Fluorine in PDB 6rh0: Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5
Protein crystallography data
The structure of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5, PDB code: 6rh0
was solved by
C.Mideros-Mora,
P.Casino,
A.Marina,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.21 /
2.87
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.616,
92.933,
174.337,
90.00,
93.49,
90.00
|
R / Rfree (%)
|
24 /
28.7
|
Other elements in 6rh0:
The structure of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5
(pdb code 6rh0). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5, PDB code: 6rh0:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6rh0
Go back to
Fluorine Binding Sites List in 6rh0
Fluorine binding site 1 out
of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F53
b:54.2
occ:0.80
|
F1
|
C:BFD53
|
0.0
|
54.2
|
0.8
|
BE
|
C:BFD53
|
1.5
|
53.3
|
0.8
|
MG
|
C:MG201
|
2.0
|
37.5
|
1.0
|
F2
|
C:BFD53
|
2.4
|
51.8
|
0.8
|
F3
|
C:BFD53
|
2.6
|
54.6
|
0.8
|
OD2
|
C:BFD53
|
3.0
|
41.8
|
1.0
|
OD1
|
C:BFD53
|
3.2
|
40.5
|
1.0
|
O
|
C:HOH323
|
3.3
|
33.5
|
1.0
|
CG
|
C:BFD53
|
3.5
|
41.1
|
1.0
|
O
|
C:MET55
|
3.6
|
44.4
|
1.0
|
O
|
A:HOH627
|
3.6
|
41.1
|
1.0
|
CB
|
C:MET55
|
3.8
|
45.6
|
1.0
|
NZ
|
C:LYS105
|
4.0
|
39.3
|
1.0
|
OD1
|
C:ASP10
|
4.2
|
47.5
|
1.0
|
N
|
C:MET55
|
4.4
|
44.2
|
1.0
|
CA
|
C:MET55
|
4.4
|
45.6
|
1.0
|
C
|
C:MET55
|
4.4
|
45.7
|
1.0
|
CB
|
C:ALA84
|
4.6
|
42.3
|
1.0
|
SD
|
C:MET55
|
4.7
|
46.5
|
1.0
|
CG
|
C:MET55
|
4.7
|
46.5
|
1.0
|
N
|
C:ALA84
|
4.8
|
41.2
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6rh0
Go back to
Fluorine Binding Sites List in 6rh0
Fluorine binding site 2 out
of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F53
b:51.8
occ:0.80
|
F2
|
C:BFD53
|
0.0
|
51.8
|
0.8
|
BE
|
C:BFD53
|
1.5
|
53.3
|
0.8
|
F1
|
C:BFD53
|
2.4
|
54.2
|
0.8
|
F3
|
C:BFD53
|
2.4
|
54.6
|
0.8
|
N
|
C:ALA84
|
2.6
|
41.2
|
1.0
|
NZ
|
C:LYS105
|
2.9
|
39.3
|
1.0
|
OD1
|
C:BFD53
|
3.0
|
40.5
|
1.0
|
CB
|
C:ALA84
|
3.2
|
42.3
|
1.0
|
CE
|
C:LYS105
|
3.2
|
38.7
|
1.0
|
CD
|
C:LYS105
|
3.3
|
38.6
|
1.0
|
C
|
C:THR83
|
3.5
|
40.9
|
1.0
|
CA
|
C:ALA84
|
3.5
|
42.1
|
1.0
|
CA
|
C:THR83
|
3.5
|
40.8
|
1.0
|
CG
|
C:BFD53
|
3.9
|
41.1
|
1.0
|
OG1
|
C:THR83
|
3.9
|
42.3
|
1.0
|
OD2
|
C:BFD53
|
4.1
|
41.8
|
1.0
|
O
|
C:HOH323
|
4.3
|
33.5
|
1.0
|
CB
|
C:THR83
|
4.3
|
41.9
|
1.0
|
MG
|
C:MG201
|
4.3
|
37.5
|
1.0
|
CG
|
C:LYS105
|
4.3
|
38.7
|
1.0
|
O
|
C:LEU82
|
4.5
|
40.8
|
1.0
|
O
|
C:THR83
|
4.6
|
41.1
|
1.0
|
N
|
C:THR83
|
4.6
|
40.6
|
1.0
|
C
|
C:ALA84
|
4.7
|
43.9
|
1.0
|
O
|
C:HOH321
|
4.9
|
28.9
|
1.0
|
N
|
C:LYS85
|
4.9
|
44.7
|
1.0
|
OD2
|
C:ASP9
|
4.9
|
43.7
|
1.0
|
CB
|
C:LYS105
|
4.9
|
39.4
|
1.0
|
C
|
C:LEU82
|
5.0
|
40.7
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6rh0
Go back to
Fluorine Binding Sites List in 6rh0
Fluorine binding site 3 out
of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F53
b:54.6
occ:0.80
|
F3
|
C:BFD53
|
0.0
|
54.6
|
0.8
|
BE
|
C:BFD53
|
1.5
|
53.3
|
0.8
|
F2
|
C:BFD53
|
2.4
|
51.8
|
0.8
|
F1
|
C:BFD53
|
2.6
|
54.2
|
0.8
|
OD1
|
C:BFD53
|
2.9
|
40.5
|
1.0
|
OG1
|
C:THR83
|
2.9
|
42.3
|
1.0
|
N
|
C:MET55
|
3.3
|
44.2
|
1.0
|
N
|
C:ALA84
|
3.4
|
41.2
|
1.0
|
CB
|
C:MET55
|
3.5
|
45.6
|
1.0
|
SD
|
C:MET55
|
3.6
|
46.5
|
1.0
|
CG
|
C:MET55
|
3.7
|
46.5
|
1.0
|
CG
|
C:BFD53
|
3.9
|
41.1
|
1.0
|
CA
|
C:MET55
|
4.0
|
45.6
|
1.0
|
CB
|
C:THR83
|
4.0
|
41.9
|
1.0
|
CB
|
C:ALA84
|
4.0
|
42.3
|
1.0
|
CA
|
C:THR83
|
4.1
|
40.8
|
1.0
|
N
|
C:ILE54
|
4.1
|
42.5
|
1.0
|
CB
|
C:ILE54
|
4.1
|
44.0
|
1.0
|
OD2
|
C:BFD53
|
4.1
|
41.8
|
1.0
|
MG
|
C:MG201
|
4.2
|
37.5
|
1.0
|
CA
|
C:ALA84
|
4.2
|
42.1
|
1.0
|
C
|
C:THR83
|
4.3
|
40.9
|
1.0
|
N
|
C:LYS85
|
4.3
|
44.7
|
1.0
|
C
|
C:ILE54
|
4.3
|
44.9
|
1.0
|
CA
|
C:ILE54
|
4.4
|
44.1
|
1.0
|
CG
|
C:LYS85
|
4.6
|
47.9
|
1.0
|
O
|
C:MET55
|
4.6
|
44.4
|
1.0
|
C
|
C:ALA84
|
4.8
|
43.9
|
1.0
|
C
|
C:MET55
|
4.8
|
45.7
|
1.0
|
CG1
|
C:ILE54
|
5.0
|
43.8
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6rh0
Go back to
Fluorine Binding Sites List in 6rh0
Fluorine binding site 4 out
of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F53
b:46.4
occ:0.80
|
F1
|
D:BFD53
|
0.0
|
46.4
|
0.8
|
BE
|
D:BFD53
|
1.5
|
45.7
|
0.8
|
F2
|
D:BFD53
|
2.4
|
44.6
|
0.8
|
MG
|
D:MG201
|
2.5
|
46.8
|
1.0
|
F3
|
D:BFD53
|
2.6
|
46.4
|
0.8
|
O
|
D:HOH317
|
3.1
|
44.0
|
1.0
|
O
|
D:HOH320
|
3.4
|
32.2
|
1.0
|
OD1
|
D:BFD53
|
3.5
|
43.5
|
1.0
|
OD2
|
D:BFD53
|
3.7
|
45.0
|
1.0
|
O
|
D:MET55
|
3.9
|
49.0
|
1.0
|
CB
|
D:ALA84
|
4.0
|
44.9
|
1.0
|
CG
|
D:BFD53
|
4.0
|
44.5
|
1.0
|
CB
|
D:MET55
|
4.1
|
50.1
|
1.0
|
NZ
|
D:LYS105
|
4.2
|
43.1
|
1.0
|
N
|
D:ALA84
|
4.5
|
44.3
|
1.0
|
SD
|
D:MET55
|
4.5
|
51.5
|
1.0
|
N
|
D:MET55
|
4.7
|
48.7
|
1.0
|
CA
|
D:MET55
|
4.7
|
50.1
|
1.0
|
C
|
D:MET55
|
4.7
|
50.3
|
1.0
|
OD1
|
D:ASP10
|
4.9
|
49.5
|
1.0
|
O
|
D:HOH306
|
4.9
|
23.8
|
1.0
|
CA
|
D:ALA84
|
4.9
|
44.8
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6rh0
Go back to
Fluorine Binding Sites List in 6rh0
Fluorine binding site 5 out
of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F53
b:44.6
occ:0.80
|
F2
|
D:BFD53
|
0.0
|
44.6
|
0.8
|
BE
|
D:BFD53
|
1.5
|
45.7
|
0.8
|
F1
|
D:BFD53
|
2.4
|
46.4
|
0.8
|
F3
|
D:BFD53
|
2.4
|
46.4
|
0.8
|
N
|
D:ALA84
|
2.5
|
44.3
|
1.0
|
NZ
|
D:LYS105
|
3.0
|
43.1
|
1.0
|
OD1
|
D:BFD53
|
3.0
|
43.5
|
1.0
|
CB
|
D:ALA84
|
3.2
|
44.9
|
1.0
|
C
|
D:THR83
|
3.2
|
44.1
|
1.0
|
CA
|
D:THR83
|
3.3
|
44.4
|
1.0
|
CD
|
D:LYS105
|
3.3
|
42.4
|
1.0
|
CE
|
D:LYS105
|
3.3
|
42.7
|
1.0
|
CA
|
D:ALA84
|
3.4
|
44.8
|
1.0
|
OG1
|
D:THR83
|
3.6
|
45.5
|
1.0
|
CB
|
D:THR83
|
4.0
|
45.5
|
1.0
|
CG
|
D:BFD53
|
4.0
|
44.5
|
1.0
|
CG
|
D:LYS105
|
4.3
|
42.4
|
1.0
|
O
|
D:LEU82
|
4.3
|
44.8
|
1.0
|
O
|
D:THR83
|
4.3
|
44.1
|
1.0
|
N
|
D:THR83
|
4.4
|
44.5
|
1.0
|
MG
|
D:MG201
|
4.4
|
46.8
|
1.0
|
OD2
|
D:BFD53
|
4.5
|
45.0
|
1.0
|
C
|
D:ALA84
|
4.6
|
46.4
|
1.0
|
O
|
D:HOH320
|
4.7
|
32.2
|
1.0
|
O
|
D:HOH306
|
4.7
|
23.8
|
1.0
|
N
|
D:LYS85
|
4.8
|
47.1
|
1.0
|
C
|
D:LEU82
|
4.8
|
44.7
|
1.0
|
OD2
|
D:ASP9
|
4.9
|
46.0
|
1.0
|
CB
|
D:LYS105
|
4.9
|
42.6
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6rh0
Go back to
Fluorine Binding Sites List in 6rh0
Fluorine binding site 6 out
of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 5.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F53
b:46.4
occ:0.80
|
F3
|
D:BFD53
|
0.0
|
46.4
|
0.8
|
BE
|
D:BFD53
|
1.5
|
45.7
|
0.8
|
F2
|
D:BFD53
|
2.4
|
44.6
|
0.8
|
F1
|
D:BFD53
|
2.6
|
46.4
|
0.8
|
OG1
|
D:THR83
|
2.7
|
45.5
|
1.0
|
OD1
|
D:BFD53
|
2.9
|
43.5
|
1.0
|
N
|
D:MET55
|
3.2
|
48.7
|
1.0
|
N
|
D:ALA84
|
3.5
|
44.3
|
1.0
|
CB
|
D:MET55
|
3.6
|
50.1
|
1.0
|
SD
|
D:MET55
|
3.7
|
51.5
|
1.0
|
CB
|
D:THR83
|
3.8
|
45.5
|
1.0
|
CG
|
D:BFD53
|
3.9
|
44.5
|
1.0
|
N
|
D:ILE54
|
3.9
|
46.6
|
1.0
|
CB
|
D:ILE54
|
3.9
|
47.8
|
1.0
|
CA
|
D:MET55
|
4.0
|
50.1
|
1.0
|
CA
|
D:THR83
|
4.0
|
44.4
|
1.0
|
CG
|
D:MET55
|
4.1
|
50.9
|
1.0
|
CB
|
D:ALA84
|
4.1
|
44.9
|
1.0
|
C
|
D:ILE54
|
4.2
|
49.1
|
1.0
|
CA
|
D:ILE54
|
4.2
|
48.1
|
1.0
|
MG
|
D:MG201
|
4.2
|
46.8
|
1.0
|
OD2
|
D:BFD53
|
4.2
|
45.0
|
1.0
|
C
|
D:THR83
|
4.3
|
44.1
|
1.0
|
CA
|
D:ALA84
|
4.3
|
44.8
|
1.0
|
O
|
D:MET55
|
4.4
|
49.0
|
1.0
|
N
|
D:LYS85
|
4.4
|
47.1
|
1.0
|
C
|
D:MET55
|
4.7
|
50.3
|
1.0
|
CG
|
D:LYS85
|
4.7
|
50.0
|
1.0
|
CG1
|
D:ILE54
|
4.8
|
47.7
|
1.0
|
CG2
|
D:ILE54
|
4.9
|
49.2
|
1.0
|
C
|
D:ALA84
|
4.9
|
46.4
|
1.0
|
C
|
D:BFD53
|
5.0
|
47.0
|
1.0
|
|
Reference:
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L.Miguel-Romero,
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P.Casino,
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Revisiting the pH-Gated Conformational Switch on the Activities of Hiska-Family Histidine Kinases. Nat Commun V. 11 769 2020.
ISSN: ESSN 2041-1723
PubMed: 32034139
DOI: 10.1038/S41467-020-14540-5
Page generated: Fri Aug 2 01:11:14 2024
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