Atomistry » Fluorine » PDB 5ddf-5dy7 » 5dgc
Atomistry »
  Fluorine »
    PDB 5ddf-5dy7 »
      5dgc »

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: Sun Dec 13 12:20:51 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy