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Fluorine in PDB 3rvp: Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89K

Protein crystallography data

The structure of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89K, PDB code: 3rvp 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) 44.58 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.487, 53.626, 160.416, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21.5

Other elements in 3rvp:

The structure of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89K also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
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 E89K (pdb code 3rvp). 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 E89K, PDB code: 3rvp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3rvp

Go back to Fluorine Binding Sites List in 3rvp
Fluorine binding site 1 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89K


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 E89K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F131

b:24.7
occ:1.00
 F1 A:BEF131 0.0 24.7 1.0
BE A:BEF131 1.4 28.8 1.0
F3 A:BEF131 2.3 26.3 1.0
F2 A:BEF131 2.4 28.0 1.0
OD1 A:ASP57 2.6 21.4 1.0
OG1 A:THR87 2.6 20.6 1.0
N A:ASP59 2.9 23.3 1.0
O A:HOH206 3.0 33.0 1.0
N A:TRP58 3.3 21.5 1.0
CB A:TRP58 3.3 24.1 1.0
CB A:THR87 3.4 17.4 1.0
CG A:ASP57 3.5 23.8 1.0
CA A:TRP58 3.6 23.9 1.0
CB A:ASP59 3.6 23.8 1.0
C A:TRP58 3.7 26.5 1.0
CA A:ASP59 3.8 25.8 1.0
CA A:THR87 3.9 19.1 1.0
N A:ALA88 3.9 20.7 1.0
OD2 A:ASP57 4.0 24.2 1.0
MN A:MN130 4.3 37.9 1.0
C A:THR87 4.4 26.2 1.0
CG A:TRP58 4.4 26.0 1.0
C A:ASP57 4.4 22.7 1.0
CG A:LYS89 4.4 24.1 1.0
O A:ASP59 4.6 27.9 1.0
N A:LYS89 4.6 23.2 1.0
CD A:LYS89 4.7 32.6 1.0
C A:ASP59 4.7 29.6 1.0
CB A:ASP57 4.7 16.8 1.0
CA A:ASP57 4.8 18.6 1.0
CG2 A:THR87 4.8 18.9 1.0
CA A:ALA88 4.9 24.9 1.0
NZ A:LYS109 4.9 21.7 1.0
O A:TRP58 4.9 23.9 1.0
CD1 A:TRP58 5.0 26.1 1.0

Fluorine binding site 2 out of 6 in 3rvp

Go back to Fluorine Binding Sites List in 3rvp
Fluorine binding site 2 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89K


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 E89K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F131

b:28.0
occ:1.00
 F2 A:BEF131 0.0 28.0 1.0
BE A:BEF131 1.4 28.8 1.0
F3 A:BEF131 2.3 26.3 1.0
F1 A:BEF131 2.4 24.7 1.0
OD1 A:ASP57 2.5 21.4 1.0
NZ A:LYS109 2.8 21.7 1.0
N A:ALA88 3.0 20.7 1.0
CE A:LYS109 3.4 25.2 1.0
CA A:THR87 3.4 19.1 1.0
CD A:LYS109 3.5 23.4 1.0
CG A:ASP57 3.6 23.8 1.0
C A:THR87 3.6 26.2 1.0
OG1 A:THR87 3.7 20.6 1.0
O A:HOH206 3.7 33.0 1.0
CB A:ALA88 3.9 16.6 1.0
OD2 A:ASP57 4.0 24.2 1.0
CB A:THR87 4.0 17.4 1.0
O A:HOH212 4.0 26.4 1.0
CA A:ALA88 4.0 24.9 1.0
MN A:MN130 4.1 37.9 1.0
O A:VAL86 4.4 23.5 1.0
N A:THR87 4.6 20.5 1.0
CG A:LYS109 4.6 21.7 1.0
N A:TRP58 4.7 21.5 1.0
CB A:ASP57 4.8 16.8 1.0
O A:THR87 4.8 29.0 1.0
OD2 A:ASP12 4.9 21.3 1.0
O A:HOH234 4.9 22.7 1.0
N A:ASP59 4.9 23.3 1.0
C A:VAL86 4.9 24.8 1.0
N A:LYS89 5.0 23.2 1.0

Fluorine binding site 3 out of 6 in 3rvp

Go back to Fluorine Binding Sites List in 3rvp
Fluorine binding site 3 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89K


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 E89K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F131

b:26.3
occ:1.00
 F3 A:BEF131 0.0 26.3 1.0
BE A:BEF131 1.4 28.8 1.0
F1 A:BEF131 2.3 24.7 1.0
F2 A:BEF131 2.3 28.0 1.0
MN A:MN130 2.3 37.9 1.0
OD1 A:ASP57 2.7 21.4 1.0
OD2 A:ASP57 3.0 24.2 1.0
CG A:ASP57 3.2 23.8 1.0
CB A:ASP59 3.3 23.8 1.0
O A:ASP59 3.4 27.9 1.0
O A:HOH212 3.4 26.4 1.0
O A:HOH206 3.4 33.0 1.0
O A:HOH213 3.5 29.8 1.0
N A:ASP59 3.5 23.3 1.0
CA A:ASP59 3.8 25.8 1.0
C A:ASP59 4.0 29.6 1.0
NZ A:LYS109 4.1 21.7 1.0
CG A:ASP59 4.4 35.1 1.0
N A:TRP58 4.5 21.5 1.0
OD2 A:ASP13 4.5 22.7 1.0
C A:TRP58 4.6 26.5 1.0
CB A:ASP57 4.7 16.8 1.0
OG1 A:THR87 4.8 20.6 1.0
OD2 A:ASP59 4.8 39.8 1.0
N A:ALA88 4.9 20.7 1.0
O A:HOH154 5.0 38.8 1.0

