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Fluorine in PDB 4le0: Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium

Protein crystallography data

The structure of Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium, PDB code: 4le0 was solved by F.Trajtenberg, N.Larrieux, A.Buschiazzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 2.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.945, 71.782, 52.193, 90.00, 104.25, 90.00
R / Rfree (%) 17.7 / 21.3

Other elements in 4le0:

The structure of Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium (pdb code 4le0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium, PDB code: 4le0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4le0

Go back to Fluorine Binding Sites List in 4le0
Fluorine binding site 1 out of 6 in the Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:18.6
occ:1.00
 F1 A:BEF202 0.0 18.6 1.0
BE A:BEF202 1.7 20.3 1.0
OG1 A:THR80 2.6 21.7 1.0
F3 A:BEF202 2.7 21.4 1.0
F2 A:BEF202 2.7 22.3 1.0
OD1 A:ASP54 2.7 18.2 1.0
N A:GLU56 2.9 18.4 1.0
N A:ILE55 3.0 16.3 1.0
CB A:ILE55 3.3 19.8 1.0
CA A:ILE55 3.4 17.1 1.0
CB A:THR80 3.5 18.0 1.0
CD2 A:PHE82 3.5 30.1 1.0
C A:ILE55 3.6 22.4 1.0
CE2 A:PHE82 3.6 33.4 1.0
CG A:ASP54 3.7 14.8 1.0
CA A:GLU56 3.9 19.4 1.0
CB A:GLU56 3.9 21.6 1.0
CA A:THR80 4.0 18.0 1.0
C A:ASP54 4.1 18.5 1.0
CG1 A:ILE55 4.2 19.0 1.0
OD2 A:ASP54 4.2 12.7 1.0
CG A:GLU56 4.2 34.0 1.0
O A:HOH361 4.2 30.2 1.0
N A:THR81 4.3 23.6 1.0
CG2 A:ILE55 4.3 20.9 1.0
MG A:MG201 4.4 22.3 1.0
O A:GLU56 4.5 22.2 1.0
CA A:ASP54 4.6 13.7 1.0
C A:GLU56 4.6 23.1 1.0
CB A:ASP54 4.7 14.0 1.0
C A:THR80 4.7 24.1 1.0
CD1 A:ILE55 4.8 22.9 1.0
O A:ILE55 4.8 22.7 1.0
CG A:PHE82 4.8 29.9 1.0
CG2 A:THR80 4.8 11.8 1.0
O A:LEU79 4.8 19.1 1.0
CZ A:PHE82 4.9 32.9 1.0

Fluorine binding site 2 out of 6 in 4le0

Go back to Fluorine Binding Sites List in 4le0
Fluorine binding site 2 out of 6 in the Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:22.3
occ:1.00
 F2 A:BEF202 0.0 22.3 1.0
BE A:BEF202 1.7 20.3 1.0
MG A:MG201 2.0 22.3 1.0
OD1 A:ASP54 2.6 18.2 1.0
O A:HOH307 2.6 25.3 1.0
F3 A:BEF202 2.7 21.4 1.0
F1 A:BEF202 2.7 18.6 1.0
O A:HOH361 2.8 30.2 1.0
OD2 A:ASP54 2.8 12.7 1.0
O A:GLU56 2.9 22.2 1.0
O A:HOH301 2.9 26.6 1.0
CG A:ASP54 3.1 14.8 1.0
N A:GLU56 3.5 18.4 1.0
CB A:GLU56 3.6 21.6 1.0
C A:GLU56 3.6 23.1 1.0
CA A:GLU56 3.7 19.4 1.0
O A:HOH355 4.0 42.5 1.0
OD1 A:ASP9 4.0 18.9 1.0
NZ A:LYS102 4.1 14.1 1.0
CE2 A:PHE82 4.2 33.4 1.0
O A:HOH362 4.2 57.6 1.0
N A:ILE55 4.5 16.3 1.0
CB A:ASP54 4.6 14.0 1.0
C A:ILE55 4.6 22.4 1.0
CG A:GLU56 4.6 34.0 1.0
O A:HOH314 4.9 46.7 1.0
CD2 A:PHE82 4.9 30.1 1.0
N A:MET57 4.9 18.4 1.0
OG1 A:THR80 5.0 21.7 1.0

Fluorine binding site 3 out of 6 in 4le0

Go back to Fluorine Binding Sites List in 4le0
Fluorine binding site 3 out of 6 in the Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:21.4
occ:1.00
 F3 A:BEF202 0.0 21.4 1.0
BE A:BEF202 1.7 20.3 1.0
OD1 A:ASP54 2.5 18.2 1.0
F2 A:BEF202 2.7 22.3 1.0
F1 A:BEF202 2.7 18.6 1.0
NZ A:LYS102 2.7 14.1 1.0
O A:HOH361 3.0 30.2 1.0
N A:THR81 3.0 23.6 1.0
CE A:LYS102 3.2 14.2 1.0
CA A:THR80 3.4 18.0 1.0
OG1 A:THR81 3.5 35.1 1.0
OG1 A:THR80 3.5 21.7 1.0
C A:THR80 3.6 24.1 1.0
CG A:ASP54 3.7 14.8 1.0
CD A:LYS102 3.7 17.3 1.0
CB A:THR81 3.8 33.1 1.0
O A:HOH301 3.9 26.6 1.0
CB A:THR80 3.9 18.0 1.0
CA A:THR81 4.0 24.7 1.0
O A:HOH314 4.2 46.7 1.0
MG A:MG201 4.2 22.3 1.0
OD2 A:ASP54 4.2 12.7 1.0
O A:LEU79 4.3 19.1 1.0
CE2 A:PHE82 4.3 33.4 1.0
N A:THR80 4.5 18.4 1.0
CD2 A:PHE82 4.6 30.1 1.0
OE1 A:GLU8 4.7 24.9 1.0
CG A:LYS102 4.7 17.3 1.0
N A:ILE55 4.8 16.3 1.0
O A:THR80 4.8 23.2 1.0
CB A:ASP54 4.9 14.0 1.0
C A:LEU79 4.9 19.9 1.0
O A:HOH307 4.9 25.3 1.0

Fluorine binding site 4 out of 6 in 4le0

Go back to Fluorine Binding Sites List in 4le0
Fluorine binding site 4 out of 6 in the Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:23.4
occ:1.00
 F1 B:BEF202 0.0 23.4 1.0
BE B:BEF202 1.7 22.8 1.0
MG B:MG201 2.0 17.1 1.0
O B:HOH335 2.7 24.6 1.0
F2 B:BEF202 2.7 23.1 1.0
F3 B:BEF202 2.7 21.8 1.0
OD1 B:ASP54 2.8 19.8 1.0
O B:HOH301 2.8 13.6 1.0
O B:GLU56 2.9 18.8 1.0
O B:HOH305 3.0 23.9 1.0
OD2 B:ASP54 3.0 22.2 1.0
CG B:ASP54 3.3 19.2 1.0
CB B:GLU56 3.4 18.4 1.0
N B:GLU56 3.6 17.8 1.0
O B:HOH310 3.7 44.6 1.0
C B:GLU56 3.7 19.2 1.0
CA B:GLU56 3.7 17.2 1.0
CE2 B:PHE82 4.1 23.9 1.0
OD1 B:ASP9 4.1 16.9 1.0
NZ B:LYS102 4.1 24.4 1.0
CG B:GLU56 4.4 17.9 1.0
N B:ILE55 4.7 18.6 1.0
C B:ILE55 4.7 19.4 1.0
O B:HOH354 4.7 45.2 1.0
CB B:ASP54 4.8 16.5 1.0
CD2 B:PHE82 4.9 21.7 1.0
CZ B:PHE82 4.9 23.1 1.0
OE2 B:GLU56 5.0 22.3 1.0
N B:MET57 5.0 15.4 1.0

