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Fluorine in PDB 6zix: Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter P1FLHDC in the Presence of Phosphomimetic BEF3-

Protein crystallography data

The structure of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter P1FLHDC in the Presence of Phosphomimetic BEF3-, PDB code: 6zix 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) 57.79 / 3.40
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 183.22, 183.22, 84.143, 90, 90, 120
R / Rfree (%) 23.9 / 27.4

Other elements in 6zix:

The structure of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter P1FLHDC in the Presence of Phosphomimetic BEF3- also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter P1FLHDC in the Presence of Phosphomimetic BEF3- (pdb code 6zix). 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 P1FLHDC in the Presence of Phosphomimetic BEF3-, PDB code: 6zix:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6zix

Go back to Fluorine Binding Sites List in 6zix
Fluorine binding site 1 out of 6 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter P1FLHDC 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 P1FLHDC in the Presence of Phosphomimetic BEF3- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:177.6
occ:1.00
F1 B:BFD302 0.0 177.6 1.0
BE B:BFD302 1.5 176.0 1.0
F2 B:BFD302 2.5 168.8 1.0
F3 B:BFD302 2.6 172.2 1.0
OD2 B:ASP56 3.0 135.3 1.0
OD1 B:ASP56 3.2 142.7 1.0
CG B:ASP56 3.3 140.6 1.0
N B:MET88 3.5 169.3 1.0
MG B:MG301 3.5 153.7 1.0
OD2 B:ASP10 3.5 145.3 1.0
SD B:MET88 3.5 193.0 1.0
CG B:MET88 3.8 185.4 1.0
CB B:MET88 3.8 181.7 1.0
CA B:THR87 4.2 158.8 1.0
CA B:MET88 4.3 173.4 1.0
C B:THR87 4.3 163.9 1.0
CG B:ASP10 4.4 147.9 1.0
ND1 B:HIS12 4.4 159.8 1.0
OG1 B:THR87 4.4 145.9 1.0
OD1 B:ASP10 4.5 142.0 1.0
CB B:ASP56 4.5 140.5 1.0
CE1 B:HIS12 4.6 164.9 1.0
O B:LEU86 4.7 176.3 1.0
CE B:MET88 4.9 194.8 1.0
OG B:SER58 4.9 193.1 1.0
CB B:LYS109 5.0 180.0 1.0
CB B:THR87 5.0 154.1 1.0

Fluorine binding site 2 out of 6 in 6zix

Go back to Fluorine Binding Sites List in 6zix
Fluorine binding site 2 out of 6 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter P1FLHDC 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 P1FLHDC in the Presence of Phosphomimetic BEF3- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:168.8
occ:1.00
F2 B:BFD302 0.0 168.8 1.0
BE B:BFD302 1.5 176.0 1.0
F1 B:BFD302 2.5 177.6 1.0
F3 B:BFD302 2.5 172.2 1.0
ND1 B:HIS12 3.4 159.8 1.0
CG2 B:VAL15 3.5 186.5 1.0
CE1 B:HIS12 4.0 164.9 1.0
OD2 B:ASP10 4.1 145.3 1.0
CG1 B:VAL15 4.2 193.6 1.0
CE A:MET88 4.3 198.3 1.0
CE1 A:HIS12 4.4 189.7 1.0
CB B:VAL15 4.4 184.3 1.0
ND1 A:HIS12 4.4 184.0 1.0
CB B:MET88 4.4 181.7 1.0
SD B:MET88 4.5 193.0 1.0
CG B:HIS12 4.6 157.8 1.0
CB B:LYS109 4.7 180.0 1.0
OD1 B:ASP10 4.7 142.0 1.0
N B:MET88 4.8 169.3 1.0
CG B:ASP10 4.8 147.9 1.0
NZ A:LYS109 4.9 176.5 1.0
CG2 A:VAL15 4.9 181.8 1.0
MG B:MG301 4.9 153.7 1.0
CB B:HIS12 5.0 156.1 1.0

Fluorine binding site 3 out of 6 in 6zix

Go back to Fluorine Binding Sites List in 6zix
Fluorine binding site 3 out of 6 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter P1FLHDC 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 P1FLHDC in the Presence of Phosphomimetic BEF3- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:172.2
occ:1.00
F3 B:BFD302 0.0 172.2 1.0
BE B:BFD302 1.5 176.0 1.0
F2 B:BFD302 2.5 168.8 1.0
F1 B:BFD302 2.6 177.6 1.0
CB B:LYS109 3.0 180.0 1.0
OD2 B:ASP10 3.6 145.3 1.0
N B:MET88 3.7 169.3 1.0
CG1 B:VAL15 3.8 193.6 1.0
O B:LEU86 3.9 176.3 1.0
C B:THR87 4.1 163.9 1.0
CA B:THR87 4.2 158.8 1.0
CA B:LYS109 4.5 182.0 1.0
C B:LEU86 4.5 167.1 1.0
CA B:MET88 4.6 173.4 1.0
N B:THR87 4.6 159.1 1.0
CG2 B:VAL15 4.6 186.5 1.0
OD1 B:ASP56 4.6 142.7 1.0
CG B:ASP10 4.7 147.9 1.0
CB B:MET88 4.7 181.7 1.0
CG B:LEU86 4.7 178.8 1.0
O B:THR87 4.8 167.7 1.0
CG B:ASP56 4.8 140.6 1.0
CB B:VAL15 4.8 184.3 1.0
OD2 B:ASP56 4.9 135.3 1.0

