Fluorine in PDB 6zii: Structure of the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium in the Presence of Phosphomimetic BEF3-
Protein crystallography data
The structure of Structure of the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium in the Presence of Phosphomimetic BEF3-, PDB code: 6zii
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)
|
28.71 /
2.50
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
38.144,
64.4,
47.131,
90,
100.14,
90
|
R / Rfree (%)
|
22.2 /
27.8
|
Other elements in 6zii:
The structure of Structure of the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium 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 the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium in the Presence of Phosphomimetic BEF3-
(pdb code 6zii). 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 the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium in the Presence of Phosphomimetic BEF3-, PDB code: 6zii:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6zii
Go back to
Fluorine Binding Sites List in 6zii
Fluorine binding site 1 out
of 6 in the Structure of the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium 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 the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium in the Presence of Phosphomimetic BEF3- within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F56
b:41.5
occ:1.00
|
F1
|
B:BFD56
|
0.0
|
41.5
|
1.0
|
BE
|
B:BFD56
|
1.5
|
41.5
|
1.0
|
MG
|
B:MG301
|
2.5
|
37.1
|
1.0
|
F2
|
B:BFD56
|
2.5
|
40.9
|
1.0
|
OD1
|
B:BFD56
|
2.6
|
29.2
|
1.0
|
F3
|
B:BFD56
|
2.6
|
41.1
|
1.0
|
OD2
|
B:BFD56
|
2.9
|
27.0
|
1.0
|
CG
|
B:BFD56
|
3.1
|
27.9
|
1.0
|
O
|
B:SER58
|
3.4
|
33.2
|
1.0
|
CB
|
B:SER58
|
3.4
|
33.5
|
1.0
|
O
|
B:HOH409
|
3.7
|
32.4
|
1.0
|
N
|
B:SER58
|
3.7
|
32.3
|
1.0
|
CA
|
B:SER58
|
3.9
|
33.0
|
1.0
|
O
|
B:HOH401
|
4.1
|
55.6
|
1.0
|
OG
|
B:SER58
|
4.1
|
34.5
|
1.0
|
C
|
B:SER58
|
4.1
|
32.7
|
1.0
|
NZ
|
B:LYS109
|
4.1
|
29.8
|
1.0
|
OD1
|
B:ASP11
|
4.6
|
30.1
|
1.0
|
CB
|
B:BFD56
|
4.6
|
27.9
|
1.0
|
N
|
B:LEU57
|
4.6
|
28.7
|
1.0
|
CG
|
B:MET88
|
4.7
|
36.5
|
1.0
|
SD
|
B:MET88
|
4.8
|
41.5
|
1.0
|
C
|
B:LEU57
|
4.9
|
31.3
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6zii
Go back to
Fluorine Binding Sites List in 6zii
Fluorine binding site 2 out
of 6 in the Structure of the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium 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 the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium in the Presence of Phosphomimetic BEF3- within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F56
b:40.9
occ:1.00
|
F2
|
B:BFD56
|
0.0
|
40.9
|
1.0
|
BE
|
B:BFD56
|
1.5
|
41.5
|
1.0
|
F3
|
B:BFD56
|
2.4
|
41.1
|
1.0
|
F1
|
B:BFD56
|
2.5
|
41.5
|
1.0
|
OG1
|
B:THR87
|
2.8
|
33.1
|
1.0
|
N
|
B:MET88
|
3.4
|
33.5
|
1.0
|
OD1
|
B:BFD56
|
3.4
|
29.2
|
1.0
|
CA
|
B:THR87
|
3.7
|
32.7
|
1.0
|
CB
|
B:THR87
|
3.7
|
32.9
|
1.0
|
CG
|
B:MET88
|
3.8
|
36.5
|
1.0
|
OG
|
B:SER58
|
3.9
|
34.5
|
1.0
|
N
|
B:SER58
|
3.9
|
32.3
|
1.0
|
CB
|
B:LEU57
|
4.1
|
30.8
|
1.0
|
CB
|
B:SER58
|
4.1
|
33.5
|
1.0
|
C
|
B:THR87
|
4.1
|
32.3
|
1.0
|
N
|
B:ASN89
|
4.2
|
35.9
|
1.0
|
CA
|
B:MET88
|
4.4
|
34.4
|
1.0
|
N
|
B:LEU57
|
4.4
|
28.7
|
1.0
|
CB
|
B:MET88
|
4.5
|
35.0
|
1.0
|
CG
|
B:BFD56
|
4.5
|
27.9
|
1.0
|
CA
|
B:SER58
|
4.6
|
33.0
|
1.0
|
C
|
B:MET88
|
4.7
|
34.9
|
1.0
|
CA
|
B:LEU57
|
4.7
|
30.3
|
1.0
|
C
|
B:LEU57
|
4.7
|
31.3
|
1.0
|
CB
|
B:ASN89
|
4.8
|
37.2
|
1.0
|
SD
|
B:MET88
|
4.8
|
41.5
|
1.0
|
MG
|
B:MG301
|
4.9
|
37.1
|
1.0
|
OD2
|
B:BFD56
|
4.9
|
27.0
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6zii
Go back to
Fluorine Binding Sites List in 6zii
Fluorine binding site 3 out
of 6 in the Structure of the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium 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 the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium in the Presence of Phosphomimetic BEF3- within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F56
b:41.1
occ:1.00
|
F3
|
B:BFD56
|
0.0
|
41.1
|
1.0
|
BE
|
B:BFD56
|
1.5
|
41.5
|
1.0
|
F2
|
B:BFD56
|
2.4
|
40.9
|
1.0
|
F1
|
B:BFD56
|
2.6
|
41.5
|
1.0
|
OD1
|
B:BFD56
|
2.9
|
29.2
|
1.0
|
NZ
|
B:LYS109
|
2.9
|
29.8
|
1.0
|
N
|
B:MET88
|
2.9
|
33.5
|
1.0
|
CE
|
B:LYS109
|
3.2
|
29.6
|
1.0
|
CA
|
B:THR87
|
3.3
|
32.7
|
1.0
|
C
|
B:THR87
|
3.4
|
32.3
|
1.0
|
CD
|
B:LYS109
|
3.4
|
29.0
|
1.0
|
CG
|
B:MET88
|
3.7
|
36.5
|
1.0
|
CB
|
B:MET88
|
3.8
|
35.0
|
1.0
|
O
|
B:LEU86
|
3.8
|
34.1
|
1.0
|
CG
|
B:BFD56
|
3.9
|
27.9
|
1.0
|
CA
|
B:MET88
|
3.9
|
34.4
|
1.0
|
OG1
|
B:THR87
|
4.0
|
33.1
|
1.0
|
CB
|
B:THR87
|
4.2
|
32.9
|
1.0
|
N
|
B:THR87
|
4.2
|
33.0
|
1.0
|
CG
|
B:LYS109
|
4.3
|
28.5
|
1.0
|
OD2
|
B:BFD56
|
4.3
|
27.0
|
1.0
|
SD
|
B:MET88
|
4.4
|
41.5
|
1.0
|
C
|
B:LEU86
|
4.4
|
32.5
|
1.0
|
O
|
B:THR87
|
4.5
|
32.4
|
1.0
|
MG
|
B:MG301
|
4.6
|
37.1
|
1.0
|
OD2
|
B:ASP10
|
4.8
|
37.2
|
1.0
|
C
|
B:MET88
|
5.0
|
34.9
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6zii
Go back to
Fluorine Binding Sites List in 6zii
Fluorine binding site 4 out
of 6 in the Structure of the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium 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 the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium in the Presence of Phosphomimetic BEF3- within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F56
b:26.9
occ:1.00
|
F1
|
A:BFD56
|
0.0
|
26.9
|
1.0
|
BE
|
A:BFD56
|
1.5
|
25.9
|
1.0
|
MG
|
A:MG301
|
2.2
|
32.7
|
1.0
|
F2
|
A:BFD56
|
2.5
|
25.1
|
1.0
|
F3
|
A:BFD56
|
2.5
|
25.5
|
1.0
|
OD2
|
A:BFD56
|
2.9
|
31.1
|
1.0
|
O
|
A:HOH403
|
3.0
|
30.0
|
1.0
|
O
|
A:SER58
|
3.0
|
36.1
|
1.0
|
OD1
|
A:BFD56
|
3.1
|
34.7
|
1.0
|
CB
|
A:SER58
|
3.3
|
35.0
|
1.0
|
CG
|
A:BFD56
|
3.3
|
32.9
|
1.0
|
N
|
A:SER58
|
3.7
|
35.0
|
1.0
|
CA
|
A:SER58
|
3.8
|
35.6
|
1.0
|
C
|
A:SER58
|
3.8
|
36.0
|
1.0
|
OG
|
A:SER58
|
4.2
|
34.6
|
1.0
|
OD1
|
A:ASP11
|
4.3
|
31.3
|
1.0
|
NZ
|
A:LYS109
|
4.8
|
28.6
|
1.0
|
CB
|
A:BFD56
|
4.8
|
32.9
|
1.0
|
