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Fluorine in PDB 5d2c: Reaction of Phosphorylated Chey with Imidazole 1 of 3

Protein crystallography data

The structure of Reaction of Phosphorylated Chey with Imidazole 1 of 3, PDB code: 5d2c 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) 81.20 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.620, 53.720, 162.450, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.5

Other elements in 5d2c:

The structure of Reaction of Phosphorylated Chey with Imidazole 1 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 1 of 3 (pdb code 5d2c). 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 1 of 3, PDB code: 5d2c:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5d2c

Go back to Fluorine Binding Sites List in 5d2c
Fluorine binding site 1 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 1 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 1 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:27.5
occ:1.00
 F1 A:BEF202 0.0 27.5 1.0
BE A:BEF202 1.5 26.5 1.0
MN A:MN201 2.2 29.4 1.0
F3 A:BEF202 2.6 24.2 1.0
F2 A:BEF202 2.6 27.1 1.0
OD1 A:ASP57 2.6 28.8 1.0
OD2 A:ASP57 2.9 28.8 1.0
N3 A:IMD204 3.0 37.1 0.8
CG A:ASP57 3.1 25.6 1.0
O A:HOH302 3.1 26.6 1.0
C5 A:IMD203 3.2 42.8 0.9
O A:LYS59 3.2 25.5 1.0
N1 A:IMD203 3.3 33.5 0.9
CB A:LYS59 3.3 32.0 1.0
N A:LYS59 3.5 27.6 1.0
C2 A:IMD204 3.7 33.6 0.8
CA A:LYS59 3.7 28.9 1.0
C A:LYS59 3.9 30.3 1.0
NZ A:LYS109 4.1 28.2 1.0
C4 A:IMD204 4.1 38.2 0.8
OD1 A:ASP13 4.4 28.8 1.0
CG A:LYS59 4.4 37.2 1.0
C4 A:IMD203 4.5 41.6 0.9
N A:TRP58 4.6 26.1 1.0
C A:TRP58 4.6 25.0 1.0
CB A:ASP57 4.6 24.6 1.0
C2 A:IMD203 4.6 44.0 0.9
CD A:LYS59 4.8 45.6 1.0
OG1 A:THR87 4.9 25.8 1.0
N1 A:IMD204 5.0 36.7 0.8
OE1 A:GLN14 5.0 35.1 1.0

Fluorine binding site 2 out of 6 in 5d2c

Go back to Fluorine Binding Sites List in 5d2c
Fluorine binding site 2 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 1 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 1 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:27.1
occ:1.00
 F2 A:BEF202 0.0 27.1 1.0
BE A:BEF202 1.6 26.5 1.0
OD1 A:ASP57 2.5 28.8 1.0
OG1 A:THR87 2.6 25.8 1.0
F1 A:BEF202 2.6 27.5 1.0
F3 A:BEF202 2.6 24.2 1.0
N A:LYS59 2.8 27.6 1.0
N A:TRP58 3.0 26.1 1.0
CB A:TRP58 3.2 25.6 1.0
N3 A:IMD204 3.3 37.1 0.8
CB A:THR87 3.3 26.9 1.0
CA A:TRP58 3.4 27.6 1.0
CG A:ASP57 3.5 25.6 1.0
C A:TRP58 3.5 25.0 1.0
C4 A:IMD204 3.7 38.2 0.8
CB A:LYS59 3.8 32.0 1.0
CA A:THR87 3.8 24.9 1.0
CA A:LYS59 3.8 28.9 1.0
N A:ALA88 4.0 25.1 1.0
CD2 A:TYR89 4.1 33.2 1.0
OD2 A:ASP57 4.1 28.8 1.0
C A:ASP57 4.2 24.5 1.0
CE2 A:TYR89 4.3 33.0 1.0
C A:THR87 4.4 25.3 1.0
CG A:TRP58 4.4 24.3 1.0
MN A:MN201 4.5 29.4 1.0
CA A:ASP57 4.6 23.1 1.0
C2 A:IMD204 4.6 33.6 0.8
CB A:ASP57 4.6 24.6 1.0
O A:LYS59 4.6 25.5 1.0
C A:LYS59 4.7 30.3 1.0
CG2 A:THR87 4.7 27.9 1.0
O A:TRP58 4.8 26.4 1.0
N A:TYR89 4.8 27.4 1.0
O A:VAL86 4.8 24.2 1.0
CG A:TYR89 4.9 35.1 1.0
NZ A:LYS109 5.0 28.2 1.0

Fluorine binding site 3 out of 6 in 5d2c

Go back to Fluorine Binding Sites List in 5d2c
Fluorine binding site 3 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 1 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 1 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:24.2
occ:1.00
 F3 A:BEF202 0.0 24.2 1.0
BE A:BEF202 1.5 26.5 1.0
F1 A:BEF202 2.6 27.5 1.0
F2 A:BEF202 2.6 27.1 1.0
OD1 A:ASP57 2.7 28.8 1.0
NZ A:LYS109 2.8 28.2 1.0
N A:ALA88 2.8 25.1 1.0
CE A:LYS109 3.3 27.5 1.0
N3 A:IMD204 3.3 37.1 0.8
CD A:LYS109 3.3 29.0 1.0
CA A:THR87 3.4 24.9 1.0
C A:THR87 3.6 25.3 1.0
OG1 A:THR87 3.7 25.8 1.0
CB A:ALA88 3.8 30.3 1.0
CG A:ASP57 3.8 25.6 1.0
CA A:ALA88 3.8 27.8 1.0
O A:HOH302 3.9 26.6 1.0
C4 A:IMD204 4.0 38.2 0.8
CB A:THR87 4.0 26.9 1.0
C2 A:IMD204 4.2 33.6 0.8
OD2 A:ASP57 4.3 28.8 1.0
O A:VAL86 4.4 24.2 1.0
MN A:MN201 4.4 29.4 1.0
CG A:LYS109 4.5 29.3 1.0
N A:THR87 4.5 26.1 1.0
O A:HOH334 4.7 35.1 1.0
C5 A:IMD203 4.7 42.8 0.9
O A:THR87 4.8 25.5 1.0
C A:ALA88 4.9 28.3 1.0
C A:VAL86 4.9 24.6 1.0
N A:TRP58 4.9 26.1 1.0
N A:TYR89 4.9 27.4 1.0

Fluorine binding site 4 out of 6 in 5d2c

Go back to Fluorine Binding Sites List in 5d2c
Fluorine binding site 4 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 1 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 1 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:28.9
occ:1.00
 F1 B:BEF202 0.0 28.9 1.0
BE B:BEF202 1.5 27.0 1.0
MN B:MN201 2.1 30.6 1.0
F3 B:BEF202 2.5 30.3 1.0
F2 B:BEF202 2.5 24.9 1.0
OD1 B:ASP57 2.5 29.5 1.0
OD2 B:ASP57 2.8 28.8 1.0
O B:HOH306 2.9 26.9 1.0
CG B:ASP57 3.0 28.6 1.0
O B:LYS59 3.2 29.9 1.0
C2 B:IMD203 3.2 50.2 1.0
N3 B:IMD204 3.3 44.0 0.9
N1 B:IMD203 3.4 44.0 1.0
CB B:LYS59 3.4 32.9 1.0
O B:HOH386 3.4 46.8 1.0
C2 B:IMD204 3.5 44.9 0.9
N B:LYS59 3.6 27.8 1.0
CA B:LYS59 3.8 30.1 1.0
C B:LYS59 3.9 30.7 1.0
NZ B:LYS109 4.1 28.7 1.0
OD1 B:ASP13 4.3 31.3 1.0
CG B:LYS59 4.5 39.9 1.0
N3 B:IMD203 4.5 52.6 1.0
CB B:ASP57 4.5 25.7 1.0
N B:TRP58 4.6 26.1 1.0
C B:TRP58 4.6 26.6 1.0
C4 B:IMD204 4.6 47.3 0.9
C5 B:IMD203 4.8 53.3 1.0
N1 B:IMD204 4.8 49.3 0.9
CD B:LYS59 4.8 46.5 1.0
OG1 B:THR87 5.0 28.4 1.0

Fluorine binding site 5 out of 6 in 5d2c

Go back to Fluorine Binding Sites List in 5d2c
Fluorine binding site 5 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 1 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 1 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:24.9
occ:1.00
 F2 B:BEF202 0.0 24.9 1.0
BE B:BEF202 1.5 27.0 1.0
OD1 B:ASP57 2.5 29.5 1.0
F1 B:BEF202 2.5 28.9 1.0
F3 B:BEF202 2.5 30.3 1.0
OG1 B:THR87 2.7 28.4 1.0
N B:LYS59 2.7 27.8 1.0
N B:TRP58 3.1 26.1 1.0
N3 B:IMD204 3.3 44.0 0.9
CB B:TRP58 3.3 27.8 1.0
CA B:TRP58 3.4 24.8 1.0
CB B:THR87 3.5 28.7 1.0
CG B:ASP57 3.5 28.6 1.0
C B:TRP58 3.5 26.6 1.0
CB B:LYS59 3.7 32.9 1.0
CA B:LYS59 3.8 30.1 1.0
CA B:THR87 3.9 26.3 1.0
OD2 B:ASP57 4.0 28.8 1.0
N B:ALA88 4.0 27.5 1.0
CD2 B:TYR89 4.1 36.8 1.0
C4 B:IMD204 4.1 47.3 0.9
C B:ASP57 4.2 24.5 1.0
C2 B:IMD204 4.3 44.9 0.9
CE2 B:TYR89 4.3 38.6 1.0
MN B:MN201 4.4 30.6 1.0
C B:THR87 4.5 28.0 1.0
CG B:TRP58 4.5 27.4 1.0
O B:LYS59 4.5 29.9 1.0
CA B:ASP57 4.5 26.0 1.0
CB B:ASP57 4.6 25.7 1.0
C B:LYS59 4.6 30.7 1.0
O B:TRP58 4.7 26.8 1.0
N B:TYR89 4.8 27.9 1.0
CG2 B:THR87 4.8 29.5 1.0
O B:VAL86 4.8 27.0 1.0
O B:HOH386 4.9 46.8 1.0
CG B:TYR89 4.9 35.9 1.0
NZ B:LYS109 5.0 28.7 1.0

Fluorine binding site 6 out of 6 in 5d2c

Go back to Fluorine Binding Sites List in 5d2c
Fluorine binding site 6 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 1 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 1 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:30.3
occ:1.00
 F3 B:BEF202 0.0 30.3 1.0
BE B:BEF202 1.5 27.0 1.0
F1 B:BEF202 2.5 28.9 1.0
F2 B:BEF202 2.5 24.9 1.0
OD1 B:ASP57 2.6 29.5 1.0
N B:ALA88 2.8 27.5 1.0
O B:HOH386 2.9 46.8 1.0
NZ B:LYS109 2.9 28.7 1.0
N3 B:IMD204 3.3 44.0 0.9
CE B:LYS109 3.3 29.9 1.0
CA B:THR87 3.4 26.3 1.0
CD B:LYS109 3.4 29.8 1.0
C B:THR87 3.6 28.0 1.0
OG1 B:THR87 3.6 28.4 1.0
CG B:ASP57 3.7 28.6 1.0
CB B:ALA88 3.8 34.6 1.0
C2 B:IMD204 3.9 44.9 0.9
CA B:ALA88 3.9 31.4 1.0
O B:HOH306 3.9 26.9 1.0
CB B:THR87 4.0 28.7 1.0
OD2 B:ASP57 4.2 28.8 1.0
O B:VAL86 4.3 27.0 1.0
MN B:MN201 4.4 30.6 1.0
C4 B:IMD204 4.4 47.3 0.9
CG B:LYS109 4.5 30.2 1.0
N B:THR87 4.6 25.5 1.0
O B:THR87 4.8 27.1 1.0
N B:TRP58 4.8 26.1 1.0
O B:HOH327 4.9 35.4 1.0
N B:TYR89 4.9 27.9 1.0
C B:ALA88 4.9 30.6 1.0
C2 B:IMD203 4.9 50.2 1.0
C B:VAL86 4.9 25.6 1.0
CB B:ASP57 4.9 25.7 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: Thu Aug 1 08:39:03 2024

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