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Fluorine in PDB 5dgc: Reaction of Phosphorylated Chey with Imidazole 2 of 3

Protein crystallography data

The structure of Reaction of Phosphorylated Chey with Imidazole 2 of 3, PDB code: 5dgc 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) 26.43 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.490, 53.580, 161.980, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 18.9

Other elements in 5dgc:

The structure of Reaction of Phosphorylated Chey with Imidazole 2 of 3 also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 6 in 5dgc

Go back to Fluorine Binding Sites List in 5dgc
Fluorine binding site 1 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 2 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 2 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:21.1
occ:1.00
 F1 A:BEF201 0.0 21.1 1.0
BE A:BEF201 1.6 21.1 1.0
MN A:MN202 2.2 21.1 1.0
F2 A:BEF201 2.5 22.0 1.0
F3 A:BEF201 2.5 20.6 1.0
OD1 A:ASP57 2.6 21.7 1.0
OD2 A:ASP57 2.9 22.1 1.0
O A:HOH311 3.1 18.9 1.0
CG A:ASP57 3.1 21.0 1.0
O A:LYS59 3.1 19.6 1.0
C2 A:IMD204 3.2 27.1 0.8
C5 A:IMD203 3.2 32.2 0.9
N1 A:IMD203 3.3 28.6 0.9
CB A:LYS59 3.3 25.9 1.0
N A:LYS59 3.5 20.9 1.0
CA A:LYS59 3.7 21.5 1.0
C A:LYS59 3.8 22.4 1.0
N3 A:IMD204 4.1 26.9 0.8
N1 A:IMD204 4.1 28.5 0.8
NZ A:LYS109 4.1 21.6 1.0
OD1 A:ASP13 4.3 20.5 1.0
CG A:LYS59 4.3 31.4 1.0
C4 A:IMD203 4.5 30.0 0.9
N A:TRP58 4.6 19.3 1.0
C A:TRP58 4.6 19.4 1.0
CB A:ASP57 4.6 18.3 1.0
C2 A:IMD203 4.6 33.3 0.9
CD A:LYS59 4.7 35.7 1.0
OG1 A:THR87 4.9 18.6 1.0
OE1 A:GLN14 5.0 30.0 1.0

Fluorine binding site 2 out of 6 in 5dgc

Go back to Fluorine Binding Sites List in 5dgc
Fluorine binding site 2 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 2 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 2 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:22.0
occ:1.00
 F2 A:BEF201 0.0 22.0 1.0
BE A:BEF201 1.6 21.1 1.0
F1 A:BEF201 2.5 21.1 1.0
F3 A:BEF201 2.5 20.6 1.0
OG1 A:THR87 2.6 18.6 1.0
OD1 A:ASP57 2.6 21.7 1.0
N A:LYS59 2.8 20.9 1.0
N A:TRP58 3.1 19.3 1.0
CB A:TRP58 3.4 20.9 1.0
CB A:THR87 3.4 19.8 1.0
CA A:TRP58 3.5 20.5 1.0
C2 A:IMD204 3.5 27.1 0.8
N3 A:IMD204 3.5 26.9 0.8
CG A:ASP57 3.6 21.0 1.0
C A:TRP58 3.6 19.4 1.0
CB A:LYS59 3.7 25.9 1.0
CA A:THR87 3.8 20.9 1.0
N A:ALA88 3.8 20.1 1.0
CA A:LYS59 3.8 21.5 1.0
OD2 A:ASP57 4.1 22.1 1.0
CD2 A:TYR89 4.1 27.1 1.0
CE2 A:TYR89 4.3 26.9 1.0
C A:ASP57 4.3 19.1 1.0
C A:THR87 4.3 20.9 1.0
MN A:MN202 4.4 21.1 1.0
CG A:TRP58 4.5 21.3 1.0
O A:LYS59 4.6 19.6 1.0
CA A:ASP57 4.6 17.7 1.0
CB A:ASP57 4.7 18.3 1.0
N A:TYR89 4.7 20.2 1.0
C A:LYS59 4.7 22.4 1.0
CG2 A:THR87 4.8 20.7 1.0
O A:TRP58 4.8 20.3 1.0
O A:VAL86 4.8 20.1 1.0
N1 A:IMD204 4.9 28.5 0.8
CA A:ALA88 4.9 22.5 1.0
CG A:TYR89 4.9 25.2 1.0
C4 A:IMD204 4.9 26.5 0.8
NZ A:LYS109 4.9 21.6 1.0

Fluorine binding site 3 out of 6 in 5dgc

Go back to Fluorine Binding Sites List in 5dgc
Fluorine binding site 3 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 2 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 2 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:20.6
occ:1.00
 F3 A:BEF201 0.0 20.6 1.0
BE A:BEF201 1.6 21.1 1.0
F2 A:BEF201 2.5 22.0 1.0
F1 A:BEF201 2.5 21.1 1.0
OD1 A:ASP57 2.6 21.7 1.0
N A:ALA88 2.8 20.1 1.0
NZ A:LYS109 2.8 21.6 1.0
CE A:LYS109 3.2 21.6 1.0
CD A:LYS109 3.3 22.4 1.0
CA A:THR87 3.4 20.9 1.0
C2 A:IMD204 3.5 27.1 0.8
C A:THR87 3.5 20.9 1.0
CB A:ALA88 3.7 24.7 1.0
OG1 A:THR87 3.7 18.6 1.0
CA A:ALA88 3.8 22.5 1.0
CG A:ASP57 3.8 21.0 1.0
O A:HOH311 3.9 18.9 1.0
N3 A:IMD204 4.0 26.9 0.8
CB A:THR87 4.1 19.8 1.0
OD2 A:ASP57 4.3 22.1 1.0
MN A:MN202 4.3 21.1 1.0
O A:VAL86 4.4 20.1 1.0
CG A:LYS109 4.5 22.2 1.0
N1 A:IMD204 4.5 28.5 0.8
N A:THR87 4.5 21.0 1.0
O A:THR87 4.7 21.1 1.0
O A:HOH333 4.8 24.9 1.0
C5 A:IMD203 4.8 32.2 0.9
C A:ALA88 4.9 22.5 1.0
N A:TRP58 4.9 19.3 1.0
C A:VAL86 4.9 19.0 1.0
N A:TYR89 4.9 20.2 1.0
OD2 A:ASP12 5.0 20.4 1.0
CB A:ASP57 5.0 18.3 1.0

Fluorine binding site 4 out of 6 in 5dgc

Go back to Fluorine Binding Sites List in 5dgc
Fluorine binding site 4 out of 6 in the Reaction of Phosphorylated Chey with Imidazole 2 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 2 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:24.5
occ:1.00
 F1 B:BEF202 0.0 24.5 1.0
BE B:BEF202 1.5 22.2 1.0
MN B:MN201 2.1 22.7 1.0
F2 B:BEF202 2.5 20.8 1.0
F3 B:BEF202 2.5 22.7 1.0
OD1 B:ASP57 2.6 20.4 1.0
OD2 B:ASP57 2.9 21.1 1.0
O B:HOH307 2.9 22.9 1.0
N1 B:IMD203 3.1 31.1 0.8
CG B:ASP57 3.1 20.3 1.0
C2 B:IMD204 3.1 30.8 0.8
O B:LYS59 3.2 20.8 1.0
C2 B:IMD203 3.3 33.8 0.8
CB B:LYS59 3.4 25.4 1.0
O B:HOH399 3.5 36.7 1.0
N B:LYS59 3.6 21.3 1.0
CA B:LYS59 3.8 23.5 1.0
N3 B:IMD204 3.9 30.1 0.8
C B:LYS59 3.9 23.0 1.0
NZ B:LYS109 4.1 18.9 1.0
N1 B:IMD204 4.2 34.5 0.8
OD1 B:ASP13 4.3 22.2 1.0
C5 B:IMD203 4.4 33.8 0.8
CG B:LYS59 4.5 30.3 1.0
N B:TRP58 4.6 19.8 1.0
CB B:ASP57 4.6 20.8 1.0
C B:TRP58 4.6 22.1 1.0
N3 B:IMD203 4.6 37.0 0.8
CD B:LYS59 4.9 35.7 1.0
OE1 B:GLN14 4.9 28.2 1.0
OG1 B:THR87 5.0 20.5 1.0

