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:
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
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