Fluorine binding site 4 out of 6 in 3rvp

Go back to Fluorine Binding Sites List in 3rvp
Fluorine binding site 4 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89K


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 E89K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F131

b:30.7
occ:1.00
 F1 B:BEF131 0.0 30.7 1.0
BE B:BEF131 1.4 32.6 1.0
F2 B:BEF131 2.3 25.2 1.0
F3 B:BEF131 2.3 27.2 1.0
OD1 B:ASP57 2.7 26.0 1.0
N B:ALA88 2.8 26.3 1.0
NZ B:LYS109 3.0 28.3 1.0
O B:HOH192 3.2 43.2 1.0
CE B:LYS109 3.4 24.6 1.0
CA B:THR87 3.5 24.1 1.0
CD B:LYS109 3.5 21.3 1.0
C B:THR87 3.6 27.0 1.0
OG1 B:THR87 3.6 26.0 1.0
CB B:ALA88 3.6 22.3 1.0
CG B:ASP57 3.7 20.3 1.0
CA B:ALA88 3.8 30.5 1.0
O B:HOH186 4.0 24.3 1.0
CB B:THR87 4.0 21.6 1.0
O B:HOH204 4.1 41.0 1.0
OD2 B:ASP57 4.1 21.8 1.0
MN B:MN130 4.3 38.5 1.0
O B:VAL86 4.5 28.5 1.0
CG B:LYS109 4.6 22.8 1.0
N B:THR87 4.7 21.9 1.0
N B:LYS89 4.7 29.9 1.0
O B:THR87 4.8 28.7 1.0
O B:HOH205 4.8 36.2 1.0
C B:ALA88 4.8 29.9 1.0
N B:TRP58 4.9 20.7 1.0
CB B:ASP57 5.0 17.2 1.0
OD2 B:ASP12 5.0 25.9 1.0

Fluorine binding site 5 out of 6 in 3rvp

Go back to Fluorine Binding Sites List in 3rvp
Fluorine binding site 5 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89K


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 E89K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F131

b:25.2
occ:1.00
 F2 B:BEF131 0.0 25.2 1.0
BE B:BEF131 1.4 32.6 1.0
MN B:MN130 2.2 38.5 1.0
F1 B:BEF131 2.3 30.7 1.0
F3 B:BEF131 2.3 27.2 1.0
OD1 B:ASP57 2.7 26.0 1.0
OD2 B:ASP57 2.7 21.8 1.0
CG B:ASP57 3.1 20.3 1.0
O B:HOH186 3.1 24.3 1.0
O B:HOH192 3.2 43.2 1.0
O B:ASP59 3.3 30.1 1.0
O B:HOH189 3.4 31.3 1.0
CB B:ASP59 3.5 29.5 1.0
N B:ASP59 3.7 21.3 1.0
O B:HOH204 3.9 41.0 1.0
NZ B:LYS109 3.9 28.3 1.0
CA B:ASP59 4.0 24.8 1.0
C B:ASP59 4.1 30.8 1.0
OD1 B:ASP13 4.4 26.1 1.0
CG B:ASP59 4.5 32.2 1.0
CB B:ASP57 4.6 17.2 1.0
N B:TRP58 4.6 20.7 1.0
OD2 B:ASP59 4.6 44.4 1.0
O B:HOH218 4.7 45.4 1.0
C B:TRP58 4.8 26.4 1.0
OG1 B:THR87 4.8 26.0 1.0
N B:ALA88 4.9 26.3 1.0

Fluorine binding site 6 out of 6 in 3rvp

Go back to Fluorine Binding Sites List in 3rvp
Fluorine binding site 6 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89K


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 E89K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F131

b:27.2
occ:1.00
 F3 B:BEF131 0.0 27.2 1.0
BE B:BEF131 1.4 32.6 1.0
F2 B:BEF131 2.3 25.2 1.0
F1 B:BEF131 2.3 30.7 1.0
OD1 B:ASP57 2.5 26.0 1.0
OG1 B:THR87 2.7 26.0 1.0
N B:ASP59 2.8 21.3 1.0
N B:TRP58 3.2 20.7 1.0
CG B:ASP57 3.4 20.3 1.0
CB B:TRP58 3.5 25.6 1.0
CB B:THR87 3.5 21.6 1.0
CB B:ASP59 3.5 29.5 1.0
CA B:TRP58 3.6 24.0 1.0
C B:TRP58 3.7 26.4 1.0
CA B:ASP59 3.7 24.8 1.0
OD2 B:ASP57 3.8 21.8 1.0
N B:ALA88 3.9 26.3 1.0
CA B:THR87 3.9 24.1 1.0
O B:HOH204 3.9 41.0 1.0
MN B:MN130 4.2 38.5 1.0
C B:ASP57 4.4 23.0 1.0
O B:ASP59 4.4 30.1 1.0
C B:THR87 4.4 27.0 1.0
C B:ASP59 4.5 30.8 1.0
CG B:LYS89 4.6 33.3 1.0
CG B:TRP58 4.6 32.9 1.0
CB B:ASP57 4.6 17.2 1.0
O B:HOH192 4.7 43.2 1.0
N B:LYS89 4.7 29.9 1.0
CA B:ASP57 4.7 18.9 1.0
O B:TRP58 4.9 30.5 1.0
NZ B:LYS109 4.9 28.3 1.0
CG2 B:THR87 4.9 24.4 1.0
CG B:ASP59 4.9 32.2 1.0
CA B:ALA88 4.9 30.5 1.0
CD B:LYS89 5.0 33.1 1.0
CB B:ALA88 5.0 22.3 1.0
O B:VAL86 5.0 28.5 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 22:23:35 2024

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