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Fluorine in PDB 3w9s: Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra

Protein crystallography data

The structure of Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra, PDB code: 3w9s was solved by C.Chen, S.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.38 / 1.70
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 49.994, 49.994, 145.859, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 17.5

Other elements in 3w9s:

The structure of Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra (pdb code 3w9s). 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 Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra, PDB code: 3w9s:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3w9s

Go back to Fluorine Binding Sites List in 3w9s
Fluorine binding site 1 out of 6 in the Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:13.7
occ:1.00
 F1 A:BEF201 0.0 13.7 1.0
BE A:BEF201 1.4 16.1 1.0
MG A:MG202 2.0 14.1 1.0
F2 A:BEF201 2.4 13.9 1.0
F3 A:BEF201 2.4 13.5 1.0
OD2 A:ASP51 2.6 14.8 1.0
OD1 A:ASP51 2.8 12.2 1.0
O A:HOH380 2.9 16.1 1.0
O A:HOH301 3.0 13.6 1.0
CG A:ASP51 3.0 12.6 1.0
O A:GLY53 3.1 13.1 1.0
N A:GLY53 3.1 13.7 1.0
CA A:GLY53 3.2 14.0 1.0
O A:HOH313 3.3 20.9 1.0
O A:HOH472 3.4 26.6 1.0
C A:GLY53 3.6 13.9 1.0
OD2 A:ASP8 4.1 13.1 1.0
NZ A:LYS101 4.3 13.9 1.0
C A:LEU52 4.4 17.5 1.0
N A:LEU52 4.4 10.8 1.0
CB A:ASP51 4.5 12.8 1.0
O A:HOH342 4.7 20.7 1.0
O A:HOH435 4.8 32.8 1.0
N A:LEU54 4.9 13.4 1.0
CA A:LEU52 4.9 12.4 1.0
OG1 A:THR79 5.0 14.6 1.0
N A:ALA80 5.0 14.5 1.0

Fluorine binding site 2 out of 6 in 3w9s

Go back to Fluorine Binding Sites List in 3w9s
Fluorine binding site 2 out of 6 in the Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:13.9
occ:1.00
 F2 A:BEF201 0.0 13.9 1.0
BE A:BEF201 1.4 16.1 1.0
F1 A:BEF201 2.4 13.7 1.0
F3 A:BEF201 2.4 13.5 1.0
OD2 A:ASP51 2.5 14.8 1.0
OG1 A:THR79 2.6 14.6 1.0
N A:GLY53 2.8 13.7 1.0
O A:HOH313 2.9 20.9 1.0
N A:LEU52 3.2 10.8 1.0
CB A:THR79 3.5 13.5 1.0
CG A:ASP51 3.5 12.6 1.0
CA A:LEU52 3.6 12.4 1.0
N A:ALA80 3.7 14.5 1.0
C A:LEU52 3.7 17.5 1.0
CB A:LEU52 3.7 14.5 1.0
CA A:THR79 3.7 11.0 1.0
CA A:GLY53 3.7 14.0 1.0
OD1 A:ASP51 4.1 12.2 1.0
C A:THR79 4.2 13.9 1.0
MG A:MG202 4.2 14.1 1.0
C A:ASP51 4.2 12.6 1.0
CG A:ARG81 4.5 20.9 1.0
N A:ARG81 4.5 17.5 1.0
CG A:LEU52 4.6 13.3 1.0
CA A:ASP51 4.6 12.5 1.0
O A:HOH472 4.6 26.6 1.0
CB A:ASP51 4.6 12.8 1.0
O A:HOH363 4.7 25.0 1.0
CA A:ALA80 4.7 15.7 1.0
O A:LEU78 4.7 14.6 1.0
O A:GLY53 4.7 13.1 1.0
C A:GLY53 4.7 13.9 1.0
CB A:ALA80 4.7 18.5 1.0
O A:LEU52 4.9 15.5 1.0
CG2 A:THR79 4.9 14.8 1.0
O A:HOH301 4.9 13.6 1.0
NZ A:LYS101 4.9 13.9 1.0

Fluorine binding site 3 out of 6 in 3w9s

Go back to Fluorine Binding Sites List in 3w9s
Fluorine binding site 3 out of 6 in the Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:13.5
occ:1.00
 F3 A:BEF201 0.0 13.5 1.0
BE A:BEF201 1.4 16.1 1.0
F2 A:BEF201 2.4 13.9 1.0
F1 A:BEF201 2.4 13.7 1.0
OD2 A:ASP51 2.5 14.8 1.0
O A:HOH472 2.8 26.6 1.0
NZ A:LYS101 2.9 13.9 1.0
N A:ALA80 2.9 14.5 1.0
CE A:LYS101 3.5 12.6 1.0
O A:HOH301 3.5 13.6 1.0
CD A:LYS101 3.6 11.6 1.0
CB A:ALA80 3.6 18.5 1.0
CG A:ASP51 3.6 12.6 1.0
CA A:THR79 3.6 11.0 1.0
C A:THR79 3.7 13.9 1.0
O A:HOH313 3.8 20.9 1.0
CA A:ALA80 3.8 15.7 1.0
OG1 A:THR79 3.9 14.6 1.0
MG A:MG202 4.0 14.1 1.0
OD1 A:ASP51 4.1 12.2 1.0
CB A:THR79 4.3 13.5 1.0
O A:LEU78 4.4 14.6 1.0
CG A:LYS101 4.7 12.8 1.0
N A:THR79 4.7 11.4 1.0
O A:HOH338 4.7 16.0 1.0
N A:GLY53 4.8 13.7 1.0
O A:HOH342 4.8 20.7 1.0
OE1 A:GLU7 4.8 14.4 1.0
O A:HOH380 4.8 16.1 1.0
CB A:ASP51 4.9 12.8 1.0
O A:THR79 4.9 13.5 1.0
C A:ALA80 4.9 16.2 1.0
N A:LEU52 5.0 10.8 1.0
N A:ARG81 5.0 17.5 1.0

Fluorine binding site 4 out of 6 in 3w9s

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Fluorine binding site 4 out of 6 in the Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:14.3
occ:1.00
 F1 B:BEF201 0.0 14.3 1.0
BE B:BEF201 1.4 19.0 1.0
F2 B:BEF201 2.4 13.9 1.0
F3 B:BEF201 2.4 14.2 1.0
OD1 B:ASP51 2.5 14.3 1.0
OG1 B:THR79 2.6 14.5 1.0
N B:GLY53 2.8 14.0 1.0
O B:HOH416 2.8 21.6 1.0
N B:LEU52 3.2 11.3 1.0
CB B:THR79 3.5 12.3 1.0
CG B:ASP51 3.5 12.8 1.0
CA B:LEU52 3.6 12.6 1.0
C B:LEU52 3.7 16.7 1.0
N B:ALA80 3.7 14.8 1.0
CB B:LEU52 3.7 14.7 1.0
CA B:GLY53 3.7 13.7 1.0
CA B:THR79 3.8 11.3 1.0
OD2 B:ASP51 4.0 11.8 1.0
MG B:MG202 4.2 13.1 1.0
C B:THR79 4.2 13.1 1.0
C B:ASP51 4.2 14.2 1.0
O B:HOH347 4.5 32.5 1.0
N B:ARG81 4.5 16.9 1.0
CA B:ASP51 4.6 12.2 1.0
CG B:LEU52 4.6 14.2 1.0
O B:HOH382 4.6 22.4 1.0
CB B:ASP51 4.6 12.1 1.0
CG B:ARG81 4.6 20.6 1.0
O B:HOH422 4.7 25.8 1.0
C B:GLY53 4.7 14.4 1.0
O B:GLY53 4.7 14.3 1.0
CA B:ALA80 4.7 16.8 1.0
O B:LEU78 4.7 13.8 1.0
CB B:ALA80 4.7 19.4 1.0
O B:LEU52 4.8 15.3 1.0
CG2 B:THR79 4.9 14.1 1.0
O B:HOH410 4.9 14.2 1.0
NZ B:LYS101 5.0 12.8 1.0