N
|
A:LEU57
|
4.8
|
33.6
|
1.0
|
C
|
A:LEU57
|
4.9
|
34.4
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6zii
Go back to
Fluorine Binding Sites List in 6zii
Fluorine binding site 5 out
of 6 in the Structure of the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium 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 the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium in the Presence of Phosphomimetic BEF3- within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F56
b:25.1
occ:1.00
|
F2
|
A:BFD56
|
0.0
|
25.1
|
1.0
|
BE
|
A:BFD56
|
1.5
|
25.9
|
1.0
|
F3
|
A:BFD56
|
2.5
|
25.5
|
1.0
|
F1
|
A:BFD56
|
2.5
|
26.9
|
1.0
|
OD1
|
A:BFD56
|
2.7
|
34.7
|
1.0
|
OG1
|
A:THR87
|
2.9
|
28.1
|
1.0
|
N
|
A:SER58
|
3.2
|
35.0
|
1.0
|
N
|
A:LEU57
|
3.4
|
33.6
|
1.0
|
CB
|
A:LEU57
|
3.5
|
34.4
|
1.0
|
CB
|
A:THR87
|
3.6
|
27.6
|
1.0
|
CG
|
A:BFD56
|
3.6
|
32.9
|
1.0
|
CA
|
A:THR87
|
3.8
|
27.7
|
1.0
|
CA
|
A:LEU57
|
3.8
|
34.3
|
1.0
|
CB
|
A:SER58
|
3.9
|
35.0
|
1.0
|
C
|
A:LEU57
|
4.0
|
34.4
|
1.0
|
OD2
|
A:BFD56
|
4.0
|
31.1
|
1.0
|
CA
|
A:SER58
|
4.1
|
35.6
|
1.0
|
N
|
A:MET88
|
4.2
|
27.8
|
1.0
|
MG
|
A:MG301
|
4.4
|
32.7
|
1.0
|
O
|
A:SER58
|
4.5
|
36.1
|
1.0
|
O
|
A:LEU86
|
4.5
|
26.5
|
1.0
|
C
|
A:BFD56
|
4.5
|
33.1
|
1.0
|
C
|
A:THR87
|
4.5
|
28.0
|
1.0
|
C
|
A:SER58
|
4.8
|
36.0
|
1.0
|
CB
|
A:BFD56
|
4.8
|
32.9
|
1.0
|
CG
|
A:LEU57
|
4.8
|
35.4
|
1.0
|
CA
|
A:BFD56
|
4.8
|
33.0
|
1.0
|
O
|
A:HOH403
|
4.9
|
30.0
|
1.0
|
N
|
A:ASN89
|
4.9
|
27.1
|
1.0
|
N
|
A:THR87
|
4.9
|
27.2
|
1.0
|
CG2
|
A:THR87
|
5.0
|
27.1
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6zii
Go back to
Fluorine Binding Sites List in 6zii
Fluorine binding site 6 out
of 6 in the Structure of the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium 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 the Isolated Rec Domain of Rcsb From Salmonella Enterica Serovar Typhimurium in the Presence of Phosphomimetic BEF3- within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F56
b:25.5
occ:1.00
|
F3
|
A:BFD56
|
0.0
|
25.5
|
1.0
|
BE
|
A:BFD56
|
1.5
|
25.9
|
1.0
|
F2
|
A:BFD56
|
2.5
|
25.1
|
1.0
|
F1
|
A:BFD56
|
2.5
|
26.9
|
1.0
|
OD1
|
A:BFD56
|
3.1
|
34.7
|
1.0
|
N
|
A:MET88
|
3.2
|
27.8
|
1.0
|
NZ
|
A:LYS109
|
3.3
|
28.6
|
1.0
|
CG
|
A:MET88
|
3.5
|
28.8
|
1.0
|
CA
|
A:THR87
|
3.8
|
27.7
|
1.0
|
CE
|
A:LYS109
|
3.8
|
28.3
|
1.0
|
OG1
|
A:THR87
|
3.9
|
28.1
|
1.0
|
O
|
A:HOH403
|
3.9
|
30.0
|
1.0
|
C
|
A:THR87
|
3.9
|
28.0
|
1.0
|
CB
|
A:MET88
|
4.0
|
28.1
|
1.0
|
CG
|
A:BFD56
|
4.0
|
32.9
|
1.0
|
CD
|
A:LYS109
|
4.1
|
28.3
|
1.0
|
CA
|
A:MET88
|
4.2
|
27.6
|
1.0
|
OD2
|
A:BFD56
|
4.2
|
31.1
|
1.0
|
MG
|
A:MG301
|
4.3
|
32.7
|
1.0
|
SD
|
A:MET88
|
4.3
|
29.8
|
1.0
|
CB
|
A:THR87
|
4.4
|
27.6
|
1.0
|
O
|
A:HOH405
|
4.5
|
30.0
|
1.0
|
O
|
A:LEU86
|
4.6
|
26.5
|
1.0
|
N
|
A:ASN89
|
4.9
|
27.1
|
1.0
|
N
|
A:THR87
|
4.9
|
27.2
|
1.0
|
C
|
A:MET88
|
5.0
|
27.2
|
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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