Fluorine in PDB 6zj2: Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-

The structure of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-, PDB code: 6zj2 was solved by J.Huesa, A.Marina, P.Casino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.99 / 3.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.356, 111.514, 146.262, 90, 90.36, 90
R / Rfree (%)	26.6 / 31.9

The structure of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3- also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Fluorine atom in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3- (pdb code 6zj2). 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 Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-, PDB code: 6zj2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3- within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:57.9 occ:1.00 F1 B:BFD301 0.0 57.9 1.0 BE B:BFD301 1.5 58.8 1.0 F2 B:BFD301 2.5 58.3 1.0 F3 B:BFD301 2.6 59.0 1.0 MG B:MG302 2.8 72.9 1.0 CB B:SER58 3.4 88.3 1.0 CB B:MET88 3.5 44.5 1.0 OG B:SER58 3.7 88.5 1.0 OD1 B:ASP56 4.0 72.9 1.0 O B:SER58 4.0 87.1 1.0 OD2 B:ASP56 4.1 69.7 1.0 N B:MET88 4.1 44.9 1.0 NZ B:LYS109 4.2 55.3 1.0 CA B:MET88 4.3 45.3 1.0 CG B:ASP56 4.4 72.5 1.0 CA B:SER58 4.5 86.5 1.0 OG1 B:THR87 4.7 47.6 1.0 C B:SER58 4.8 87.8 1.0 CE1 B:HIS12 4.8 92.7 1.0 N B:SER58 4.8 83.2 1.0 C B:MET88 4.9 45.5 1.0

Fluorine binding site 2 out of 6 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3- within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:58.3 occ:1.00 F2 B:BFD301 0.0 58.3 1.0 BE B:BFD301 1.5 58.8 1.0 F3 B:BFD301 2.4 59.0 1.0 F1 B:BFD301 2.5 57.9 1.0 OD1 B:ASP56 2.5 72.9 1.0 OG1 B:THR87 2.5 47.6 1.0 OG B:SER58 2.7 88.5 1.0 CB B:SER58 3.0 88.3 1.0 N B:SER58 3.2 83.2 1.0 N B:MET88 3.3 44.9 1.0 CG B:ASP56 3.5 72.5 1.0 CB B:THR87 3.6 47.2 1.0 CA B:SER58 3.6 86.5 1.0 CA B:THR87 3.8 46.3 1.0 OD2 B:ASP56 3.8 69.7 1.0 MG B:MG302 3.9 72.9 1.0 C B:THR87 4.0 45.0 1.0 N B:ASN89 4.1 46.3 1.0 O B:SER58 4.1 87.1 1.0 CB B:MET88 4.2 44.5 1.0 CA B:MET88 4.2 45.3 1.0 N B:LEU57 4.3 76.7 1.0 C B:LEU57 4.3 79.7 1.0 C B:SER58 4.4 87.8 1.0 CB B:LEU57 4.4 77.0 1.0 C B:MET88 4.5 45.5 1.0 CA B:LEU57 4.6 77.7 1.0 CB B:ASN89 4.8 47.7 1.0 CB B:ASP56 4.8 73.7 1.0 CG2 B:THR87 4.9 47.5 1.0 CA B:ASN89 5.0 47.3 1.0 C B:ASP56 5.0 76.5 1.0

Fluorine binding site 3 out of 6 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3- within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:59.0 occ:1.00 F3 B:BFD301 0.0 59.0 1.0 BE B:BFD301 1.5 58.8 1.0 F2 B:BFD301 2.4 58.3 1.0 F1 B:BFD301 2.6 57.9 1.0 N B:MET88 2.6 44.9 1.0 OD1 B:ASP56 2.7 72.9 1.0 NZ B:LYS109 2.8 55.3 1.0 CE B:LYS109 3.0 55.5 1.0 CG B:ASP56 3.1 72.5 1.0 CB B:MET88 3.3 44.5 1.0 OD2 B:ASP56 3.3 69.7 1.0 C B:THR87 3.4 45.0 1.0 CA B:THR87 3.4 46.3 1.0 CD B:LYS109 3.4 56.0 1.0 CA B:MET88 3.5 45.3 1.0 OG1 B:THR87 3.7 47.6 1.0 MG B:MG302 3.7 72.9 1.0 CG B:LYS109 4.1 56.8 1.0 CB B:THR87 4.2 47.2 1.0 CB B:ASP56 4.3 73.7 1.0 O B:LEU86 4.4 47.9 1.0 N B:THR87 4.5 46.9 1.0 O B:THR87 4.5 43.9 1.0 C B:MET88 4.6 45.5 1.0 N B:ASN89 4.7 46.3 1.0 OD2 B:ASP10 4.8 98.6 1.0 C B:LEU86 4.9 48.6 1.0 O B:SER58 4.9 87.1 1.0 CB B:SER58 5.0 88.3 1.0

Fluorine binding site 4 out of 6 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3- within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:83.9 occ:1.00 F1 A:BFD301 0.0 83.9 1.0 BE A:BFD301 1.5 82.9 1.0 MG A:MG302 2.1 71.2 1.0 F2 A:BFD301 2.4 82.9 1.0 F3 A:BFD301 2.6 81.4 1.0 OD1 A:ASP56 2.6 50.9 1.0 OD2 A:ASP56 3.1 53.1 1.0 CG A:ASP56 3.2 52.6 1.0 CB A:SER58 3.4 65.9 1.0 O A:SER58 3.6 66.6 1.0 N A:SER58 3.7 63.0 1.0 CA A:SER58 3.9 65.1 1.0 OG A:SER58 4.0 67.3 1.0 CB A:MET88 4.1 51.9 1.0 C A:SER58 4.2 65.6 1.0 N A:MET88 4.2 50.2 1.0 OD1 A:ASP11 4.6 64.7 1.0 CB A:ASP56 4.6 53.0 1.0 CE1 A:HIS12 4.8 70.5 1.0 CA A:MET88 4.8 52.3 1.0 N A:LEU57 4.8 56.7 1.0 C A:LEU57 4.9 59.0 1.0 OD2 A:ASP11 5.0 66.9 1.0

Fluorine binding site 5 out of 6 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3- within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:82.9 occ:1.00 F2 A:BFD301 0.0 82.9 1.0 BE A:BFD301 1.5 82.9 1.0 F1 A:BFD301 2.4 83.9 1.0 F3 A:BFD301 2.5 81.4 1.0 OD1 A:ASP56 2.6 50.9 1.0 N A:MET88 2.6 50.2 1.0 OG1 A:THR87 2.7 48.2 1.0 CA A:THR87 3.1 47.6 1.0 C A:THR87 3.3 48.4 1.0 CB A:THR87 3.4 47.6 1.0 CA A:MET88 3.6 52.3 1.0 N A:ASN89 3.6 57.2 1.0 CB A:MET88 3.7 51.9 1.0 CG A:ASP56 3.8 52.6 1.0 CB A:LEU57 3.9 58.5 1.0 N A:SER58 3.9 63.0 1.0 N A:LEU57 4.0 56.7 1.0 C A:MET88 4.1 54.5 1.0 OG A:SER58 4.4 67.3 1.0 OD2 A:ASP56 4.4 53.1 1.0 CB A:SER58 4.4 65.9 1.0 CA A:LEU57 4.4 58.5 1.0 MG A:MG302 4.4 71.2 1.0 N A:THR87 4.5 46.4 1.0 O A:THR87 4.6 47.7 1.0 O A:LEU86 4.6 45.8 1.0 CB A:ASN89 4.6 59.5 1.0 C A:LEU57 4.7 59.0 1.0 CA A:ASN89 4.7 59.6 1.0 CA A:SER58 4.8 65.1 1.0 CG2 A:THR87 4.8 47.4 1.0 CB A:ASP56 4.9 53.0 1.0 C A:LEU86 5.0 44.9 1.0

Fluorine binding site 6 out of 6 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3- within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:81.4 occ:1.00 F3 A:BFD301 0.0 81.4 1.0 BE A:BFD301 1.5 82.9 1.0 F2 A:BFD301 2.5 82.9 1.0 OD1 A:ASP56 2.6 50.9 1.0 F1 A:BFD301 2.6 83.9 1.0 N A:MET88 2.7 50.2 1.0 CG A:ASP56 3.2 52.6 1.0 CA A:THR87 3.3 47.6 1.0 C A:THR87 3.3 48.4 1.0 O A:LEU86 3.5 45.8 1.0 CB A:MET88 3.5 51.9 1.0 CA A:MET88 3.7 52.3 1.0 OD2 A:ASP56 3.8 53.1 1.0 CB A:ASP56 3.9 53.0 1.0 N A:THR87 4.1 46.4 1.0 MG A:MG302 4.1 71.2 1.0 C A:LEU86 4.2 44.9 1.0 O A:THR87 4.4 47.7 1.0 OG1 A:THR87 4.4 48.2 1.0 CB A:THR87 4.5 47.6 1.0 CB A:LYS109 4.7 67.9 1.0 CA A:ASP56 4.8 53.4 1.0 N A:LEU57 4.8 56.7 1.0 C A:MET88 4.9 54.5 1.0 OD2 A:ASP10 4.9 61.9 1.0

J.Huesa, J.Giner-Lamia, M.G.Pucciarelli, F.Paredes-Martinez, F.Garcia-Del Portillo, A.Marina, P.Casino. Structure-Based Analyses of Salmonella Rcsb Variants Unravel New Features of the Rcs Regulon Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAB060