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Fluorine in PDB 6rgy: Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5

Protein crystallography data

The structure of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5, PDB code: 6rgy 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) 87.11 / 2.20
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 68.470, 92.710, 174.522, 90.00, 93.39, 90.00
R / Rfree (%) 18.6 / 22.7

Other elements in 6rgy:

The structure of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5 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 7.5 (pdb code 6rgy). 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 7.5, PDB code: 6rgy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6rgy

Go back to Fluorine Binding Sites List in 6rgy
Fluorine binding site 1 out of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5


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

b:43.8
occ:1.00
 F1 C:BFD53 0.0 43.8 1.0
BE C:BFD53 1.7 39.9 1.0
MG C:MG201 1.8 42.9 1.0
OD1 C:BFD53 2.7 33.9 1.0
O C:HOH311 2.7 48.5 1.0
O C:HOH327 2.8 38.1 1.0
OD2 C:BFD53 2.8 40.2 1.0
F2 C:BFD53 2.8 42.5 1.0
O C:MET55 2.8 39.2 1.0
O A:HOH680 2.9 47.0 1.0
F3 C:BFD53 2.9 46.4 1.0
CG C:BFD53 3.1 37.8 1.0
CB C:MET55 3.5 44.1 1.0
C C:MET55 3.7 40.2 1.0
N C:MET55 3.7 38.7 1.0
CA C:MET55 3.8 39.9 1.0
OD1 C:ASP10 3.8 45.1 1.0
O A:HOH684 4.1 43.8 1.0
NZ C:LYS105 4.3 35.0 1.0
CG C:MET55 4.4 49.6 1.0
CB C:BFD53 4.6 34.4 1.0
C C:ILE54 4.8 42.5 1.0
N C:ILE54 4.8 39.9 1.0
CG C:ASP10 4.8 46.8 1.0
OD1 C:ASP9 4.9 41.1 1.0
SD C:MET55 4.9 62.9 1.0
N C:MET56 4.9 42.6 1.0

Fluorine binding site 2 out of 6 in 6rgy

Go back to Fluorine Binding Sites List in 6rgy
Fluorine binding site 2 out of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5


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

b:42.5
occ:1.00
 F2 C:BFD53 0.0 42.5 1.0
BE C:BFD53 1.7 39.9 1.0
F1 C:BFD53 2.8 43.8 1.0
N C:ALA84 2.8 35.5 1.0
O A:HOH680 2.8 47.0 1.0
F3 C:BFD53 2.8 46.4 1.0
NZ C:LYS105 3.0 35.0 1.0
OD1 C:BFD53 3.1 33.9 1.0
CB C:ALA84 3.2 39.8 1.0
CD C:LYS105 3.4 33.4 1.0
CE C:LYS105 3.5 35.1 1.0
CA C:ALA84 3.6 39.7 1.0
C C:THR83 3.7 33.9 1.0
CA C:THR83 3.8 34.4 1.0
O C:HOH311 3.8 48.5 1.0
OG1 C:THR83 4.1 38.6 1.0
CG C:BFD53 4.2 37.8 1.0
MG C:MG201 4.4 42.9 1.0
CB C:THR83 4.5 36.6 1.0
OD2 C:BFD53 4.6 40.2 1.0
CG C:LYS105 4.6 33.1 1.0
O C:HOH334 4.7 28.7 1.0
O A:HOH684 4.7 43.8 1.0
C C:ALA84 4.7 41.8 1.0
N C:LYS85 4.8 44.7 1.0
O C:LEU82 4.8 38.5 1.0
O C:THR83 4.8 36.4 1.0
N C:THR83 4.9 36.1 1.0

Fluorine binding site 3 out of 6 in 6rgy

Go back to Fluorine Binding Sites List in 6rgy
Fluorine binding site 3 out of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5


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

b:46.4
occ:1.00
 F3 C:BFD53 0.0 46.4 1.0
BE C:BFD53 1.7 39.9 1.0
OG1 C:THR83 2.7 38.6 1.0
OD1 C:BFD53 2.8 33.9 1.0
F2 C:BFD53 2.8 42.5 1.0
N C:MET55 2.9 38.7 1.0
F1 C:BFD53 2.9 43.8 1.0
N C:ILE54 3.4 39.9 1.0
CG C:MET55 3.5 49.6 1.0
CB C:ILE54 3.5 40.6 1.0
CB C:MET55 3.6 44.1 1.0
CA C:ILE54 3.7 40.2 1.0
CB C:THR83 3.7 36.6 1.0
C C:ILE54 3.8 42.5 1.0
CA C:MET55 3.8 39.9 1.0
N C:ALA84 3.8 35.5 1.0
CG C:BFD53 3.9 37.8 1.0
CA C:THR83 4.1 34.4 1.0
SD C:MET55 4.2 62.9 1.0
OD2 C:BFD53 4.4 40.2 1.0
O A:HOH680 4.4 47.0 1.0
N C:LYS85 4.4 44.7 1.0
C C:THR83 4.4 33.9 1.0
CG1 C:ILE54 4.4 40.6 1.0
CG2 C:ILE54 4.4 43.7 1.0
O C:MET55 4.5 39.2 1.0
C C:BFD53 4.5 39.5 1.0
MG C:MG201 4.5 42.9 1.0
CD C:LYS85 4.6 65.8 1.0
C C:MET55 4.6 40.2 1.0
CB C:ALA84 4.7 39.8 1.0
CA C:ALA84 4.7 39.7 1.0
CA C:BFD53 4.9 37.9 1.0
CB C:LYS85 4.9 52.0 1.0
O C:ILE54 5.0 41.9 1.0
CB C:BFD53 5.0 34.4 1.0
CG2 C:THR83 5.0 36.8 1.0
CG C:LYS85 5.0 61.2 1.0

Fluorine binding site 4 out of 6 in 6rgy

Go back to Fluorine Binding Sites List in 6rgy
Fluorine binding site 4 out of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5


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

b:38.9
occ:1.00
 F1 D:BFD53 0.0 38.9 1.0
BE D:BFD53 1.7 38.0 1.0
MG D:MG201 1.9 41.3 1.0
O D:HOH319 2.5 38.0 1.0
OD1 D:BFD53 2.5 38.2 1.0
O D:HOH327 2.6 39.8 1.0
OD2 D:BFD53 2.7 41.1 1.0
F2 D:BFD53 2.7 41.1 1.0
O D:MET55 2.8 36.5 1.0
O B:HOH671 2.9 48.5 1.0
F3 D:BFD53 2.9 46.4 1.0
CG D:BFD53 3.0 39.6 1.0
CB D:MET55 3.6 47.3 1.0
N D:MET55 3.7 39.3 1.0
C D:MET55 3.7 41.5 1.0
CA D:MET55 3.8 42.1 1.0
OD1 D:ASP10 3.9 46.2 1.0
O B:HOH657 4.0 58.2 1.0
O B:HOH678 4.2 46.9 1.0
NZ D:LYS105 4.3 40.8 1.0
CB D:BFD53 4.5 36.8 1.0
OD1 D:ASP9 4.6 42.6 1.0
CG D:MET55 4.6 55.3 1.0
C D:ILE54 4.8 42.8 1.0
N D:ILE54 4.8 41.5 1.0
SD D:MET55 4.8 65.6 1.0
CG D:ASP10 4.9 46.3 1.0
O B:HOH614 5.0 55.0 1.0
N D:MET56 5.0 43.1 1.0

Fluorine binding site 5 out of 6 in 6rgy

Go back to Fluorine Binding Sites List in 6rgy
Fluorine binding site 5 out of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5


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

b:41.1
occ:1.00
 F2 D:BFD53 0.0 41.1 1.0
BE D:BFD53 1.7 38.0 1.0
F1 D:BFD53 2.7 38.9 1.0
NZ D:LYS105 2.8 40.8 1.0
F3 D:BFD53 2.8 46.4 1.0
O B:HOH671 2.9 48.5 1.0
N D:ALA84 2.9 35.1 1.0
OD1 D:BFD53 2.9 38.2 1.0
CD D:LYS105 3.3 36.0 1.0
CB D:ALA84 3.3 38.4 1.0
CE D:LYS105 3.4 39.2 1.0
O D:HOH319 3.7 38.0 1.0
CA D:THR83 3.7 34.8 1.0
CA D:ALA84 3.7 39.0 1.0
C D:THR83 3.7 34.7 1.0
O B:HOH614 3.8 55.0 1.0
CG D:BFD53 4.0 39.6 1.0
OG1 D:THR83 4.1 41.7 1.0
MG D:MG201 4.3 41.3 1.0
OD2 D:BFD53 4.4 41.1 1.0
CB D:THR83 4.5 38.8 1.0
O B:HOH622 4.5 54.8 1.0
O D:LEU82 4.6 39.5 1.0
CG D:LYS105 4.6 35.8 1.0
O D:HOH337 4.7 31.3 1.0
N D:THR83 4.7 36.8 1.0
O B:HOH678 4.8 46.9 1.0
C D:ALA84 4.9 41.9 1.0
O D:THR83 4.9 35.2 1.0
OD2 D:ASP9 4.9 44.1 1.0
N D:LYS85 5.0 45.0 1.0
O D:HOH327 5.0 39.8 1.0

Fluorine binding site 6 out of 6 in 6rgy

Go back to Fluorine Binding Sites List in 6rgy
Fluorine binding site 6 out of 6 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5


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

b:46.4
occ:1.00
 F3 D:BFD53 0.0 46.4 1.0
BE D:BFD53 1.7 38.0 1.0
OG1 D:THR83 2.6 41.7 1.0
OD1 D:BFD53 2.7 38.2 1.0
F2 D:BFD53 2.8 41.1 1.0
F1 D:BFD53 2.9 38.9 1.0
N D:MET55 2.9 39.3 1.0
N D:ILE54 3.4 41.5 1.0
CB D:ILE54 3.5 41.0 1.0
CB D:THR83 3.6 38.8 1.0
CA D:ILE54 3.7 40.8 1.0
CG D:BFD53 3.7 39.6 1.0
CB D:MET55 3.7 47.3 1.0
C D:ILE54 3.7 42.8 1.0
N D:ALA84 3.8 35.1 1.0
CG D:MET55 3.8 55.3 1.0
CA D:MET55 3.9 42.1 1.0
CA D:THR83 3.9 34.8 1.0
SD D:MET55 4.2 65.6 1.0
OD2 D:BFD53 4.3 41.1 1.0
CG1 D:ILE54 4.3 40.7 1.0
CG D:LYS85 4.4 58.2 1.0
C D:THR83 4.4 34.7 1.0
O B:HOH671 4.4 48.5 1.0
N D:LYS85 4.5 45.0 1.0
C D:BFD53 4.5 41.2 1.0
O D:MET55 4.5 36.5 1.0
MG D:MG201 4.5 41.3 1.0
CG2 D:ILE54 4.5 44.3 1.0
CB D:ALA84 4.6 38.4 1.0
C D:MET55 4.7 41.5 1.0
CA D:ALA84 4.7 39.0 1.0
CA D:BFD53 4.8 39.6 1.0
CB D:BFD53 4.8 36.8 1.0
O D:ILE54 4.9 43.3 1.0
CG2 D:THR83 5.0 37.4 1.0
O D:LEU82 5.0 39.5 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 01:11:13 2024

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