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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:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom

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

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