Fluorine binding site 5 out of 6 in 4le0

Go back to Fluorine Binding Sites List in 4le0
Fluorine binding site 5 out of 6 in the Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:23.1
occ:1.00
 F2 B:BEF202 0.0 23.1 1.0
BE B:BEF202 1.7 22.8 1.0
OD1 B:ASP54 2.6 19.8 1.0
F3 B:BEF202 2.7 21.8 1.0
OG1 B:THR80 2.7 20.5 1.0
F1 B:BEF202 2.7 23.4 1.0
N B:GLU56 2.8 17.8 1.0
N B:ILE55 3.0 18.6 1.0
CB B:ILE55 3.3 16.7 1.0
CA B:ILE55 3.4 16.1 1.0
CD2 B:PHE82 3.5 21.7 1.0
CB B:THR80 3.5 18.3 1.0
CE2 B:PHE82 3.5 23.9 1.0
C B:ILE55 3.6 19.4 1.0
CG B:ASP54 3.7 19.2 1.0
CB B:GLU56 3.8 18.4 1.0
CA B:GLU56 3.8 17.2 1.0
CG B:GLU56 4.0 17.9 1.0
CA B:THR80 4.1 16.5 1.0
C B:ASP54 4.2 22.2 1.0
OD2 B:ASP54 4.2 22.2 1.0
CG2 B:ILE55 4.3 14.7 1.0
CG1 B:ILE55 4.3 15.2 1.0
MG B:MG201 4.4 17.1 1.0
N B:THR81 4.4 19.3 1.0
O B:GLU56 4.5 18.8 1.0
O B:HOH305 4.5 23.9 1.0
C B:GLU56 4.6 19.2 1.0
CA B:ASP54 4.7 15.7 1.0
CB B:ASP54 4.7 16.5 1.0
O B:ILE55 4.8 17.7 1.0
CG B:PHE82 4.8 20.7 1.0
C B:THR80 4.8 20.7 1.0
CZ B:PHE82 4.9 23.1 1.0
CD1 B:ILE55 4.9 10.0 1.0
CG2 B:THR80 4.9 7.3 1.0
O B:LEU79 4.9 24.3 1.0
CD B:GLU56 5.0 23.2 1.0

Fluorine binding site 6 out of 6 in 4le0

Go back to Fluorine Binding Sites List in 4le0
Fluorine binding site 6 out of 6 in the Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Receiver Domain of Desr in Complex with Beryllofluoride and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:21.8
occ:1.00
 F3 B:BEF202 0.0 21.8 1.0
BE B:BEF202 1.7 22.8 1.0
F2 B:BEF202 2.7 23.1 1.0
F1 B:BEF202 2.7 23.4 1.0
OD1 B:ASP54 2.7 19.8 1.0
NZ B:LYS102 2.8 24.4 1.0
O B:HOH305 2.8 23.9 1.0
N B:THR81 3.0 19.3 1.0
CE B:LYS102 3.3 22.3 1.0
CA B:THR80 3.4 16.5 1.0
OG1 B:THR81 3.4 23.9 1.0
OG1 B:THR80 3.4 20.5 1.0
C B:THR80 3.6 20.7 1.0
CB B:THR81 3.7 24.1 1.0
CD B:LYS102 3.8 23.1 1.0
CG B:ASP54 3.8 19.2 1.0
O B:HOH301 3.9 13.6 1.0
CB B:THR80 3.9 18.3 1.0
CA B:THR81 4.0 19.7 1.0
CE2 B:PHE82 4.1 23.9 1.0
MG B:MG201 4.3 17.1 1.0
OD2 B:ASP54 4.3 22.2 1.0
O B:LEU79 4.4 24.3 1.0
CD2 B:PHE82 4.4 21.7 1.0
O B:HOH307 4.4 19.4 1.0
N B:THR80 4.6 17.9 1.0
CG B:LYS102 4.8 20.1 1.0
O B:THR80 4.8 19.0 1.0
N B:ILE55 4.9 18.6 1.0
N B:PHE82 4.9 17.9 1.0
OE1 B:GLU8 4.9 18.9 1.0
C B:LEU79 4.9 22.8 1.0
CB B:ASP54 5.0 16.5 1.0

Reference:

F.Trajtenberg, A.Albanesi, N.Ruetalo, H.Botti, A.Mechaly, L.Cybulski, N.Larrieux, D.De Mendoza, A.Buschiazzo. A Non-Canonical Protein Surface Is Key in Allosteric Control of Response Regulators To Be Published.
Page generated: Sun Dec 13 12:07:02 2020

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