Fluorine in PDB 6rgz: Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 6.5
Protein crystallography data
The structure of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 6.5, PDB code: 6rgz
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)
|
28.90 /
2.35
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.736,
93.608,
173.927,
90.00,
93.35,
90.00
|
R / Rfree (%)
|
21.5 /
26.5
|
Other elements in 6rgz:
The structure of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 6.5 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 6.5
(pdb code 6rgz). 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 6.5, PDB code: 6rgz:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6rgz
Go back to
Fluorine Binding Sites List in 6rgz
Fluorine binding site 1 out
of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 6.5
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 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F53
b:37.6
occ:0.80
|
F1
|
C:BFD53
|
0.0
|
37.6
|
0.8
|
BE
|
C:BFD53
|
1.5
|
39.0
|
0.8
|
MG
|
C:MG201
|
2.0
|
43.3
|
1.0
|
F2
|
C:BFD53
|
2.4
|
39.2
|
0.8
|
F3
|
C:BFD53
|
2.6
|
41.4
|
0.8
|
OD1
|
C:BFD53
|
2.7
|
39.5
|
1.0
|
OD2
|
C:BFD53
|
2.8
|
41.6
|
1.0
|
O
|
C:HOH305
|
2.9
|
44.3
|
1.0
|
O
|
B:HOH654
|
2.9
|
48.7
|
1.0
|
O
|
C:HOH324
|
3.1
|
45.6
|
1.0
|
O
|
C:MET55
|
3.1
|
46.5
|
1.0
|
CG
|
C:BFD53
|
3.1
|
40.5
|
1.0
|
CB
|
C:MET55
|
3.4
|
50.8
|
1.0
|
N
|
C:MET55
|
3.7
|
46.1
|
1.0
|
CA
|
C:MET55
|
3.8
|
48.9
|
1.0
|
C
|
C:MET55
|
3.8
|
49.0
|
1.0
|
O
|
C:HOH335
|
4.1
|
51.1
|
1.0
|
OD1
|
C:ASP10
|
4.3
|
50.6
|
1.0
|
NZ
|
C:LYS105
|
4.4
|
34.8
|
1.0
|
CG
|
C:MET55
|
4.4
|
54.0
|
1.0
|
SD
|
C:MET55
|
4.6
|
58.0
|
1.0
|
CB
|
C:BFD53
|
4.7
|
40.3
|
1.0
|
N
|
C:ILE54
|
4.7
|
43.1
|
1.0
|
C
|
C:ILE54
|
4.8
|
46.2
|
1.0
|
CB
|
C:ALA84
|
5.0
|
40.3
|
1.0
|
N
|
C:ALA84
|
5.0
|
39.1
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6rgz
Go back to
Fluorine Binding Sites List in 6rgz
Fluorine binding site 2 out
of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 6.5
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 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F53
b:39.2
occ:0.80
|
F2
|
C:BFD53
|
0.0
|
39.2
|
0.8
|
BE
|
C:BFD53
|
1.5
|
39.0
|
0.8
|
F1
|
C:BFD53
|
2.4
|
37.6
|
0.8
|
F3
|
C:BFD53
|
2.5
|
41.4
|
0.8
|
OD1
|
C:BFD53
|
2.6
|
39.5
|
1.0
|
N
|
C:ALA84
|
2.8
|
39.1
|
1.0
|
NZ
|
C:LYS105
|
3.0
|
34.8
|
1.0
|
O
|
B:HOH654
|
3.1
|
48.7
|
1.0
|
CB
|
C:ALA84
|
3.4
|
40.3
|
1.0
|
CD
|
C:LYS105
|
3.5
|
33.9
|
1.0
|
CE
|
C:LYS105
|
3.5
|
33.9
|
1.0
|
CA
|
C:THR83
|
3.7
|
38.6
|
1.0
|
C
|
C:THR83
|
3.7
|
38.7
|
1.0
|
CA
|
C:ALA84
|
3.7
|
40.7
|
1.0
|
CG
|
C:BFD53
|
3.7
|
40.5
|
1.0
|
O
|
C:HOH305
|
3.8
|
44.3
|
1.0
|
OG1
|
C:THR83
|
3.8
|
42.1
|
1.0
|
MG
|
C:MG201
|
4.1
|
43.3
|
1.0
|
OD2
|
C:BFD53
|
4.1
|
41.6
|
1.0
|
CB
|
C:THR83
|
4.3
|
40.7
|
1.0
|
O
|
C:LEU82
|
4.5
|
38.4
|
1.0
|
O
|
C:HOH335
|
4.6
|
51.1
|
1.0
|
CG
|
C:LYS105
|
4.7
|
34.2
|
1.0
|
O
|
C:HOH321
|
4.7
|
38.1
|
1.0
|
N
|
C:THR83
|
4.8
|
38.2
|
1.0
|
C
|
C:ALA84
|
4.8
|
43.3
|
1.0
|
N
|
C:LYS85
|
4.8
|
45.7
|
1.0
|
O
|
C:THR83
|
4.9
|
37.7
|
1.0
|
OD2
|
C:ASP9
|
4.9
|
45.2
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6rgz
Go back to
Fluorine Binding Sites List in 6rgz
Fluorine binding site 3 out
of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 6.5
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 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F53
b:41.4
occ:0.80
|
F3
|
C:BFD53
|
0.0
|
41.4
|
0.8
|
BE
|
C:BFD53
|
1.5
|
39.0
|
0.8
|
F2
|
C:BFD53
|
2.5
|
39.2
|
0.8
|
OD1
|
C:BFD53
|
2.5
|
39.5
|
1.0
|
F1
|
C:BFD53
|
2.6
|
37.6
|
0.8
|
OG1
|
C:THR83
|
2.6
|
42.1
|
1.0
|
N
|
C:MET55
|
3.0
|
46.1
|
1.0
|
N
|
C:ILE54
|
3.2
|
43.1
|
1.0
|
CG
|
C:BFD53
|
3.5
|
40.5
|
1.0
|
CB
|
C:ILE54
|
3.5
|
44.8
|
1.0
|
CB
|
C:THR83
|
3.6
|
40.7
|
1.0
|
CA
|
C:ILE54
|
3.6
|
44.8
|
1.0
|
C
|
C:ILE54
|
3.7
|
46.2
|
1.0
|
N
|
C:ALA84
|
3.8
|
39.1
|
1.0
|
CB
|
C:MET55
|
3.8
|
50.8
|
1.0
|
CA
|
C:THR83
|
3.9
|
38.6
|
1.0
|
CA
|
C:MET55
|
3.9
|
48.9
|
1.0
|
OD2
|
C:BFD53
|
4.0
|
41.6
|
1.0
|
CG
|
C:MET55
|
4.2
|
54.0
|
1.0
|
C
|
C:BFD53
|
4.3
|
43.0
|
1.0
|
MG
|
C:MG201
|
4.3
|
43.3
|
1.0
|
CG1
|
C:ILE54
|
4.3
|
44.2
|
1.0
|
C
|
C:THR83
|
4.3
|
38.7
|
1.0
|
SD
|
C:MET55
|
4.5
|
58.0
|
1.0
|
CA
|
C:BFD53
|
4.5
|
40.5
|
1.0
|
O
|
C:MET55
|
4.5
|
46.5
|
1.0
|
CB
|
C:BFD53
|
4.6
|
40.3
|
1.0
|
N
|
C:LYS85
|
4.6
|
45.7
|
1.0
|
CG2
|
C:ILE54
|
4.6
|
47.3
|
1.0
|
O
|
B:HOH654
|
4.6
|
48.7
|
1.0
|
C
|
C:MET55
|
4.7
|
49.0
|
1.0
|
CA
|
C:ALA84
|
4.8
|
40.7
|
1.0
|
O
|
C:LEU82
|
4.8
|
38.4
|
1.0
|
CB
|
C:ALA84
|
4.8
|
40.3
|
1.0
|
CG
|
C:LYS85
|
4.9
|
53.0
|
1.0
|
CG2
|
C:THR83
|
4.9
|
42.1
|
1.0
|
O
|
C:ILE54
|
4.9
|
47.8
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6rgz
Go back to
Fluorine Binding Sites List in 6rgz
Fluorine binding site 4 out
of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 6.5
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 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F53
b:37.6
occ:0.80
|
F1
|
D:BFD53
|
0.0
|
37.6
|
0.8
|
BE
|
D:BFD53
|
1.5
|
39.2
|
0.8
|
MG
|
D:MG201
|
2.0
|
44.1
|
1.0
|
F2
|
D:BFD53
|
2.4
|
39.4
|
0.8
|
F3
|
D:BFD53
|
2.6
|
41.1
|
0.8
|
OD1
|
D:BFD53
|
2.7
|
41.9
|
1.0
|
OD2
|
D:BFD53
|
2.8
|
42.8
|
1.0
|
O
|
A:HOH653
|
2.8
|
46.7
|
1.0
|
O
|
D:HOH308
|
2.9
|
44.2
|
1.0
|
O
|
D:MET55
|
3.0
|
49.7
|
1.0
|
CG
|
D:BFD53
|
3.1
|
42.8
|
1.0
|
O
|
D:HOH315
|
3.1
|
48.9
|
1.0
|
CB
|
D:MET55
|
3.4
|
53.1
|
1.0
|
N
|
D:MET55
|
3.6
|
48.9
|
1.0
|
CA
|
D:MET55
|
3.8
|
51.4
|
1.0
|
C
|
D:MET55
|
3.8
|
51.3
|
1.0
|
OD1
|
D:ASP10
|
4.1
|
51.5
|
1.0
|
CG
|
D:MET55
|
4.3
|
55.5
|
1.0
|
NZ
|
D:LYS105
|
4.4
|
39.6
|
1.0
|
O
|
A:HOH652
|
4.4
|
59.9
|
1.0
|
SD
|
D:MET55
|
4.5
|
59.2
|
1.0
|
CB
|
D:BFD53
|
4.6
|
42.5
|
1.0
|
N
|
D:ILE54
|
4.7
|
45.5
|
1.0
|
C
|
D:ILE54
|
4.7
|
49.2
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6rgz
Go back to
Fluorine Binding Sites List in 6rgz
Fluorine binding site 5 out
of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 6.5
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 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F53
b:39.4
occ:0.80
|
F2
|
D:BFD53
|
0.0
|
39.4
|
0.8
|
BE
|
D:BFD53
|
1.5
|
39.2
|
0.8
|
F1
|
D:BFD53
|
2.4
|
37.6
|
0.8
|
F3
|
D:BFD53
|
2.5
|
41.1
|
0.8
|
OD1
|
D:BFD53
|
2.6
|
41.9
|
1.0
|
O
|
A:HOH653
|
2.8
|
46.7
|
1.0
|
N
|
D:ALA84
|
2.9
|
39.8
|
1.0
|
NZ
|
D:LYS105
|
2.9
|
39.6
|
1.0
|
CB
|
D:ALA84
|
3.4
|
41.9
|
1.0
|
CE
|
D:LYS105
|
3.6
|
37.9
|
1.0
|
CD
|
D:LYS105
|
3.6
|
38.2
|
1.0
|
CG
|
D:BFD53
|
3.7
|
42.8
|
1.0
|
O
|
D:HOH308
|
3.7
|
44.2
|
1.0
|
CA
|
D:THR83
|
3.7
|
37.9
|
1.0
|
C
|
D:THR83
|
3.7
|
38.4
|
1.0
|
CA
|
D:ALA84
|
3.7
|
41.7
|
1.0
|
OG1
|
D:THR83
|
3.9
|
41.3
|
1.0
|
MG
|
D:MG201
|
4.0
|
44.1
|
1.0
|
OD2
|
D:BFD53
|
4.1
|
42.8
|
1.0
|
CB
|
D:THR83
|
4.4
|
39.8
|
1.0
|
O
|
D:LEU82
|
4.6
|
37.2
|
1.0
|
O
|
D:HOH317
|
4.7
|
37.0
|
1.0
|
CG
|
D:LYS105
|
4.8
|
37.8
|
1.0
|
N
|
D:THR83
|
4.8
|
37.6
|
1.0
|
O
|
A:HOH606
|
4.8
|
50.1
|
1.0
|
O
|
A:HOH652
|
4.8
|
59.9
|
1.0
|
C
|
D:ALA84
|
4.9
|
44.6
|
1.0
|
O
|
D:THR83
|
4.9
|
37.3
|
1.0
|
OD2
|
D:ASP9
|
4.9
|
45.9
|
1.0
|
CB
|
D:BFD53
|
5.0
|
42.5
|
1.0
|
N
|
D:LYS85
|
5.0
|
47.0
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6rgz
Go back to
Fluorine Binding Sites List in 6rgz
Fluorine binding site 6 out
of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 6.5
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 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F53
b:41.1
occ:0.80
|
F3
|
D:BFD53
|
0.0
|
41.1
|
0.8
|
BE
|
D:BFD53
|
1.5
|
39.2
|
0.8
|
F2
|
D:BFD53
|
2.5
|
39.4
|
0.8
|
OD1
|
D:BFD53
|
2.5
|
41.9
|
1.0
|
F1
|
D:BFD53
|
2.6
|
37.6
|
0.8
|
OG1
|
D:THR83
|
2.6
|
41.3
|
1.0
|
N
|
D:MET55
|
3.0
|
48.9
|
1.0
|
N
|
D:ILE54
|
3.2
|
45.5
|
1.0
|
CG
|
D:BFD53
|
3.5
|
42.8
|
1.0
|
CB
|
D:THR83
|
3.5
|
39.8
|
1.0
|
CB
|
D:ILE54
|
3.5
|
47.4
|
1.0
|
CA
|
D:ILE54
|
3.7
|
47.6
|
1.0
|
N
|
D:ALA84
|
3.7
|
39.8
|
1.0
|
CA
|
D:THR83
|
3.8
|
37.9
|
1.0
|
C
|
D:ILE54
|
3.8
|
49.2
|
1.0
|
CB
|
D:MET55
|
3.9
|
53.1
|
1.0
|
OD2
|
D:BFD53
|
4.0
|
42.8
|
1.0
|
CG
|
D:MET55
|
4.0
|
55.5
|
1.0
|
CA
|
D:MET55
|
4.0
|
51.4
|
1.0
|
C
|
D:THR83
|
4.3
|
38.4
|
1.0
|
SD
|
D:MET55
|
4.3
|
59.2
|
1.0
|
C
|
D:BFD53
|
4.3
|
45.2
|
1.0
|
CG1
|
D:ILE54
|
4.3
|
46.4
|
1.0
|
MG
|
D:MG201
|
4.4
|
44.1
|
1.0
|
O
|
A:HOH653
|
4.4
|
46.7
|
1.0
|
CA
|
D:BFD53
|
4.6
|
42.8
|
1.0
|
CG2
|
D:ILE54
|
4.6
|
49.9
|
1.0
|
O
|
D:MET55
|
4.6
|
49.7
|
1.0
|
CB
|
D:BFD53
|
4.6
|
42.5
|
1.0
|
N
|
D:LYS85
|
4.6
|
47.0
|
1.0
|
CB
|
D:ALA84
|
4.7
|
41.9
|
1.0
|
CA
|
D:ALA84
|
4.7
|
41.7
|
1.0
|
C
|
D:MET55
|
4.8
|
51.3
|
1.0
|
O
|
D:LEU82
|
4.9
|
37.2
|
1.0
|
CG2
|
D:THR83
|
4.9
|
41.0
|
1.0
|
NZ
|
D:LYS105
|
5.0
|
39.6
|
1.0
|
|
Reference:
C.Mideros-Mora,
L.Miguel-Romero,
A.Felipe-Ruiz,
P.Casino,
A.Marina.
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
|