Fluorine in PDB 4ldz: Crystal Structure of the Full-Length Response Regulator Desr in the Active State

The structure of Crystal Structure of the Full-Length Response Regulator Desr in the Active State, PDB code: 4ldz was solved by F.Trajtenberg, N.Larrieux, A.Buschiazzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.92 / 2.31
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.612, 77.646, 139.751, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.1

The structure of Crystal Structure of the Full-Length Response Regulator Desr in the Active State also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of the Full-Length Response Regulator Desr in the Active State (pdb code 4ldz). 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 Full-Length Response Regulator Desr in the Active State, PDB code: 4ldz:
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 Full-Length Response Regulator Desr in the Active State


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 Full-Length Response Regulator Desr in the Active State within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:41.5 occ:1.00 F1 A:BEF202 0.0 41.5 1.0 BE A:BEF202 1.7 36.3 1.0 OG1 A:THR80 2.7 36.5 1.0 OD1 A:ASP54 2.7 29.1 1.0 F2 A:BEF202 2.7 33.5 1.0 F3 A:BEF202 2.7 34.6 1.0 N A:GLU56 2.8 32.6 1.0 N A:ILE55 2.9 30.4 1.0 CB A:ILE55 3.2 33.2 1.0 CA A:ILE55 3.3 30.9 1.0 CD2 A:PHE82 3.3 44.7 1.0 CE2 A:PHE82 3.4 47.8 1.0 C A:ILE55 3.5 35.3 1.0 CB A:THR80 3.6 33.3 1.0 CG A:ASP54 3.6 32.1 1.0 CA A:GLU56 3.8 33.2 1.0 CB A:GLU56 3.8 35.3 1.0 C A:ASP54 4.1 34.4 1.0 CG1 A:ILE55 4.1 31.9 1.0 OD2 A:ASP54 4.1 30.9 1.0 CA A:THR80 4.1 31.9 1.0 CG A:GLU56 4.2 41.9 1.0 CG2 A:ILE55 4.3 34.7 1.0 MG A:MG201 4.3 35.3 1.0 N A:THR81 4.4 36.0 1.0 O A:GLU56 4.5 38.8 1.0 O3 A:GOL203 4.5 79.0 1.0 CA A:ASP54 4.6 28.5 1.0 C A:GLU56 4.6 38.7 1.0 CG A:PHE82 4.7 45.5 1.0 CB A:ASP54 4.7 29.0 1.0 O A:ILE55 4.7 35.3 1.0 CZ A:PHE82 4.7 47.1 1.0 CD1 A:ILE55 4.7 37.8 1.0 C A:THR80 4.8 38.6 1.0 CG2 A:THR80 4.9 27.1 1.0 CD A:GLU56 5.0 56.0 1.0 O A:LEU79 5.0 32.5 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the Full-Length Response Regulator Desr in the Active State


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 Full-Length Response Regulator Desr in the Active State within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:33.5 occ:1.00 F2 A:BEF202 0.0 33.5 1.0 BE A:BEF202 1.7 36.3 1.0 OD1 A:ASP54 2.6 29.1 1.0 F3 A:BEF202 2.7 34.6 1.0 F1 A:BEF202 2.7 41.5 1.0 NZ A:LYS102 2.9 37.9 1.0 O3 A:GOL203 2.9 79.0 1.0 N A:THR81 2.9 36.0 1.0 OG1 A:THR81 3.2 51.8 1.0 OG1 A:THR80 3.4 36.5 1.0 CA A:THR80 3.5 31.9 1.0 CE A:LYS102 3.5 30.1 1.0 C A:THR80 3.6 38.6 1.0 CB A:THR81 3.6 47.5 1.0 CG A:ASP54 3.7 32.1 1.0 CE2 A:PHE82 3.8 47.8 1.0 CD A:LYS102 3.9 29.0 1.0 CA A:THR81 3.9 37.8 1.0 CB A:THR80 4.0 33.3 1.0 O A:HOH303 4.0 30.9 1.0 MG A:MG201 4.1 35.3 1.0 CD2 A:PHE82 4.1 44.7 1.0 OD2 A:ASP54 4.2 30.9 1.0 C3 A:GOL203 4.2 78.6 1.0 O1 A:GOL203 4.4 71.3 1.0 O A:LEU79 4.4 32.5 1.0 C2 A:GOL203 4.4 76.4 1.0 C1 A:GOL203 4.6 74.6 1.0 N A:THR80 4.7 30.6 1.0 CZ A:PHE82 4.7 47.1 1.0 O A:THR80 4.8 40.9 1.0 N A:ILE55 4.8 30.4 1.0 N A:PHE82 4.8 42.6 1.0 OE1 A:GLU8 4.9 46.0 1.0 O A:HOH302 4.9 37.2 1.0 CB A:ASP54 4.9 29.0 1.0 CG A:LYS102 4.9 25.9 1.0 C A:THR81 4.9 45.1 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the Full-Length Response Regulator Desr in the Active State


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 Full-Length Response Regulator Desr in the Active State within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:34.6 occ:1.00 F3 A:BEF202 0.0 34.6 1.0 BE A:BEF202 1.7 36.3 1.0 MG A:MG201 1.9 35.3 1.0 F2 A:BEF202 2.7 33.5 1.0 F1 A:BEF202 2.7 41.5 1.0 OD1 A:ASP54 2.7 29.1 1.0 O A:HOH302 2.7 37.2 1.0 OD2 A:ASP54 2.8 30.9 1.0 O A:GLU56 2.9 38.8 1.0 O3 A:GOL203 2.9 79.0 1.0 CG A:ASP54 3.1 32.1 1.0 O A:HOH303 3.1 30.9 1.0 CB A:GLU56 3.3 35.3 1.0 N A:GLU56 3.5 32.6 1.0 CA A:GLU56 3.6 33.2 1.0 C A:GLU56 3.6 38.7 1.0 CE2 A:PHE82 3.7 47.8 1.0 O A:HOH355 3.9 52.1 1.0 C3 A:GOL203 3.9 78.6 1.0 OD1 A:ASP9 4.0 40.0 1.0 NZ A:LYS102 4.2 37.9 1.0 C2 A:GOL203 4.2 76.4 1.0 CG A:GLU56 4.4 41.9 1.0 CZ A:PHE82 4.6 47.1 1.0 CD2 A:PHE82 4.6 44.7 1.0 C A:ILE55 4.6 35.3 1.0 N A:ILE55 4.6 30.4 1.0 CB A:ASP54 4.6 29.0 1.0 CG A:ASP9 4.9 44.0 1.0 N A:MET57 4.9 34.9 1.0 OG1 A:THR80 5.0 36.5 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the Full-Length Response Regulator Desr in the Active State


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 Full-Length Response Regulator Desr in the Active State within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:32.4 occ:1.00 F1 B:BEF202 0.0 32.4 1.0 BE B:BEF202 1.7 33.3 1.0 OG1 B:THR80 2.6 28.9 1.0 F3 B:BEF202 2.6 35.1 1.0 OD1 B:ASP54 2.7 29.1 1.0 F2 B:BEF202 2.7 30.6 1.0 N B:GLU56 3.0 33.6 1.0 N B:ILE55 3.0 29.5 1.0 CB B:ILE55 3.4 32.9 1.0 CB B:THR80 3.4 26.0 1.0 CA B:ILE55 3.4 30.8 1.0 CD2 B:PHE82 3.5 46.0 1.0 CE2 B:PHE82 3.5 49.1 1.0 CG B:ASP54 3.6 31.8 1.0 C B:ILE55 3.7 35.9 1.0 CA B:THR80 3.9 28.9 1.0 CA B:GLU56 4.0 34.2 1.0 CB B:GLU56 4.0 36.6 1.0 OD2 B:ASP54 4.1 35.2 1.0 C B:ASP54 4.1 31.9 1.0 N B:THR81 4.1 30.6 1.0 CG1 B:ILE55 4.2 32.3 1.0 MG B:MG201 4.3 36.0 1.0 CG B:GLU56 4.4 42.7 1.0 CG2 B:ILE55 4.5 32.4 1.0 CA B:ASP54 4.5 26.9 1.0 C B:THR80 4.6 33.1 1.0 O B:GLU56 4.6 36.4 1.0 CB B:ASP54 4.6 27.4 1.0 NZ B:LYS102 4.7 34.5 1.0 C B:GLU56 4.7 38.0 1.0 O B:LEU79 4.8 34.1 1.0 CG B:PHE82 4.8 44.0 1.0 CG2 B:THR80 4.8 19.8 1.0 CD1 B:ILE55 4.8 35.0 1.0 CZ B:PHE82 4.8 47.9 1.0 O B:ILE55 4.9 35.8 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the Full-Length Response Regulator Desr in the Active State


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 Full-Length Response Regulator Desr in the Active State within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:30.6 occ:1.00 F2 B:BEF202 0.0 30.6 1.0 BE B:BEF202 1.7 33.3 1.0 NZ B:LYS102 2.5 34.5 1.0 F1 B:BEF202 2.7 32.4 1.0 OD1 B:ASP54 2.7 29.1 1.0 F3 B:BEF202 2.7 35.1 1.0 N B:THR81 2.9 30.6 1.0 OG1 B:THR81 3.1 37.8 1.0 CE B:LYS102 3.3 29.2 1.0 CA B:THR80 3.5 28.9 1.0 CB B:THR81 3.6 38.7 1.0 C B:THR80 3.6 33.1 1.0 OG1 B:THR80 3.6 28.9 1.0 CG B:ASP54 3.8 31.8 1.0 CD B:LYS102 3.8 28.3 1.0 O B:HOH301 3.8 30.2 1.0 CA B:THR81 3.8 32.8 1.0 CE2 B:PHE82 4.1 49.1 1.0 MG B:MG201 4.1 36.0 1.0 CB B:THR80 4.1 26.0 1.0 OD2 B:ASP54 4.2 35.2 1.0 CD2 B:PHE82 4.4 46.0 1.0 O B:LEU79 4.4 34.1 1.0 N B:THR80 4.7 28.8 1.0 O B:THR80 4.7 32.3 1.0 OE1 B:GLU8 4.8 37.3 1.0 CG B:LYS102 4.9 27.6 1.0 N B:PHE82 4.9 38.4 1.0 CZ B:PHE82 5.0 47.9 1.0 N B:ILE55 5.0 29.5 1.0 C B:THR81 5.0 40.7 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the Full-Length Response Regulator Desr in the Active State


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 Full-Length Response Regulator Desr in the Active State within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:35.1 occ:1.00 F3 B:BEF202 0.0 35.1 1.0 BE B:BEF202 1.7 33.3 1.0 MG B:MG201 1.9 36.0 1.0 F1 B:BEF202 2.6 32.4 1.0 F2 B:BEF202 2.7 30.6 1.0 OD1 B:ASP54 2.8 29.1 1.0 OD2 B:ASP54 2.8 35.2 1.0 O B:GLU56 2.8 36.4 1.0 O B:HOH302 2.9 39.3 1.0 O B:HOH301 3.0 30.2 1.0 CG B:ASP54 3.1 31.8 1.0 CB B:GLU56 3.3 36.6 1.0 N B:GLU56 3.4 33.6 1.0 CA B:GLU56 3.5 34.2 1.0 C B:GLU56 3.5 38.0 1.0 CE2 B:PHE82 3.9 49.1 1.0 OD1 B:ASP9 4.0 43.7 1.0 NZ B:LYS102 4.1 34.5 1.0 CG B:GLU56 4.5 42.7 1.0 C B:ILE55 4.5 35.9 1.0 N B:ILE55 4.5 29.5 1.0 CB B:ASP54 4.6 27.4 1.0 CD2 B:PHE82 4.7 46.0 1.0 CZ B:PHE82 4.8 47.9 1.0 N B:MET57 4.8 35.7 1.0 CG B:ASP9 4.9 45.6 1.0 OG1 B:THR80 5.0 28.9 1.0 CA B:ILE55 5.0 30.8 1.0

F.Trajtenberg, A.Albanesi, N.Ruetalo, H.Botti, A.Mechaly, L.Cybulski, N.Larrieux, D.De Mendoza, A.Buschiazzo. A Non-Canonical Protein Surface Is Key in Allosteric Control of Response Regulators To Be Published.