Fluorine binding site 5 out of 6 in 3w9s

Go back to Fluorine Binding Sites List in 3w9s
Fluorine binding site 5 out of 6 in the Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:13.9
occ:1.00
 F2 B:BEF201 0.0 13.9 1.0
BE B:BEF201 1.4 19.0 1.0
MG B:MG202 2.0 13.1 1.0
F1 B:BEF201 2.4 14.3 1.0
F3 B:BEF201 2.4 14.2 1.0
OD1 B:ASP51 2.6 14.3 1.0
OD2 B:ASP51 2.8 11.8 1.0
O B:HOH351 2.9 15.3 1.0
O B:HOH410 2.9 14.2 1.0
CG B:ASP51 3.0 12.8 1.0
O B:GLY53 3.1 14.3 1.0
N B:GLY53 3.1 14.0 1.0
CA B:GLY53 3.2 13.7 1.0
O B:HOH347 3.2 32.5 1.0
O B:HOH416 3.2 21.6 1.0
O B:HOH422 3.5 25.8 1.0
C B:GLY53 3.6 14.4 1.0
OD1 B:ASP8 4.1 14.1 1.0
NZ B:LYS101 4.3 12.8 1.0
C B:LEU52 4.4 16.7 1.0
N B:LEU52 4.4 11.3 1.0
CB B:ASP51 4.5 12.1 1.0
O B:HOH441 4.7 32.1 1.0
O B:HOH458 4.7 20.3 1.0
N B:LEU54 4.9 14.6 1.0
CA B:LEU52 4.9 12.6 1.0
OG1 B:THR79 5.0 14.5 1.0
O B:HOH382 5.0 22.4 1.0

Fluorine binding site 6 out of 6 in 3w9s

Go back to Fluorine Binding Sites List in 3w9s
Fluorine binding site 6 out of 6 in the Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure Analysis of the N-Terminal Receiver Domain of Response Regulator Pmra within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:14.2
occ:1.00
 F3 B:BEF201 0.0 14.2 1.0
BE B:BEF201 1.4 19.0 1.0
F1 B:BEF201 2.4 14.3 1.0
F2 B:BEF201 2.4 13.9 1.0
OD1 B:ASP51 2.5 14.3 1.0
NZ B:LYS101 2.9 12.8 1.0
N B:ALA80 2.9 14.8 1.0
O B:HOH422 2.9 25.8 1.0
CE B:LYS101 3.5 11.6 1.0
O B:HOH410 3.5 14.2 1.0
CD B:LYS101 3.6 11.7 1.0
CG B:ASP51 3.6 12.8 1.0
CB B:ALA80 3.6 19.4 1.0
CA B:THR79 3.6 11.3 1.0
O B:HOH416 3.7 21.6 1.0
C B:THR79 3.7 13.1 1.0
CA B:ALA80 3.9 16.8 1.0
OG1 B:THR79 3.9 14.5 1.0
MG B:MG202 4.0 13.1 1.0
OD2 B:ASP51 4.0 11.8 1.0
O B:HOH347 4.2 32.5 1.0
CB B:THR79 4.3 12.3 1.0
O B:LEU78 4.4 13.8 1.0
O B:HOH353 4.7 14.9 1.0
CG B:LYS101 4.7 11.6 1.0
N B:THR79 4.7 12.2 1.0
N B:GLY53 4.8 14.0 1.0
O B:HOH351 4.8 15.3 1.0
OE1 B:GLU7 4.8 14.9 1.0
O B:HOH458 4.8 20.3 1.0
CB B:ASP51 4.9 12.1 1.0
O B:THR79 4.9 13.1 1.0
N B:LEU52 4.9 11.3 1.0
C B:ALA80 4.9 17.5 1.0
N B:ARG81 5.0 16.9 1.0

Reference:

S.C.Lou, Y.C.Lou, M.Rajasekaran, Y.W.Chang, C.D.Hsiao, C.Chen. Structural Basis of A Physical Blockage Mechanism For the Interaction of Response Regulator Pmra with Connector Protein Pmrd From Klebsiella Pneumoniae J.Biol.Chem. V. 288 25551 2013.
ISSN: ISSN 0021-9258
PubMed: 23861396
DOI: 10.1074/JBC.M113.481978
Page generated: Mon Jul 14 20:04:08 2025

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