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Fluorine in PDB 3rvj: Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Q

Protein crystallography data

The structure of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Q, PDB code: 3rvj 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) 27.58 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.584, 53.697, 160.663, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.1

Other elements in 3rvj:

The structure of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Q 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 E89Q (pdb code 3rvj). 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 E89Q, PDB code: 3rvj:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3rvj

Go back to Fluorine Binding Sites List in 3rvj
Fluorine binding site 1 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Q


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 E89Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F131

b:26.4
occ:1.00
 F1 A:BEF131 0.0 26.4 1.0
BE A:BEF131 1.4 32.5 1.0
F2 A:BEF131 2.3 27.2 1.0
F3 A:BEF131 2.4 24.1 1.0
OD1 A:ASP57 2.7 25.4 1.0
N A:ALA88 2.8 23.2 1.0
NZ A:LYS109 2.9 25.0 1.0
O A:HOH221 3.4 42.1 1.0
CE A:LYS109 3.4 25.4 1.0
O A:HOH255 3.5 41.1 1.0
CA A:THR87 3.5 21.7 1.0
CD A:LYS109 3.5 26.4 1.0
CB A:ALA88 3.6 26.6 1.0
C A:THR87 3.6 26.0 1.0
OG1 A:THR87 3.6 25.7 1.0
CA A:ALA88 3.8 24.5 1.0
CG A:ASP57 3.8 23.9 1.0
O A:HOH214 4.0 26.9 1.0
CB A:THR87 4.0 23.2 1.0
MN A:MN130 4.2 29.3 1.0
OD2 A:ASP57 4.3 23.9 1.0
O A:VAL86 4.6 23.3 1.0
CG A:LYS109 4.6 27.2 1.0
N A:THR87 4.7 23.3 1.0
N A:TRP58 4.7 25.5 1.0
O A:THR87 4.8 27.0 1.0
C A:ALA88 4.8 31.1 1.0
N A:GLN89 4.8 26.1 1.0
CB A:ASP57 5.0 25.2 1.0
N A:ASP59 5.0 25.9 1.0
OD2 A:ASP12 5.0 27.0 1.0

Fluorine binding site 2 out of 6 in 3rvj

Go back to Fluorine Binding Sites List in 3rvj
Fluorine binding site 2 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Q


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 E89Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F131

b:27.2
occ:1.00
 F2 A:BEF131 0.0 27.2 1.0
BE A:BEF131 1.4 32.5 1.0
MN A:MN130 2.3 29.3 1.0
F3 A:BEF131 2.3 24.1 1.0
F1 A:BEF131 2.3 26.4 1.0
OD1 A:ASP57 2.5 25.4 1.0
OD2 A:ASP57 3.1 23.9 1.0
O A:HOH221 3.1 42.1 1.0
CG A:ASP57 3.2 23.9 1.0
O A:HOH214 3.2 26.9 1.0
O A:HOH212 3.3 26.4 1.0
O A:ASP59 3.3 26.4 1.0
CB A:ASP59 3.3 24.7 1.0
N A:ASP59 3.5 25.9 1.0
O A:HOH255 3.6 41.1 1.0
CA A:ASP59 3.8 27.0 1.0
C A:ASP59 3.9 27.6 1.0
NZ A:LYS109 4.1 25.0 1.0
CG A:ASP59 4.4 36.1 1.0
OD1 A:ASP13 4.4 24.9 1.0
N A:TRP58 4.5 25.5 1.0
C A:TRP58 4.6 25.6 1.0
CB A:ASP57 4.7 25.2 1.0
OD2 A:ASP59 4.7 37.3 1.0
OG1 A:THR87 4.8 25.7 1.0
N A:ALA88 4.9 23.2 1.0

Fluorine binding site 3 out of 6 in 3rvj

Go back to Fluorine Binding Sites List in 3rvj
Fluorine binding site 3 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Q


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 E89Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F131

b:24.1
occ:1.00
 F3 A:BEF131 0.0 24.1 1.0
BE A:BEF131 1.4 32.5 1.0
F2 A:BEF131 2.3 27.2 1.0
F1 A:BEF131 2.4 26.4 1.0
OD1 A:ASP57 2.5 25.4 1.0
OG1 A:THR87 2.6 25.7 1.0
O A:HOH221 2.7 42.1 1.0
N A:ASP59 2.9 25.9 1.0
N A:TRP58 3.1 25.5 1.0
CB A:TRP58 3.3 24.7 1.0
CB A:THR87 3.5 23.2 1.0
CA A:TRP58 3.5 25.0 1.0
CG A:ASP57 3.6 23.9 1.0
C A:TRP58 3.7 25.6 1.0
CB A:ASP59 3.7 24.7 1.0
N A:ALA88 3.8 23.2 1.0
CA A:ASP59 3.8 27.0 1.0
CA A:THR87 3.9 21.7 1.0
CG A:GLN89 4.0 28.1 1.0
OD2 A:ASP57 4.1 23.9 1.0
MN A:MN130 4.3 29.3 1.0
C A:ASP57 4.3 25.6 1.0
NE2 A:GLN89 4.3 41.9 1.0
C A:THR87 4.4 26.0 1.0
N A:GLN89 4.5 26.1 1.0
CG A:TRP58 4.5 25.8 1.0
O A:ASP59 4.5 26.4 1.0
CA A:ASP57 4.6 23.0 1.0
C A:ASP59 4.6 27.6 1.0
CB A:ASP57 4.7 25.2 1.0
CD A:GLN89 4.8 43.1 1.0
CA A:ALA88 4.8 24.5 1.0
CG2 A:THR87 4.8 23.0 1.0
CB A:ALA88 4.9 26.6 1.0
O A:TRP58 4.9 25.3 1.0
NZ A:LYS109 4.9 25.0 1.0
O A:HOH255 5.0 41.1 1.0

Fluorine binding site 4 out of 6 in 3rvj

Go back to Fluorine Binding Sites List in 3rvj
Fluorine binding site 4 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Q


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 E89Q within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F131

b:34.2
occ:1.00
 F1 B:BEF131 0.0 34.2 1.0
BE B:BEF131 1.4 32.8 1.0
F3 B:BEF131 2.3 33.2 1.0
F2 B:BEF131 2.3 30.0 1.0
OD1 B:ASP57 2.5 27.5 1.0
OG1 B:THR87 2.7 27.2 1.0
N B:ASP59 2.8 28.3 1.0
O B:HOH200 3.1 42.0 1.0
N B:TRP58 3.2 25.8 1.0
CG B:ASP57 3.4 28.2 1.0
CB B:TRP58 3.4 29.0 1.0
CA B:TRP58 3.6 28.2 1.0
CB B:THR87 3.6 26.1 1.0
CB B:ASP59 3.6 30.4 1.0
C B:TRP58 3.7 25.8 1.0
CA B:ASP59 3.8 30.2 1.0
OD2 B:ASP57 3.8 28.7 1.0
N B:ALA88 3.9 26.5 1.0
CA B:THR87 4.0 26.1 1.0
MN B:MN130 4.2 33.1 1.0
C B:ASP57 4.3 27.6 1.0
O B:ASP59 4.4 31.6 1.0
C B:THR87 4.5 27.5 1.0
C B:ASP59 4.5 30.4 1.0
N B:GLN89 4.6 35.0 1.0
CB B:ASP57 4.6 26.9 1.0
CG B:TRP58 4.6 33.2 1.0
CA B:ASP57 4.6 24.7 1.0
NZ B:LYS109 4.8 25.1 1.0
O B:HOH179 4.8 49.2 1.0
O B:HOH218 4.8 48.8 1.0
O B:TRP58 4.8 28.3 1.0
CB B:GLN89 4.9 34.9 1.0
CG2 B:THR87 5.0 31.0 1.0
CA B:ALA88 5.0 30.1 1.0

Fluorine binding site 5 out of 6 in 3rvj

Go back to Fluorine Binding Sites List in 3rvj
Fluorine binding site 5 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Q


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 E89Q within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F131

b:30.0
occ:1.00
 F2 B:BEF131 0.0 30.0 1.0
BE B:BEF131 1.4 32.8 1.0
MN B:MN130 2.2 33.1 1.0
F3 B:BEF131 2.3 33.2 1.0
F1 B:BEF131 2.3 34.2 1.0
OD1 B:ASP57 2.7 27.5 1.0
OD2 B:ASP57 2.9 28.7 1.0
O B:HOH197 3.0 25.2 1.0
O B:HOH198 3.1 31.1 1.0
CG B:ASP57 3.1 28.2 1.0
O B:ASP59 3.3 31.6 1.0
CB B:ASP59 3.6 30.4 1.0
N B:ASP59 3.7 28.3 1.0
O B:HOH200 3.8 42.0 1.0
O B:HOH218 3.9 48.8 1.0
NZ B:LYS109 3.9 25.1 1.0
CA B:ASP59 4.0 30.2 1.0
C B:ASP59 4.0 30.4 1.0
OD1 B:ASP13 4.4 31.5 1.0
CG B:ASP59 4.5 36.9 1.0
O B:HOH190 4.5 53.1 1.0
N B:TRP58 4.6 25.8 1.0
CB B:ASP57 4.6 26.9 1.0
C B:TRP58 4.8 25.8 1.0
OD2 B:ASP59 4.8 45.5 1.0
OG1 B:THR87 4.8 27.2 1.0
O B:HOH159 4.9 44.3 1.0
N B:ALA88 4.9 26.5 1.0

Fluorine binding site 6 out of 6 in 3rvj

Go back to Fluorine Binding Sites List in 3rvj
Fluorine binding site 6 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89Q


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 E89Q within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F131

b:33.2
occ:1.00
 F3 B:BEF131 0.0 33.2 1.0
BE B:BEF131 1.4 32.8 1.0
F2 B:BEF131 2.3 30.0 1.0
F1 B:BEF131 2.3 34.2 1.0
OD1 B:ASP57 2.6 27.5 1.0
N B:ALA88 2.8 26.5 1.0
NZ B:LYS109 2.9 25.1 1.0
CA B:THR87 3.4 26.1 1.0
CE B:LYS109 3.5 25.7 1.0
OG1 B:THR87 3.5 27.2 1.0
C B:THR87 3.6 27.5 1.0
CD B:LYS109 3.6 30.6 1.0
CB B:ALA88 3.7 30.6 1.0
CG B:ASP57 3.7 28.2 1.0
CA B:ALA88 3.8 30.1 1.0
O B:HOH200 3.9 42.0 1.0
CB B:THR87 4.0 26.1 1.0
O B:HOH197 4.0 25.2 1.0
OD2 B:ASP57 4.1 28.7 1.0
MN B:MN130 4.2 33.1 1.0
O B:HOH159 4.4 44.3 1.0
O B:VAL86 4.5 27.0 1.0
CG B:LYS109 4.6 27.5 1.0
N B:GLN89 4.6 35.0 1.0
N B:THR87 4.6 23.9 1.0
C B:ALA88 4.8 35.2 1.0
O B:THR87 4.8 24.9 1.0
N B:TRP58 4.8 25.8 1.0
O B:HOH218 4.9 48.8 1.0
CB B:ASP57 4.9 26.9 1.0
N B:ASP59 5.0 28.3 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 22:23:06 2024

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