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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:

Magnesium (Mg) 2 atoms

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:

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

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