Fluorine binding site 4 out of 6 in 6zix

Go back to Fluorine Binding Sites List in 6zix
Fluorine binding site 4 out of 6 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter P1FLHDC 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 P1FLHDC in the Presence of Phosphomimetic BEF3- within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:189.8
occ:1.00
F1 A:BFD302 0.0 189.8 1.0
BE A:BFD302 1.5 179.2 1.0
MG A:MG301 1.9 165.0 1.0
F2 A:BFD302 2.5 163.8 1.0
OD2 A:ASP56 2.6 181.1 1.0
F3 A:BFD302 2.6 183.4 1.0
O A:SER58 2.7 170.4 1.0
OD1 A:ASP56 3.0 192.7 1.0
CG A:ASP56 3.1 184.7 1.0
CB A:SER58 3.4 179.4 1.0
C A:SER58 3.6 174.3 1.0
OD2 A:ASP11 3.6 156.5 1.0
CA A:SER58 3.8 178.1 1.0
N A:SER58 3.8 179.5 1.0
OG A:SER58 4.1 177.6 1.0
OD1 A:ASP11 4.3 164.9 1.0
CG A:ASP11 4.3 165.6 1.0
OD1 A:ASP10 4.6 177.1 1.0
CB A:ASP56 4.6 184.6 1.0
NZ A:LYS109 4.7 176.5 1.0
CG A:MET88 4.8 200.4 1.0
N A:MET59 4.9 171.7 1.0
CE A:MET88 4.9 198.3 1.0

Fluorine binding site 5 out of 6 in 6zix

Go back to Fluorine Binding Sites List in 6zix
Fluorine binding site 5 out of 6 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter P1FLHDC 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 P1FLHDC in the Presence of Phosphomimetic BEF3- within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:163.8
occ:1.00
F2 A:BFD302 0.0 163.8 1.0
BE A:BFD302 1.5 179.2 1.0
F3 A:BFD302 2.5 183.4 1.0
F1 A:BFD302 2.5 189.8 1.0
OG A:SER58 2.9 177.6 1.0
OG1 A:THR87 3.0 170.9 1.0
CB A:SER58 3.2 179.4 1.0
CG A:MET88 3.6 200.4 1.0
OD1 A:ASP56 3.7 192.7 1.0
N A:SER58 3.8 179.5 1.0
N A:MET88 3.8 176.4 1.0
CA A:SER58 4.0 178.1 1.0
CB A:THR87 4.1 171.0 1.0
MG A:MG301 4.2 165.0 1.0
CA A:THR87 4.2 168.4 1.0
O A:SER58 4.4 170.4 1.0
CG A:ASP56 4.5 184.7 1.0
N A:ASN89 4.5 175.4 1.0
OD2 A:ASP56 4.5 181.1 1.0
C A:THR87 4.5 166.3 1.0
CB A:MET88 4.6 199.0 1.0
SD A:MET88 4.6 205.3 1.0
CA A:MET88 4.7 186.7 1.0
CB A:LEU57 4.7 148.7 1.0
C A:SER58 4.7 174.3 1.0
C A:LEU57 4.9 171.5 1.0

Fluorine binding site 6 out of 6 in 6zix

Go back to Fluorine Binding Sites List in 6zix
Fluorine binding site 6 out of 6 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter P1FLHDC 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 P1FLHDC in the Presence of Phosphomimetic BEF3- within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:183.4
occ:1.00
F3 A:BFD302 0.0 183.4 1.0
BE A:BFD302 1.5 179.2 1.0
F2 A:BFD302 2.5 163.8 1.0
F1 A:BFD302 2.6 189.8 1.0
N A:MET88 2.9 176.4 1.0
OD1 A:ASP56 3.1 192.7 1.0
MG A:MG301 3.3 165.0 1.0
CG A:MET88 3.4 200.4 1.0
CA A:THR87 3.4 168.4 1.0
C A:THR87 3.6 166.3 1.0
CD A:LYS109 3.6 172.7 1.0
NZ A:LYS109 3.7 176.5 1.0
CB A:MET88 3.7 199.0 1.0
OD2 A:ASP56 3.8 181.1 1.0
CG A:ASP56 3.8 184.7 1.0
OG1 A:THR87 3.8 170.9 1.0
CE A:LYS109 3.9 174.6 1.0
CA A:MET88 3.9 186.7 1.0
O A:LEU86 4.0 173.2 1.0
CE A:MET88 4.1 198.3 1.0
CB A:THR87 4.2 171.0 1.0
N A:THR87 4.5 167.1 1.0
SD A:MET88 4.5 205.3 1.0
CG A:LYS109 4.6 168.5 1.0
C A:LEU86 4.7 169.2 1.0
O A:THR87 4.7 159.2 1.0
C A:MET88 4.9 185.8 1.0
N A:ASN89 5.0 175.4 1.0
OD1 A:ASP10 5.0 177.1 1.0
OD2 A:ASP10 5.0 184.0 1.0

Reference:

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
Page generated: Fri Aug 2 05:14:44 2024

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