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Fluorine in PDB 3rvn: Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y

Protein crystallography data

The structure of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y, PDB code: 3rvn was solved by C.A.Starbird, R.M.Immormino, R.E.Silversmith, R.B.Bourret, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.60 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.436, 53.613, 161.310, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.5

Other elements in 3rvn:

The structure of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y (pdb code 3rvn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y, PDB code: 3rvn:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3rvn

Go back to Fluorine Binding Sites List in 3rvn
Fluorine binding site 1 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F131

b:24.1
occ:1.00
 F1 A:BEF131 0.0 24.1 1.0
BE A:BEF131 1.4 29.5 1.0
F2 A:BEF131 2.3 26.2 1.0
F3 A:BEF131 2.3 23.5 1.0
OD1 A:ASP57 2.6 22.5 1.0
N A:ALA88 2.9 19.9 1.0
NZ A:LYS109 3.0 22.2 1.0
O A:HOH237 3.2 42.7 1.0
O A:HOH226 3.3 36.5 1.0
CA A:THR87 3.4 20.0 1.0
OG1 A:THR87 3.5 20.3 1.0
CE A:LYS109 3.6 22.6 1.0
C A:THR87 3.6 22.1 1.0
CD A:LYS109 3.7 23.9 1.0
CG A:ASP57 3.7 23.8 1.0
CB A:ALA88 3.8 23.1 1.0
CB A:THR87 3.9 22.6 1.0
CA A:ALA88 3.9 20.6 1.0
O A:HOH146 4.1 25.5 1.0
MN A:MN130 4.2 31.9 1.0
OD2 A:ASP57 4.2 24.3 1.0
O A:VAL86 4.4 22.5 1.0
N A:THR87 4.6 19.8 1.0
N A:TRP58 4.7 29.1 1.0
CG A:LYS109 4.8 25.1 1.0
O A:THR87 4.8 25.9 1.0
N A:TYR89 4.9 27.3 1.0
N A:ASP59 4.9 25.9 1.0
C A:ALA88 4.9 29.6 1.0
CB A:ASP57 4.9 22.0 1.0
C A:VAL86 5.0 25.3 1.0

Fluorine binding site 2 out of 6 in 3rvn

Go back to Fluorine Binding Sites List in 3rvn
Fluorine binding site 2 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F131

b:26.2
occ:1.00
 F2 A:BEF131 0.0 26.2 1.0
BE A:BEF131 1.4 29.5 1.0
MN A:MN130 2.2 31.9 1.0
F1 A:BEF131 2.3 24.1 1.0
F3 A:BEF131 2.3 23.5 1.0
OD1 A:ASP57 2.5 22.5 1.0
OD2 A:ASP57 2.8 24.3 1.0
CG A:ASP57 3.0 23.8 1.0
O A:ASP59 3.2 27.5 1.0
O A:HOH146 3.3 25.5 1.0
CB A:ASP59 3.3 28.2 1.0
O A:HOH237 3.4 42.7 1.0
O A:HOH174 3.4 30.9 1.0
N A:ASP59 3.5 25.9 1.0
O A:HOH226 3.6 36.5 1.0
CA A:ASP59 3.8 25.8 1.0
C A:ASP59 3.9 30.5 1.0
NZ A:LYS109 4.1 22.2 1.0
OD1 A:ASP13 4.3 29.1 1.0
CG A:ASP59 4.3 31.4 1.0
N A:TRP58 4.3 29.1 1.0
CB A:ASP57 4.4 22.0 1.0
O A:HOH245 4.5 38.8 1.0
OD2 A:ASP59 4.6 33.0 1.0
C A:TRP58 4.6 27.6 1.0
OG1 A:THR87 4.8 20.3 1.0
CA A:TRP58 5.0 25.3 1.0

Fluorine binding site 3 out of 6 in 3rvn

Go back to Fluorine Binding Sites List in 3rvn
Fluorine binding site 3 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F131

b:23.5
occ:1.00
 F3 A:BEF131 0.0 23.5 1.0
BE A:BEF131 1.4 29.5 1.0
F2 A:BEF131 2.3 26.2 1.0
F1 A:BEF131 2.3 24.1 1.0
OD1 A:ASP57 2.6 22.5 1.0
OG1 A:THR87 2.7 20.3 1.0
N A:ASP59 2.8 25.9 1.0
N A:TRP58 3.0 29.1 1.0
O A:HOH226 3.2 36.5 1.0
CB A:TRP58 3.2 26.4 1.0
CB A:THR87 3.4 22.6 1.0
CA A:TRP58 3.4 25.3 1.0
CG A:ASP57 3.4 23.8 1.0
C A:TRP58 3.6 27.6 1.0
CB A:ASP59 3.6 28.2 1.0
CA A:ASP59 3.8 25.8 1.0
CA A:THR87 3.9 20.0 1.0
OD2 A:ASP57 3.9 24.3 1.0
N A:ALA88 4.1 19.9 1.0
C A:ASP57 4.1 25.2 1.0
CD2 A:TYR89 4.2 31.5 1.0
CE2 A:TYR89 4.3 29.4 1.0
MN A:MN130 4.3 31.9 1.0
CA A:ASP57 4.4 21.6 1.0
CG A:TRP58 4.5 25.7 1.0
O A:ASP59 4.5 27.5 1.0
C A:THR87 4.5 22.1 1.0
CB A:ASP57 4.5 22.0 1.0
C A:ASP59 4.6 30.5 1.0
CG2 A:THR87 4.8 16.5 1.0
O A:TRP58 4.8 28.1 1.0
CG A:TYR89 4.8 29.5 1.0
O A:VAL86 4.8 22.5 1.0
N A:TYR89 4.9 27.3 1.0
NZ A:LYS109 4.9 22.2 1.0
O A:HOH237 4.9 42.7 1.0
CZ A:TYR89 5.0 34.0 1.0

Fluorine binding site 4 out of 6 in 3rvn

Go back to Fluorine Binding Sites List in 3rvn
Fluorine binding site 4 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F131

b:24.9
occ:1.00
 F1 B:BEF131 0.0 24.9 1.0
BE B:BEF131 1.4 28.4 1.0
F3 B:BEF131 2.3 25.7 1.0
F2 B:BEF131 2.3 28.2 1.0
OD1 B:ASP57 2.5 22.3 1.0
OG1 B:THR87 2.6 26.2 1.0
N B:ASP59 2.8 26.9 1.0
N B:TRP58 3.0 29.2 1.0
CB B:TRP58 3.3 26.4 1.0
CB B:THR87 3.4 26.8 1.0
CG B:ASP57 3.4 23.8 1.0
CA B:TRP58 3.5 26.5 1.0
C B:TRP58 3.6 26.7 1.0
CB B:ASP59 3.7 25.8 1.0
CA B:THR87 3.8 27.5 1.0
CA B:ASP59 3.8 26.9 1.0
N B:ALA88 3.9 27.9 1.0
OD2 B:ASP57 3.9 24.6 1.0
C B:ASP57 4.2 26.2 1.0
MN B:MN130 4.2 32.4 1.0
C B:THR87 4.4 25.1 1.0
O B:ASP59 4.5 28.1 1.0
CA B:ASP57 4.5 21.8 1.0
CB B:ASP57 4.5 22.6 1.0
CG B:TRP58 4.6 29.4 1.0
C B:ASP59 4.6 27.0 1.0
O B:HOH175 4.7 34.0 1.0
NZ B:LYS109 4.7 25.8 1.0
N B:TYR89 4.7 29.6 1.0
CG B:TYR89 4.7 29.8 1.0
CG2 B:THR87 4.8 24.0 1.0
CD1 B:TYR89 4.8 35.3 1.0
O B:TRP58 4.8 29.1 1.0
O B:VAL86 4.8 25.9 1.0
CD2 B:TYR89 4.8 32.9 1.0
CE1 B:TYR89 4.9 39.0 1.0
CA B:ALA88 4.9 27.5 1.0
CE2 B:TYR89 5.0 32.4 1.0
CB B:ALA88 5.0 27.0 1.0
CZ B:TYR89 5.0 33.3 1.0

Fluorine binding site 5 out of 6 in 3rvn

Go back to Fluorine Binding Sites List in 3rvn
Fluorine binding site 5 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F131

b:28.2
occ:1.00
 F2 B:BEF131 0.0 28.2 1.0
BE B:BEF131 1.4 28.4 1.0
MN B:MN130 2.2 32.4 1.0
F1 B:BEF131 2.3 24.9 1.0
F3 B:BEF131 2.3 25.7 1.0
OD1 B:ASP57 2.6 22.3 1.0
OD2 B:ASP57 2.9 24.6 1.0
O B:HOH137 3.1 23.3 1.0
O B:HOH175 3.1 34.0 1.0
CG B:ASP57 3.1 23.8 1.0
O B:HOH153 3.2 29.4 1.0
O B:ASP59 3.3 28.1 1.0
CB B:ASP59 3.4 25.8 1.0
N B:ASP59 3.5 26.9 1.0
CA B:ASP59 3.8 26.9 1.0
NZ B:LYS109 4.0 25.8 1.0
C B:ASP59 4.0 27.0 1.0
O B:HOH238 4.2 44.6 1.0
CG B:ASP59 4.4 27.8 1.0
OD1 B:ASP13 4.4 28.6 1.0
N B:TRP58 4.4 29.2 1.0
C B:TRP58 4.6 26.7 1.0
CB B:ASP57 4.6 22.6 1.0
OD2 B:ASP59 4.7 33.8 1.0
OG1 B:THR87 4.7 26.2 1.0
N B:ALA88 4.9 27.9 1.0
O B:HOH193 5.0 47.2 1.0

Fluorine binding site 6 out of 6 in 3rvn

Go back to Fluorine Binding Sites List in 3rvn
Fluorine binding site 6 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F131

b:25.7
occ:1.00
 F3 B:BEF131 0.0 25.7 1.0
BE B:BEF131 1.4 28.4 1.0
F1 B:BEF131 2.3 24.9 1.0
F2 B:BEF131 2.3 28.2 1.0
OD1 B:ASP57 2.6 22.3 1.0
NZ B:LYS109 2.8 25.8 1.0
N B:ALA88 2.8 27.9 1.0
O B:HOH175 3.1 34.0 1.0
CA B:THR87 3.4 27.5 1.0
OG1 B:THR87 3.5 26.2 1.0
CE B:LYS109 3.5 27.9 1.0
C B:THR87 3.6 25.1 1.0
CB B:ALA88 3.6 27.0 1.0
CD B:LYS109 3.6 26.6 1.0
CG B:ASP57 3.7 23.8 1.0
CA B:ALA88 3.8 27.5 1.0
CB B:THR87 3.9 26.8 1.0
O B:HOH137 4.0 23.3 1.0
OD2 B:ASP57 4.2 24.6 1.0
MN B:MN130 4.3 32.4 1.0
O B:VAL86 4.4 25.9 1.0
O B:HOH239 4.6 38.8 1.0
N B:THR87 4.6 21.6 1.0
CG B:LYS109 4.6 26.8 1.0
N B:TRP58 4.7 29.2 1.0
O B:THR87 4.8 27.7 1.0
N B:TYR89 4.8 29.6 1.0
C B:ALA88 4.9 31.2 1.0
N B:ASP59 4.9 26.9 1.0
CB B:ASP57 4.9 22.6 1.0
OD2 B:ASP12 4.9 27.3 1.0
C B:VAL86 5.0 23.9 1.0

Reference:

R.M.Immormino, C.A.Starbird, R.E.Silversmith, R.B.Bourret. Probing Mechanistic Similarities Between Response Regulator Signaling Proteins and Haloacid Dehalogenase Phosphatases. Biochemistry V. 54 3514 2015.
ISSN: ISSN 0006-2960
PubMed: 25928369
DOI: 10.1021/ACS.BIOCHEM.5B00286
Page generated: Wed Jul 31 22:23:34 2024

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