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Fluorine in PDB 5dkf: Reaction of Phosphorylated Chey with Imidazole 3 of 3

Protein crystallography data

The structure of Reaction of Phosphorylated Chey with Imidazole 3 of 3, PDB code: 5dkf was solved by S.Page, R.E.Silversmith, R.B.Bourret, E.J.Collins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.30 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.580, 53.740, 162.610, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 17.8

Other elements in 5dkf:

The structure of Reaction of Phosphorylated Chey with Imidazole 3 of 3 also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Reaction of Phosphorylated Chey with Imidazole 3 of 3 (pdb code 5dkf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Reaction of Phosphorylated Chey with Imidazole 3 of 3, PDB code: 5dkf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5dkf

Go back to Fluorine Binding Sites List in 5dkf
Fluorine binding site 1 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 3 of 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Reaction of Phosphorylated Chey with Imidazole 3 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:12.8
occ:1.00
 F1 A:BEF202 0.0 12.8 1.0
BE A:BEF202 1.5 16.4 1.0
MN A:MN201 2.2 12.9 1.0
F3 A:BEF202 2.6 12.6 1.0
F2 A:BEF202 2.6 13.4 1.0
OD1 A:ASP57 2.7 12.2 1.0
N3 A:IMD204 3.0 22.1 0.8
OD2 A:ASP57 3.0 12.1 1.0
C5 A:IMD203 3.0 23.2 0.8
O A:HOH312 3.1 11.2 1.0
N1 A:IMD203 3.1 16.1 0.8
CG A:ASP57 3.2 11.1 1.0
O A:LYS59 3.2 11.5 1.0
CB A:LYS59 3.4 15.7 1.0
N A:LYS59 3.6 11.6 1.0
CA A:LYS59 3.8 12.6 1.0
C2 A:IMD204 3.9 20.2 0.8
C A:LYS59 3.9 13.0 1.0
C4 A:IMD204 3.9 20.0 0.8
NZ A:LYS109 4.1 12.1 1.0
OD1 A:ASP13 4.3 13.2 1.0
C4 A:IMD203 4.4 22.6 0.8
CG A:LYS59 4.4 20.8 1.0
C2 A:IMD203 4.5 22.8 0.8
N A:TRP58 4.7 9.8 1.0
C A:TRP58 4.7 11.0 1.0
CB A:ASP57 4.7 10.2 1.0
CD A:LYS59 4.7 26.5 1.0
OE1 A:GLN14 5.0 20.4 1.0
OG1 A:THR87 5.0 10.5 1.0

Fluorine binding site 2 out of 6 in 5dkf

Go back to Fluorine Binding Sites List in 5dkf
Fluorine binding site 2 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 3 of 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Reaction of Phosphorylated Chey with Imidazole 3 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:13.4
occ:1.00
 F2 A:BEF202 0.0 13.4 1.0
BE A:BEF202 1.6 16.4 1.0
OG1 A:THR87 2.6 10.5 1.0
OD1 A:ASP57 2.6 12.2 1.0
F3 A:BEF202 2.6 12.6 1.0
F1 A:BEF202 2.6 12.8 1.0
N A:LYS59 2.8 11.6 1.0
N A:TRP58 3.1 9.8 1.0
CB A:TRP58 3.3 10.7 1.0
CB A:THR87 3.4 10.1 1.0
CA A:TRP58 3.5 10.7 1.0
C2 A:IMD204 3.5 20.2 0.8
N3 A:IMD204 3.5 22.1 0.8
CG A:ASP57 3.6 11.1 1.0
C A:TRP58 3.6 11.0 1.0
CB A:LYS59 3.8 15.7 1.0
CA A:THR87 3.8 10.2 1.0
CA A:LYS59 3.9 12.6 1.0
N A:ALA88 3.9 11.7 1.0
CD2 A:TYR89 4.1 17.4 1.0
OD2 A:ASP57 4.2 12.1 1.0
CE2 A:TYR89 4.2 17.8 1.0
C A:ASP57 4.3 9.3 1.0
C A:THR87 4.4 11.2 1.0
MN A:MN201 4.5 12.9 1.0
CG A:TRP58 4.5 11.0 1.0
CA A:ASP57 4.6 9.3 1.0
O A:LYS59 4.6 11.5 1.0
CB A:ASP57 4.7 10.2 1.0
N A:TYR89 4.7 13.0 1.0
C A:LYS59 4.7 13.0 1.0
CG2 A:THR87 4.7 10.3 1.0
O A:TRP58 4.8 10.7 1.0
CG A:TYR89 4.8 16.4 1.0
C4 A:IMD204 4.9 20.0 0.8
N1 A:IMD204 4.9 28.8 0.8
O A:VAL86 4.9 9.4 1.0
CA A:ALA88 4.9 13.3 1.0
NZ A:LYS109 5.0 12.1 1.0

Fluorine binding site 3 out of 6 in 5dkf

Go back to Fluorine Binding Sites List in 5dkf
Fluorine binding site 3 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 3 of 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Reaction of Phosphorylated Chey with Imidazole 3 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:12.6
occ:1.00
 F3 A:BEF202 0.0 12.6 1.0
BE A:BEF202 1.5 16.4 1.0
F1 A:BEF202 2.6 12.8 1.0
F2 A:BEF202 2.6 13.4 1.0
OD1 A:ASP57 2.7 12.2 1.0
N A:ALA88 2.8 11.7 1.0
NZ A:LYS109 2.8 12.1 1.0
CE A:LYS109 3.3 12.1 1.0
CD A:LYS109 3.3 12.6 1.0
CA A:THR87 3.4 10.2 1.0
N3 A:IMD204 3.4 22.1 0.8
C A:THR87 3.5 11.2 1.0
CB A:ALA88 3.7 15.5 1.0
OG1 A:THR87 3.7 10.5 1.0
CA A:ALA88 3.8 13.3 1.0
CG A:ASP57 3.8 11.1 1.0
O A:HOH312 4.0 11.2 1.0
C2 A:IMD204 4.0 20.2 0.8
CB A:THR87 4.1 10.1 1.0
OD2 A:ASP57 4.4 12.1 1.0
MN A:MN201 4.4 12.9 1.0
O A:VAL86 4.4 9.4 1.0
C4 A:IMD204 4.4 20.0 0.8
CG A:LYS109 4.5 12.8 1.0
N A:THR87 4.5 10.0 1.0
O A:THR87 4.7 10.9 1.0
O A:HOH340 4.7 19.3 1.0
C5 A:IMD203 4.8 23.2 0.8
C A:ALA88 4.9 14.1 1.0
C A:VAL86 4.9 9.2 1.0
N A:TYR89 4.9 13.0 1.0
N A:TRP58 4.9 9.8 1.0

Fluorine binding site 4 out of 6 in 5dkf

Go back to Fluorine Binding Sites List in 5dkf
Fluorine binding site 4 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 3 of 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Reaction of Phosphorylated Chey with Imidazole 3 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:14.5
occ:1.00
 F1 B:BEF202 0.0 14.5 1.0
BE B:BEF202 1.5 13.7 1.0
MN B:MN201 2.2 14.4 1.0
F3 B:BEF202 2.6 10.7 1.0
F2 B:BEF202 2.6 11.8 1.0
OD1 B:ASP57 2.7 12.1 1.0
N3 B:IMD203 2.9 29.7 0.8
OD2 B:ASP57 3.0 12.4 1.0
C5 B:IMD204 3.0 24.9 0.8
N1 B:IMD204 3.1 20.1 0.8
O B:HOH312 3.1 11.3 1.0
O B:LYS59 3.1 12.7 1.0
CG B:ASP57 3.3 12.0 1.0
CB B:LYS59 3.3 18.4 1.0
O B:HOH409 3.5 29.4 1.0
N B:LYS59 3.6 13.0 1.0
CA B:LYS59 3.8 14.8 1.0
C4 B:IMD203 3.8 23.6 0.8
C B:LYS59 3.9 14.8 1.0
C2 B:IMD203 4.0 27.3 0.8
NZ B:LYS109 4.3 11.1 1.0
OD1 B:ASP13 4.3 13.8 1.0
C4 B:IMD204 4.4 26.9 0.8
CG B:LYS59 4.4 22.1 1.0
C2 B:IMD204 4.4 27.7 0.8
CD B:LYS59 4.7 27.9 1.0
C B:TRP58 4.7 11.7 1.0
N B:TRP58 4.7 10.4 1.0
CB B:ASP57 4.7 10.8 1.0
OE1 B:GLN14 5.0 22.7 1.0

Fluorine binding site 5 out of 6 in 5dkf

Go back to Fluorine Binding Sites List in 5dkf
Fluorine binding site 5 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 3 of 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Reaction of Phosphorylated Chey with Imidazole 3 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:11.8
occ:1.00
 F2 B:BEF202 0.0 11.8 1.0
BE B:BEF202 1.6 13.7 1.0
OD1 B:ASP57 2.5 12.1 1.0
F3 B:BEF202 2.6 10.7 1.0
OG1 B:THR87 2.6 11.9 1.0
F1 B:BEF202 2.6 14.5 1.0
N B:LYS59 2.8 13.0 1.0
N B:TRP58 3.1 10.4 1.0
CB B:TRP58 3.3 11.6 1.0
CB B:THR87 3.4 12.3 1.0
C4 B:IMD203 3.4 23.6 0.8
CA B:TRP58 3.5 10.9 1.0
N3 B:IMD203 3.5 29.7 0.8
CG B:ASP57 3.6 12.0 1.0
C B:TRP58 3.6 11.7 1.0
CB B:LYS59 3.8 18.4 1.0
CA B:THR87 3.8 11.6 1.0
CA B:LYS59 3.9 14.8 1.0
N B:ALA88 4.0 13.6 1.0
OD2 B:ASP57 4.1 12.4 1.0
CD2 B:TYR89 4.1 18.4 1.0
C B:ASP57 4.3 9.6 1.0
CE2 B:TYR89 4.3 19.8 1.0
C B:THR87 4.4 13.2 1.0
MN B:MN201 4.4 14.4 1.0
CG B:TRP58 4.5 11.5 1.0
O B:LYS59 4.6 12.7 1.0
CA B:ASP57 4.6 10.2 1.0
CB B:ASP57 4.6 10.8 1.0
C B:LYS59 4.7 14.8 1.0
N B:TYR89 4.8 15.0 1.0
CG2 B:THR87 4.8 12.9 1.0
O B:TRP58 4.8 11.4 1.0
C5 B:IMD203 4.8 32.5 0.8
O B:VAL86 4.8 10.8 1.0
CG B:TYR89 4.9 18.8 1.0
C2 B:IMD203 4.9 27.3 0.8
O B:HOH409 5.0 29.4 1.0
NZ B:LYS109 5.0 11.1 1.0

Fluorine binding site 6 out of 6 in 5dkf

Go back to Fluorine Binding Sites List in 5dkf
Fluorine binding site 6 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 3 of 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Reaction of Phosphorylated Chey with Imidazole 3 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:10.7
occ:1.00
 F3 B:BEF202 0.0 10.7 1.0
BE B:BEF202 1.6 13.7 1.0
F2 B:BEF202 2.6 11.8 1.0
OD1 B:ASP57 2.6 12.1 1.0
F1 B:BEF202 2.6 14.5 1.0
O B:HOH409 2.8 29.4 1.0
NZ B:LYS109 2.9 11.1 1.0
N B:ALA88 2.9 13.6 1.0
CE B:LYS109 3.3 11.8 1.0
CD B:LYS109 3.4 12.6 1.0
CA B:THR87 3.5 11.6 1.0
N3 B:IMD203 3.5 29.7 0.8
C B:THR87 3.6 13.2 1.0
CG B:ASP57 3.8 12.0 1.0
OG1 B:THR87 3.8 11.9 1.0
CB B:ALA88 3.8 17.0 1.0
O B:HOH312 3.9 11.3 1.0
CA B:ALA88 3.9 15.5 1.0
C4 B:IMD203 3.9 23.6 0.8
CB B:THR87 4.1 12.3 1.0
OD2 B:ASP57 4.3 12.4 1.0
MN B:MN201 4.3 14.4 1.0
O B:VAL86 4.4 10.8 1.0
C2 B:IMD203 4.5 27.3 0.8
CG B:LYS109 4.5 12.6 1.0
N B:THR87 4.6 11.1 1.0
C5 B:IMD204 4.7 24.9 0.8
O B:THR87 4.8 12.0 1.0
N B:TRP58 4.9 10.4 1.0
C B:ALA88 4.9 16.1 1.0
N B:TYR89 4.9 15.0 1.0
C B:VAL86 4.9 10.5 1.0
CB B:ASP57 5.0 10.8 1.0

Reference:

S.C.Page, R.E.Silversmith, E.J.Collins, R.B.Bourret. Imidazole As A Small Molecule Analogue in Two-Component Signal Transduction. Biochemistry V. 54 7248 2015.
ISSN: ISSN 0006-2960
PubMed: 26569142
DOI: 10.1021/ACS.BIOCHEM.5B01082
Page generated: Tue Jul 15 03:02:54 2025

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