Atomistry » Fluorine » PDB 3rjc-3s9y » 3rvn
Atomistry »
  Fluorine »
    PDB 3rjc-3s9y »
      3rvn »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy