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Fluorine in PDB 6rfv: Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7

Protein crystallography data

The structure of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7, PDB code: 6rfv 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) 30.00 / 2.83
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 68.673, 93.579, 172.703, 90.00, 93.32, 90.00
R / Rfree (%) 24.3 / 30.9

Other elements in 6rfv:

The structure of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7 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 7 (pdb code 6rfv). 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 7, PDB code: 6rfv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6rfv

Go back to Fluorine Binding Sites List in 6rfv
Fluorine binding site 1 out of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F53

b:45.4
occ:0.80
 F1 C:BFD53 0.0 45.4 0.8
BE C:BFD53 1.5 48.1 0.8
MG C:MG201 1.9 50.5 1.0
F2 C:BFD53 2.4 51.9 0.8
O C:MET55 2.6 47.2 1.0
F3 C:BFD53 2.6 46.9 0.8
OD2 C:BFD53 2.6 38.3 1.0
O C:HOH306 2.8 37.2 1.0
OD1 C:BFD53 3.1 35.3 1.0
CG C:BFD53 3.3 37.3 1.0
CB C:MET55 3.4 52.7 1.0
C C:MET55 3.5 50.2 1.0
CA C:MET55 3.7 50.5 1.0
N C:MET55 3.7 47.2 1.0
OD1 C:ASP10 3.8 50.5 1.0
O C:HOH320 3.9 41.0 1.0
O A:HOH637 4.1 30.8 1.0
SD C:MET55 4.2 57.1 1.0
CG C:MET55 4.3 55.0 1.0
O A:HOH630 4.6 29.5 1.0
OD2 C:ASP9 4.6 45.2 1.0
CB C:BFD53 4.7 37.9 1.0
N C:MET56 4.7 53.1 1.0
C C:ILE54 4.7 46.2 1.0
NZ C:LYS105 4.7 33.7 1.0
CG C:ASP10 4.8 52.0 1.0

Fluorine binding site 2 out of 6 in 6rfv

Go back to Fluorine Binding Sites List in 6rfv
Fluorine binding site 2 out of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F53

b:51.9
occ:0.80
 F2 C:BFD53 0.0 51.9 0.8
BE C:BFD53 1.5 48.1 0.8
F1 C:BFD53 2.4 45.4 0.8
F3 C:BFD53 2.5 46.9 0.8
OD1 C:BFD53 2.5 35.3 1.0
CE C:LYS105 3.0 34.1 1.0
NZ C:LYS105 3.1 33.7 1.0
O A:HOH637 3.2 30.8 1.0
N C:ALA84 3.3 38.9 1.0
CG C:BFD53 3.4 37.3 1.0
MG C:MG201 3.4 50.5 1.0
OD2 C:BFD53 3.5 38.3 1.0
CB C:ALA84 3.7 42.0 1.0
O C:HOH320 3.8 41.0 1.0
OG1 C:THR83 3.9 38.6 1.0
CA C:THR83 4.0 38.1 1.0
C C:THR83 4.1 38.0 1.0
CA C:ALA84 4.1 40.9 1.0
OD2 C:ASP9 4.3 45.2 1.0
CD C:LYS105 4.5 32.9 1.0
CB C:THR83 4.6 38.9 1.0
O C:LEU82 4.7 38.7 1.0
SD C:MET55 4.7 57.1 1.0
CB C:BFD53 4.7 37.9 1.0
O C:MET55 4.8 47.2 1.0
O C:HOH306 4.9 37.2 1.0
O C:HOH323 4.9 36.0 1.0
N C:MET55 4.9 47.2 1.0

Fluorine binding site 3 out of 6 in 6rfv

Go back to Fluorine Binding Sites List in 6rfv
Fluorine binding site 3 out of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F53

b:46.9
occ:0.80
 F3 C:BFD53 0.0 46.9 0.8
BE C:BFD53 1.5 48.1 0.8
F2 C:BFD53 2.5 51.9 0.8
OD1 C:BFD53 2.5 35.3 1.0
F1 C:BFD53 2.6 45.4 0.8
N C:MET55 2.7 47.2 1.0
OG1 C:THR83 2.9 38.6 1.0
N C:ILE54 3.3 43.1 1.0
CG C:BFD53 3.3 37.3 1.0
CB C:MET55 3.4 52.7 1.0
CG C:MET55 3.5 55.0 1.0
SD C:MET55 3.5 57.1 1.0
C C:ILE54 3.5 46.2 1.0
CA C:MET55 3.5 50.5 1.0
CB C:ILE54 3.6 47.0 1.0
OD2 C:BFD53 3.6 38.3 1.0
CA C:ILE54 3.7 45.6 1.0
O C:MET55 4.0 47.2 1.0
CB C:THR83 4.0 38.9 1.0
N C:ALA84 4.1 38.9 1.0
C C:MET55 4.2 50.2 1.0
CA C:THR83 4.3 38.1 1.0
MG C:MG201 4.3 50.5 1.0
CG1 C:ILE54 4.4 46.9 1.0
C C:BFD53 4.4 42.6 1.0
CB C:BFD53 4.6 37.9 1.0
O C:ILE54 4.6 47.1 1.0
CG2 C:ILE54 4.7 49.6 1.0
CA C:BFD53 4.7 39.3 1.0
C C:THR83 4.8 38.0 1.0
CG C:LYS85 4.8 50.7 1.0
CB C:ALA84 4.9 42.0 1.0
N C:LYS85 5.0 45.5 1.0

Fluorine binding site 4 out of 6 in 6rfv

Go back to Fluorine Binding Sites List in 6rfv
Fluorine binding site 4 out of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F53

b:45.4
occ:0.80
 F1 D:BFD53 0.0 45.4 0.8
BE D:BFD53 1.5 44.6 0.8
F2 D:BFD53 2.4 45.2 0.8
NZ D:LYS105 2.4 39.4 1.0
F3 D:BFD53 2.6 43.4 0.8
OD1 D:BFD53 2.9 42.4 1.0
N D:ALA84 3.1 42.6 1.0
CD D:LYS105 3.1 37.0 1.0
CE D:LYS105 3.4 37.5 1.0
CB D:ALA84 3.4 43.4 1.0
O D:HOH301 3.6 32.6 1.0
CG D:BFD53 3.8 43.8 1.0
CA D:THR83 3.8 43.0 1.0
C D:THR83 3.9 42.5 1.0
CA D:ALA84 3.9 43.4 1.0
OD2 D:BFD53 4.0 44.5 1.0
O D:HOH303 4.0 37.8 1.0
OG1 D:THR83 4.1 46.1 1.0
MG D:MG201 4.2 35.4 1.0
OD2 D:ASP9 4.3 44.8 1.0
O D:LEU82 4.5 44.4 1.0
CG D:LYS105 4.6 36.5 1.0
CB D:THR83 4.6 45.0 1.0
N D:THR83 4.9 42.8 1.0
O D:THR83 4.9 42.0 1.0

Fluorine binding site 5 out of 6 in 6rfv

Go back to Fluorine Binding Sites List in 6rfv
Fluorine binding site 5 out of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F53

b:45.2
occ:0.80
 F2 D:BFD53 0.0 45.2 0.8
BE D:BFD53 1.5 44.6 0.8
OD1 D:BFD53 2.4 42.4 1.0
OG1 D:THR83 2.4 46.1 1.0
F1 D:BFD53 2.4 45.4 0.8
F3 D:BFD53 2.5 43.4 0.8
N D:ALA84 3.2 42.6 1.0
CB D:THR83 3.4 45.0 1.0
N D:MET55 3.4 51.2 1.0
CG D:BFD53 3.5 43.8 1.0
N D:ILE54 3.5 47.4 1.0
CA D:THR83 3.5 43.0 1.0
CB D:ILE54 3.9 49.2 1.0
C D:THR83 3.9 42.5 1.0
OD2 D:BFD53 4.0 44.5 1.0
CA D:ILE54 4.1 49.5 1.0
CB D:MET55 4.1 55.7 1.0
C D:ILE54 4.2 50.8 1.0
SD D:MET55 4.3 60.8 1.0
CA D:ALA84 4.3 43.4 1.0
CA D:MET55 4.3 54.5 1.0
CB D:ALA84 4.3 43.4 1.0
N D:LYS85 4.3 48.0 1.0
NZ D:LYS105 4.4 39.4 1.0
CG D:MET55 4.5 57.6 1.0
CG1 D:ILE54 4.5 48.4 1.0
C D:BFD53 4.6 47.2 1.0
O D:MET55 4.6 52.4 1.0
CB D:BFD53 4.7 44.7 1.0
CA D:BFD53 4.7 44.8 1.0
MG D:MG201 4.7 35.4 1.0
CG2 D:THR83 4.8 45.1 1.0
O D:LEU82 4.8 44.4 1.0
C D:ALA84 4.8 46.2 1.0
N D:THR83 4.8 42.8 1.0
C D:MET55 4.9 54.4 1.0
O D:HOH301 4.9 32.6 1.0
CG2 D:ILE54 4.9 51.3 1.0
CD D:LYS105 5.0 37.0 1.0

Fluorine binding site 6 out of 6 in 6rfv

Go back to Fluorine Binding Sites List in 6rfv
Fluorine binding site 6 out of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F53

b:43.4
occ:0.80
 F3 D:BFD53 0.0 43.4 0.8
BE D:BFD53 1.5 44.6 0.8
MG D:MG201 2.3 35.4 1.0
F2 D:BFD53 2.5 45.2 0.8
F1 D:BFD53 2.6 45.4 0.8
OD2 D:BFD53 2.6 44.5 1.0
OD1 D:BFD53 2.7 42.4 1.0
O D:MET55 2.8 52.4 1.0
CG D:BFD53 3.0 43.8 1.0
O D:HOH301 3.0 32.6 1.0
CB D:MET55 3.4 55.7 1.0
N D:MET55 3.6 51.2 1.0
C D:MET55 3.6 54.4 1.0
CA D:MET55 3.7 54.5 1.0
OD1 D:ASP10 4.0 55.1 1.0
NZ D:LYS105 4.3 39.4 1.0
CG D:MET55 4.4 57.6 1.0
SD D:MET55 4.5 60.8 1.0
CB D:BFD53 4.5 44.7 1.0
N D:ILE54 4.6 47.4 1.0
C D:ILE54 4.6 50.8 1.0
OD2 D:ASP9 4.8 44.8 1.0
OG1 D:THR83 4.9 46.1 1.0
N D:MET56 4.9 56.1 1.0
CG D:ASP10 5.0 56.1 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 01:09:38 2024

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