Fluorine in PDB 3rvl: Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R

The structure of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R, PDB code: 3rvl 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)	25.92 / 1.55
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	37.630, 72.436, 107.280, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.2

The structure of Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Fluorine atom in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R (pdb code 3rvl). 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 E89R, PDB code: 3rvl:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R


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 E89R within 5.0Å range: probe atom residue distance (Å) B Occ A:F130 b:13.1 occ:1.00 F1 A:BEF130 0.0 13.1 1.0 BE A:BEF130 1.5 10.2 1.0 H A:ALA88 2.0 12.5 1.0 HE3 A:LYS109 2.4 23.9 1.0 F3 A:BEF130 2.4 12.4 1.0 F2 A:BEF130 2.4 12.4 1.0 OD1 A:ASP57 2.5 11.5 1.0 HZ1 A:LYS109 2.6 15.3 1.0 HA A:THR87 2.8 11.7 1.0 N A:ALA88 2.8 10.4 1.0 O A:HOH151 2.9 15.1 1.0 HG1 A:THR87 3.0 13.5 1.0 CE A:LYS109 3.1 19.9 1.0 NZ A:LYS109 3.1 12.8 1.0 HZ2 A:LYS109 3.1 15.3 1.0 HB3 A:ALA88 3.2 13.8 1.0 HB2 A:ALA88 3.3 13.8 1.0 HE2 A:LYS109 3.4 23.9 1.0 CB A:ALA88 3.6 11.5 1.0 CA A:THR87 3.6 9.8 1.0 CG A:ASP57 3.6 10.4 1.0 C A:THR87 3.7 11.1 1.0 OG1 A:THR87 3.7 11.2 1.0 CA A:ALA88 3.8 10.1 1.0 O A:HOH135 3.8 12.9 1.0 HZ3 A:LYS109 3.9 15.3 1.0 H A:TRP58 3.9 13.3 1.0 O A:HOH157 4.0 17.8 1.0 CB A:THR87 4.2 9.8 1.0 OD2 A:ASP57 4.2 11.8 1.0 MN A:MN131 4.2 15.2 1.0 H A:ARG89 4.2 12.6 1.0 H A:ASP59 4.2 12.7 1.0 CD A:LYS109 4.3 30.3 1.0 HB A:THR87 4.4 11.8 1.0 HD2 A:LYS109 4.4 36.4 1.0 HG3 A:LYS109 4.4 16.6 1.0 HA A:ALA88 4.5 12.1 1.0 HB1 A:ALA88 4.5 13.8 1.0 HB2 A:LYS109 4.5 15.6 1.0 HB2 A:ASP59 4.6 13.2 1.0 HG3 A:ARG89 4.7 14.6 1.0 O A:VAL86 4.7 10.8 1.0 HA A:ASP57 4.7 9.8 1.0 N A:ARG89 4.8 10.5 1.0 N A:TRP58 4.8 11.1 1.0 N A:THR87 4.8 9.8 1.0 C A:ALA88 4.8 9.8 1.0 CG A:LYS109 4.8 13.8 1.0 O A:THR87 4.8 10.8 1.0 CB A:ASP57 4.9 11.5 1.0 HB3 A:TRP58 4.9 14.5 1.0 N A:ASP59 5.0 10.6 1.0

Fluorine binding site 2 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R


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 E89R within 5.0Å range: probe atom residue distance (Å) B Occ A:F130 b:12.4 occ:1.00 F2 A:BEF130 0.0 12.4 1.0 BE A:BEF130 1.4 10.2 1.0 MN A:MN131 2.2 15.2 1.0 F3 A:BEF130 2.4 12.4 1.0 F1 A:BEF130 2.4 13.1 1.0 OD1 A:ASP57 2.6 11.5 1.0 HB2 A:ASP59 2.7 13.2 1.0 OD2 A:ASP57 2.9 11.8 1.0 H A:ASP59 2.9 12.7 1.0 O A:HOH135 3.0 12.9 1.0 O A:HOH145 3.0 11.1 1.0 O A:ASP59 3.1 10.3 1.0 CG A:ASP57 3.1 10.4 1.0 O A:HOH151 3.3 15.1 1.0 O A:HOH157 3.4 17.8 1.0 N A:ASP59 3.5 10.6 1.0 CB A:ASP59 3.5 11.0 1.0 HZ1 A:LYS109 3.6 15.3 1.0 CA A:ASP59 3.8 9.5 1.0 C A:ASP59 3.8 10.9 1.0 H A:TRP58 3.9 13.3 1.0 HB3 A:ASP59 4.0 13.2 1.0 HG1 A:THR87 4.1 13.5 1.0 H A:ALA88 4.3 12.5 1.0 OD1 A:ASP13 4.3 11.7 1.0 NZ A:LYS109 4.4 12.8 1.0 HZ2 A:LYS109 4.4 15.3 1.0 C A:TRP58 4.5 13.1 1.0 N A:TRP58 4.5 11.1 1.0 CG A:ASP59 4.6 11.2 1.0 HE3 A:LYS109 4.6 23.9 1.0 CB A:ASP57 4.6 11.5 1.0 HB3 A:TRP58 4.6 14.5 1.0 OD2 A:ASP59 4.6 12.3 1.0 HB3 A:ALA88 4.7 13.8 1.0 HA A:ASP59 4.7 11.4 1.0 HA A:THR87 4.8 11.7 1.0 HG3 A:MET60 4.9 10.6 1.0 OG1 A:THR87 4.9 11.2 1.0 HB3 A:ASP57 5.0 13.8 1.0 CA A:TRP58 5.0 9.5 1.0

Fluorine binding site 3 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R


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 E89R within 5.0Å range: probe atom residue distance (Å) B Occ A:F130 b:12.4 occ:1.00 F3 A:BEF130 0.0 12.4 1.0 BE A:BEF130 1.4 10.2 1.0 HG1 A:THR87 1.9 13.5 1.0 H A:ASP59 2.1 12.7 1.0 H A:TRP58 2.3 13.3 1.0 F2 A:BEF130 2.4 12.4 1.0 F1 A:BEF130 2.4 13.1 1.0 OD1 A:ASP57 2.4 11.5 1.0 HB3 A:TRP58 2.5 14.5 1.0 OG1 A:THR87 2.7 11.2 1.0 N A:ASP59 2.9 10.6 1.0 N A:TRP58 3.1 11.1 1.0 CB A:TRP58 3.3 12.1 1.0 H A:ALA88 3.3 12.5 1.0 HA A:THR87 3.3 11.7 1.0 HB2 A:ASP59 3.4 13.2 1.0 HB A:THR87 3.4 11.8 1.0 CG A:ASP57 3.4 10.4 1.0 HG3 A:ARG89 3.4 14.6 1.0 CA A:TRP58 3.5 9.5 1.0 CB A:THR87 3.5 9.8 1.0 C A:TRP58 3.6 13.1 1.0 HB2 A:TRP58 3.6 14.5 1.0 O A:HOH157 3.7 17.8 1.0 CA A:THR87 3.9 9.8 1.0 OD2 A:ASP57 3.9 11.8 1.0 H A:ARG89 3.9 12.6 1.0 N A:ALA88 4.0 10.4 1.0 CA A:ASP59 4.0 9.5 1.0 CB A:ASP59 4.0 11.0 1.0 C A:ASP57 4.2 12.0 1.0 HD2 A:ARG89 4.2 13.2 1.0 HA A:ASP57 4.3 9.8 1.0 MN A:MN131 4.3 15.2 1.0 HZ1 A:LYS109 4.3 15.3 1.0 CG A:ARG89 4.3 12.1 1.0 HE3 A:LYS109 4.4 23.9 1.0 C A:THR87 4.4 11.1 1.0 HB3 A:ALA88 4.4 13.8 1.0 CG A:ASP59 4.4 11.2 1.0 OD2 A:ASP59 4.4 12.3 1.0 HA A:TRP58 4.4 11.4 1.0 O A:ASP59 4.5 10.3 1.0 CG A:TRP58 4.5 9.3 1.0 CB A:ASP57 4.5 11.5 1.0 HD3 A:ARG89 4.5 13.2 1.0 CA A:ASP57 4.6 8.2 1.0 O A:HOH151 4.6 15.1 1.0 CD A:ARG89 4.6 11.0 1.0 C A:ASP59 4.7 10.9 1.0 N A:ARG89 4.7 10.5 1.0 HA A:ASP59 4.7 11.4 1.0 O A:TRP58 4.8 12.3 1.0 HB2 A:ARG89 4.8 13.2 1.0 CG2 A:THR87 4.9 11.0 1.0 HB3 A:ASP59 4.9 13.2 1.0 HG2 A:ARG89 4.9 14.6 1.0 HE2 A:LYS109 4.9 23.9 1.0 CA A:ALA88 5.0 10.1 1.0 CE A:LYS109 5.0 19.9 1.0 HG21 A:THR87 5.0 13.2 1.0

Fluorine binding site 4 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R


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 E89R within 5.0Å range: probe atom residue distance (Å) B Occ B:F130 b:10.1 occ:1.00 F1 B:BEF130 0.0 10.1 1.0 BE B:BEF130 1.5 6.3 1.0 H B:ALA88 2.0 10.5 1.0 HZ2 B:LYS109 2.2 12.2 1.0 F3 B:BEF130 2.4 10.3 1.0 F2 B:BEF130 2.4 10.6 1.0 OD1 B:ASP57 2.5 9.8 1.0 HA B:THR87 2.8 10.5 1.0 HD2 B:LYS109 2.8 26.4 1.0 O B:HOH233 2.9 13.1 1.0 N B:ALA88 2.9 8.8 1.0 HG1 B:THR87 2.9 12.3 1.0 NZ B:LYS109 3.0 10.2 1.0 HB3 B:ALA88 3.2 11.6 1.0 HE3 B:LYS109 3.4 17.2 1.0 HB2 B:ALA88 3.4 11.6 1.0 HZ1 B:LYS109 3.5 12.2 1.0 CE B:LYS109 3.5 14.3 1.0 HZ3 B:LYS109 3.6 12.2 1.0 CD B:LYS109 3.6 22.0 1.0 CA B:THR87 3.6 8.7 1.0 CG B:ASP57 3.6 9.6 1.0 CB B:ALA88 3.6 9.7 1.0 OG1 B:THR87 3.6 10.3 1.0 C B:THR87 3.7 8.5 1.0 O B:HOH136 3.8 10.2 1.0 CA B:ALA88 3.8 10.4 1.0 H B:TRP58 3.9 11.0 1.0 HD3 B:LYS109 4.0 26.4 1.0 O B:HOH144 4.0 17.0 1.0 CB B:THR87 4.1 8.5 1.0 OD2 B:ASP57 4.1 8.8 1.0 H B:ARG89 4.2 11.2 1.0 MN B:MN131 4.2 13.2 1.0 H B:ASP59 4.2 11.0 1.0 HB B:THR87 4.3 10.2 1.0 HE2 B:LYS109 4.5 17.2 1.0 HA B:ALA88 4.5 12.5 1.0 HB1 B:ALA88 4.6 11.6 1.0 O B:VAL86 4.6 8.9 1.0 HG3 B:ARG89 4.6 11.5 1.0 HB2 B:LYS109 4.7 12.8 1.0 HB2 B:ASP59 4.7 9.2 1.0 HA B:ASP57 4.7 10.2 1.0 HG3 B:LYS109 4.7 14.2 1.0 N B:ARG89 4.8 9.4 1.0 N B:TRP58 4.8 9.1 1.0 CG B:LYS109 4.8 11.8 1.0 N B:THR87 4.8 8.2 1.0 C B:ALA88 4.8 9.1 1.0 CB B:ASP57 4.9 9.6 1.0 HB3 B:TRP58 4.9 12.9 1.0 O B:THR87 4.9 9.1 1.0 O B:HOH213 5.0 17.7 1.0 N B:ASP59 5.0 9.2 1.0

Fluorine binding site 5 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R


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 E89R within 5.0Å range: probe atom residue distance (Å) B Occ B:F130 b:10.6 occ:1.00 F2 B:BEF130 0.0 10.6 1.0 BE B:BEF130 1.5 6.3 1.0 MN B:MN131 2.2 13.2 1.0 F3 B:BEF130 2.4 10.3 1.0 F1 B:BEF130 2.4 10.1 1.0 OD1 B:ASP57 2.6 9.8 1.0 HB2 B:ASP59 2.6 9.2 1.0 H B:ASP59 2.8 11.0 1.0 OD2 B:ASP57 2.9 8.8 1.0 O B:HOH136 3.0 10.2 1.0 O B:HOH143 3.1 9.6 1.0 CG B:ASP57 3.1 9.6 1.0 O B:ASP59 3.1 10.4 1.0 O B:HOH233 3.3 13.1 1.0 O B:HOH144 3.3 17.0 1.0 N B:ASP59 3.4 9.2 1.0 CB B:ASP59 3.5 7.7 1.0 HZ2 B:LYS109 3.6 12.2 1.0 CA B:ASP59 3.7 9.8 1.0 C B:ASP59 3.8 9.5 1.0 H B:TRP58 3.8 11.0 1.0 HB3 B:ASP59 4.0 9.2 1.0 HG1 B:THR87 4.1 12.3 1.0 OD1 B:ASP13 4.3 10.4 1.0 H B:ALA88 4.3 10.5 1.0 NZ B:LYS109 4.4 10.2 1.0 HZ1 B:LYS109 4.5 12.2 1.0 N B:TRP58 4.5 9.1 1.0 C B:TRP58 4.5 12.0 1.0 CG B:ASP59 4.5 12.7 1.0 O B:HOH213 4.6 17.7 1.0 OD2 B:ASP59 4.6 12.5 1.0 HB3 B:TRP58 4.6 12.9 1.0 CB B:ASP57 4.6 9.6 1.0 HB3 B:ALA88 4.7 11.6 1.0 HA B:ASP59 4.7 11.7 1.0 HZ3 B:LYS109 4.8 12.2 1.0 HA B:THR87 4.8 10.5 1.0 OG1 B:THR87 4.9 10.3 1.0 HG3 B:MET60 4.9 10.7 1.0 CA B:TRP58 5.0 8.8 1.0 HG3 B:ARG89 5.0 11.5 1.0

Fluorine binding site 6 out of 6 in the Structure of the Chey-BEF3 Complex with Substitutions at 59 and 89: N59D and E89R


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 E89R within 5.0Å range: probe atom residue distance (Å) B Occ B:F130 b:10.3 occ:1.00 F3 B:BEF130 0.0 10.3 1.0 BE B:BEF130 1.4 6.3 1.0 HG1 B:THR87 1.9 12.3 1.0 H B:ASP59 2.1 11.0 1.0 H B:TRP58 2.3 11.0 1.0 F2 B:BEF130 2.4 10.6 1.0 F1 B:BEF130 2.4 10.1 1.0 OD1 B:ASP57 2.5 9.8 1.0 HB3 B:TRP58 2.5 12.9 1.0 OG1 B:THR87 2.6 10.3 1.0 N B:ASP59 2.9 9.2 1.0 N B:TRP58 3.1 9.1 1.0 CB B:TRP58 3.3 10.7 1.0 HG3 B:ARG89 3.3 11.5 1.0 HB B:THR87 3.3 10.2 1.0 H B:ALA88 3.4 10.5 1.0 HB2 B:ASP59 3.4 9.2 1.0 HA B:THR87 3.4 10.5 1.0 CG B:ASP57 3.4 9.6 1.0 CA B:TRP58 3.4 8.8 1.0 CB B:THR87 3.5 8.5 1.0 HB2 B:TRP58 3.6 12.9 1.0 C B:TRP58 3.6 12.0 1.0 O B:HOH144 3.7 17.0 1.0 H B:ARG89 3.9 11.2 1.0 CA B:THR87 3.9 8.7 1.0 OD2 B:ASP57 3.9 8.8 1.0 CA B:ASP59 4.0 9.8 1.0 CB B:ASP59 4.0 7.7 1.0 N B:ALA88 4.0 8.8 1.0 HD2 B:ARG89 4.2 13.6 1.0 CG B:ARG89 4.2 9.6 1.0 C B:ASP57 4.2 8.7 1.0 HZ2 B:LYS109 4.3 12.2 1.0 HA B:ASP57 4.3 10.2 1.0 MN B:MN131 4.3 13.2 1.0 CG B:ASP59 4.4 12.7 1.0 OD2 B:ASP59 4.4 12.5 1.0 HA B:TRP58 4.4 10.5 1.0 C B:THR87 4.5 8.5 1.0 HB3 B:ALA88 4.5 11.6 1.0 HD3 B:ARG89 4.5 13.6 1.0 CG B:TRP58 4.5 8.5 1.0 O B:ASP59 4.5 10.4 1.0 CD B:ARG89 4.6 11.4 1.0 CA B:ASP57 4.6 8.5 1.0 CB B:ASP57 4.6 9.6 1.0 O B:HOH233 4.6 13.1 1.0 N B:ARG89 4.7 9.4 1.0 C B:ASP59 4.7 9.5 1.0 HA B:ASP59 4.7 11.7 1.0 HB2 B:ARG89 4.7 12.0 1.0 O B:TRP58 4.8 12.3 1.0 HG2 B:ARG89 4.8 11.5 1.0 CG2 B:THR87 4.8 9.7 1.0 HB3 B:ASP59 4.9 9.2 1.0 HG21 B:THR87 5.0 11.7 1.0 HE3 B:LYS109 5.0 17.2 1.0 O B:VAL86 5.0 8.9 1.0 HD2 B:LYS109 5.0 26.4 1.0 O B:HOH136 5.0 10.2 1.0

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