Fluorine binding site 5 out of 6 in 5dgc

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

b:20.8
occ:1.00
 F2 B:BEF202 0.0 20.8 1.0
BE B:BEF202 1.5 22.2 1.0
F1 B:BEF202 2.5 24.5 1.0
F3 B:BEF202 2.5 22.7 1.0
OD1 B:ASP57 2.6 20.4 1.0
OG1 B:THR87 2.6 20.5 1.0
N B:LYS59 2.8 21.3 1.0
N B:TRP58 3.1 19.8 1.0
CB B:TRP58 3.4 21.0 1.0
N3 B:IMD204 3.4 30.1 0.8
CB B:THR87 3.4 20.9 1.0
CA B:TRP58 3.5 19.9 1.0
CG B:ASP57 3.5 20.3 1.0
C B:TRP58 3.6 22.1 1.0
C2 B:IMD204 3.6 30.8 0.8
CB B:LYS59 3.7 25.4 1.0
CA B:LYS59 3.8 23.5 1.0
CA B:THR87 3.8 20.6 1.0
N B:ALA88 3.9 22.8 1.0
OD2 B:ASP57 4.0 21.1 1.0
CD2 B:TYR89 4.1 27.7 1.0
C B:ASP57 4.3 18.5 1.0
CE2 B:TYR89 4.3 30.4 1.0
MN B:MN201 4.4 22.7 1.0
C B:THR87 4.4 21.6 1.0
O B:LYS59 4.5 20.8 1.0
CG B:TRP58 4.6 19.6 1.0
CA B:ASP57 4.6 19.0 1.0
CB B:ASP57 4.6 20.8 1.0
C B:LYS59 4.6 23.0 1.0
C4 B:IMD204 4.7 30.7 0.8
N B:TYR89 4.8 23.0 1.0
O B:TRP58 4.8 21.5 1.0
O B:VAL86 4.8 21.5 1.0
CG2 B:THR87 4.8 22.0 1.0
O B:HOH399 4.9 36.7 1.0
CG B:TYR89 4.9 27.4 1.0
N1 B:IMD204 4.9 34.5 0.8
NZ B:LYS109 4.9 18.9 1.0
CA B:ALA88 5.0 24.3 1.0

Fluorine binding site 6 out of 6 in 5dgc

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

b:22.7
occ:1.00
 F3 B:BEF202 0.0 22.7 1.0
BE B:BEF202 1.5 22.2 1.0
F1 B:BEF202 2.5 24.5 1.0
F2 B:BEF202 2.5 20.8 1.0
OD1 B:ASP57 2.7 20.4 1.0
N B:ALA88 2.8 22.8 1.0
O B:HOH399 2.9 36.7 1.0
NZ B:LYS109 2.9 18.9 1.0
CE B:LYS109 3.3 20.0 1.0
CD B:LYS109 3.4 20.0 1.0
CA B:THR87 3.4 20.6 1.0
C2 B:IMD204 3.5 30.8 0.8
C B:THR87 3.5 21.6 1.0
CB B:ALA88 3.7 26.1 1.0
OG1 B:THR87 3.7 20.5 1.0
CA B:ALA88 3.8 24.3 1.0
CG B:ASP57 3.8 20.3 1.0
O B:HOH307 3.9 22.9 1.0
N3 B:IMD204 3.9 30.1 0.8
CB B:THR87 4.1 20.9 1.0
O B:VAL86 4.3 21.5 1.0
OD2 B:ASP57 4.3 21.1 1.0
MN B:MN201 4.3 22.7 1.0
CG B:LYS109 4.5 21.1 1.0
N1 B:IMD204 4.5 34.5 0.8
N B:THR87 4.5 21.1 1.0
O B:THR87 4.7 19.6 1.0
O B:HOH304 4.8 28.1 1.0
C B:ALA88 4.9 24.6 1.0
C2 B:IMD203 4.9 33.8 0.8
N B:TRP58 4.9 19.8 1.0
C B:VAL86 4.9 19.9 1.0
N B:TYR89 4.9 23.0 1.0
CB B:ASP57 5.0 20.8 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: Thu Aug 1 08:44:54 2024

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