0 MG A:MG1126 4.3 16.7 1.0 C A:GLY84 4.4 19.2 1.0 N A:SER83 4.5 11.8 1.0 CG A:LYS105 4.6 17.8 1.0 NE2 A:HIS85 4.6 22.0 1.0 O A:SER83 4.7 16.9 1.0 CG A:HIS85 4.8 20.9 1.0 C A:ILE82 4.8 14.3 1.0 OD2 A:ASP9 4.8 22.0 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:F1125 b:18.7 occ:1.00 F2 A:BEF1125 0.0 18.7 1.0 BE A:BEF1125 1.7 19.3 1.0 OG A:SER83 2.5 16.3 1.0 OD1 A:ASP53 2.7 12.8 1.0 N A:TRP55 2.8 17.3 1.0 F1 A:BEF1125 2.9 16.1 1.0 F3 A:BEF1125 2.9 17.0 1.0 N A:ILE54 2.9 14.2 1.0 CB A:ILE54 3.3 17.4 1.0 CB A:SER83 3.3 15.2 1.0 CD2 A:HIS85 3.4 21.8 1.0 CA A:ILE54 3.4 14.6 1.0 C A:ILE54 3.5 18.3 1.0 CG A:ASP53 3.6 15.4 1.0 CB A:TRP55 3.8 21.4 1.0 CB A:HIS85 3.8 18.0 1.0 CA A:TRP55 3.8 19.9 1.0 CG A:HIS85 3.9 20.9 1.0 CA A:SER83 3.9 12.4 1.0 OD2 A:ASP53 4.1 18.8 1.0 C A:ASP53 4.1 16.8 1.0 N A:GLY84 4.2 15.6 1.0 N A:HIS85 4.2 17.6 1.0 CG1 A:ILE54 4.3 18.0 1.0 CG2 A:ILE54 4.3 18.6 1.0 CD1 A:TRP55 4.4 26.9 1.0 CG A:TRP55 4.4 24.4 1.0 MG A:MG1126 4.4 16.7 1.0 O A:TRP55 4.5 20.3 1.0 NE2 A:HIS85 4.5 22.0 1.0 CA A:ASP53 4.5 11.0 1.0 C A:SER83 4.6 17.4 1.0 C A:TRP55 4.6 22.7 1.0 CA A:HIS85 4.6 17.5 1.0 CB A:ASP53 4.6 13.8 1.0 O A:ILE82 4.7 15.8 1.0 O A:ILE54 4.7 17.6 1.0 CD1 A:ILE54 4.8 21.2 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:F1125 b:17.0 occ:1.00 F3 A:BEF1125 0.0 17.0 1.0 BE A:BEF1125 1.7 19.3 1.0 MG A:MG1126 1.9 16.7 1.0 O A:HOH2001 2.7 20.0 1.0 OD2 A:ASP53 2.7 18.8 1.0 OD1 A:ASP53 2.7 12.8 1.0 O A:HOH2004 2.8 24.0 1.0 F1 A:BEF1125 2.8 16.1 1.0 O A:TRP55 2.9 20.3 1.0 F2 A:BEF1125 2.9 18.7 1.0 CG A:ASP53 3.1 15.4 1.0 CB A:TRP55 3.3 21.4 1.0 CD2 A:HIS85 3.6 21.8 1.0 N A:TRP55 3.6 17.3 1.0 C A:TRP55 3.7 22.7 1.0 CA A:TRP55 3.7 19.9 1.0 OD1 A:ASP10 3.9 19.0 1.0 NE2 A:HIS85 3.9 22.0 1.0 NZ A:LYS105 4.2 21.0 1.0 CG A:TRP55 4.5 24.4 1.0 CB A:ASP53 4.6 13.8 1.0 N A:ILE54 4.6 14.2 1.0 OE2 A:GLU11 4.7 29.3 1.0 C A:ILE54 4.8 18.3 1.0 CG A:HIS85 4.8 20.9 1.0 CG A:ASP10 4.9 23.0 1.0 N A:LEU56 5.0 21.2 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:F1125 b:15.6 occ:1.00 F1 B:BEF1125 0.0 15.6 1.0 BE B:BEF1125 1.7 17.4 1.0 OG B:SER83 2.5 17.4 1.0 OD1 B:ASP53 2.7 13.6 1.0 N B:TRP55 2.8 16.8 1.0 F3 B:BEF1125 2.8 15.2 1.0 F2 B:BEF1125 2.8 16.8 1.0 N B:ILE54 3.0 14.5 1.0 CD2 B:HIS85 3.3 21.8 1.0 CB B:SER83 3.4 15.9 1.0 CB B:ILE54 3.4 18.0 1.0 CA B:ILE54 3.5 14.9 1.0 CG B:ASP53 3.6 16.6 1.0 C B:ILE54 3.6 19.4 1.0 CB B:TRP55 3.7 20.4 1.0 CA B:TRP55 3.8 19.3 1.0 CB B:HIS85 3.8 17.6 1.0 CG B:HIS85 3.9 20.7 1.0 CA B:SER83 3.9 12.1 1.0 OD2 B:ASP53 4.1 18.0 1.0 C B:ASP53 4.2 16.5 1.0 N B:GLY84 4.2 14.2 1.0 N B:HIS85 4.2 16.2 1.0 CD1 B:TRP55 4.3 26.3 1.0 CG B:TRP55 4.4 23.8 1.0 CG1 B:ILE54 4.4 17.2 1.0 MG B:MG1126 4.4 17.6 1.0 CG2 B:ILE54 4.4 21.2 1.0 O B:TRP55 4.4 20.3 1.0 NE2 B:HIS85 4.5 21.3 1.0 C B:TRP55 4.5 22.2 1.0 CA B:ASP53 4.6 10.2 1.0 C B:SER83 4.6 15.2 1.0 CA B:HIS85 4.6 17.2 1.0 CB B:ASP53 4.7 12.5 1.0 O B:ILE82 4.7 16.5 1.0 O B:HOH2027 4.7 34.6 1.0 O B:ILE54 4.8 15.6 1.0 CD1 B:ILE54 4.9 23.6 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:F1125 b:16.8 occ:1.00 F2 B:BEF1125 0.0 16.8 1.0 BE B:BEF1125 1.7 17.4 1.0 MG B:MG1126 1.8 17.6 1.0 OD2 B:ASP53 2.6 18.0 1.0 OD1 B:ASP53 2.7 13.6 1.0 O B:HOH2002 2.8 25.5 1.0 O B:TRP55 2.8 20.3 1.0 O B:HOH2001 2.8 19.5 1.0 F1 B:BEF1125 2.8 15.6 1.0 F3 B:BEF1125 2.8 15.2 1.0 CG B:ASP53 3.0 16.6 1.0 CB B:TRP55 3.3 20.4 1.0 O B:HOH2027 3.5 34.6 1.0 N B:TRP55 3.6 16.8 1.0 C B:TRP55 3.6 22.2 1.0 CA B:TRP55 3.7 19.3 1.0 CD2 B:HIS85 3.7 21.8 1.0 OD1 B:ASP10 3.9 20.9 1.0 NE2 B:HIS85 4.0 21.3 1.0 NZ B:LYS105 4.2 21.2 1.0 CB B:ASP53 4.5 12.5 1.0 CG B:TRP55 4.5 23.8 1.0 N B:ILE54 4.6 14.5 1.0 C B:ILE54 4.7 19.4 1.0 OE2 B:GLU11 4.7 29.2 1.0 CG B:HIS85 4.8 20.7 1.0 CG B:ASP10 4.9 24.5 1.0 N B:LEU56 4.9 20.2 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Receiver Domain of Ntrx From Brucella Abortus in Complex with Beryllofluoride and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:F1125 b:15.2 occ:1.00 F3 B:BEF1125 0.0 15.2 1.0 BE B:BEF1125 1.7 17.4 1.0 OD1 B:ASP53 2.7 13.6 1.0 N B:GLY84 2.8 14.2 1.0 NZ B:LYS105 2.8 21.2 1.0 F1 B:BEF1125 2.8 15.6 1.0 O B:HOH2027 2.8 34.6 1.0 F2 B:BEF1125 2.8 16.8 1.0 CE B:LYS105 3.3 23.2 1.0 CA B:SER83 3.3 12.1 1.0 CD B:LYS105 3.5 24.7 1.0 C B:SER83 3.5 15.2 1.0 OG B:SER83 3.6 17.4 1.0 CA B:GLY84 3.8 14.4 1.0 CD2 B:HIS85 3.8 21.8 1.0 CG B:ASP53 3.8 16.6 1.0 CB B:SER83 3.9 15.9 1.0 O B:HOH2001 3.9 19.5 1.0 O B:ILE82 4.2 16.5 1.0 OD2 B:ASP53 4.3 18.0 1.0 N B:HIS85 4.3 16.2 1.0 MG B:MG1126 4.3 17.6 1.0 O B:HOH2003 4.4 21.3 1.0 C B:GLY84 4.5 20.5 1.0 N B:SER83 4.5 13.2 1.0 CG B:LYS105 4.6 19.2 1.0 NE2 B:HIS85 4.6 21.3 1.0 O B:SER83 4.7 14.9 1.0 CG B:HIS85 4.8 20.7 1.0 C B:ILE82 4.8 17.5 1.0 OD2 B:ASP9 4.8 19.4 1.0

I.Fernandez, L.H.Otero, S.Klinke, M.C.Carrica, F.A.Goldbaum. Snapshots of Conformational Changes Shed Light Into the Ntrx Receiver Domain Signal Transduction Mechanism J.Mol.Biol. V. 427 3258 2015.
ISSN: ISSN 0022-2836
PubMed: 26113057
DOI: 10.1016/J.JMB.2015.06.010