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Fluorine in PDB 3ffx: Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+

Protein crystallography data

The structure of Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+, PDB code: 3ffx was solved by Y.Pazy, E.J.Collins, R.B.Bourret, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.97 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.564, 53.408, 161.839, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21

Other elements in 3ffx:

The structure of Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+ also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+ (pdb code 3ffx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+, PDB code: 3ffx:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3ffx

Go back to Fluorine Binding Sites List in 3ffx
Fluorine binding site 1 out of 6 in the Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F130

b:26.1
occ:1.00
 F1 A:BEF130 0.0 26.1 1.0
BE A:BEF130 1.7 23.0 1.0
MN A:MN202 2.0 26.0 1.0
O A:HOH318 2.7 22.5 1.0
O A:HOH343 2.8 51.5 1.0
F3 A:BEF130 2.9 21.2 1.0
OD1 A:ASP57 2.9 18.9 1.0
F2 A:BEF130 2.9 23.5 1.0
O A:ARG59 3.0 22.2 1.0
OD2 A:ASP57 3.0 22.3 1.0
O A:HOH223 3.1 20.0 1.0
CB A:ARG59 3.2 23.4 0.5
CG A:ASP57 3.3 19.5 1.0
CB A:ARG59 3.4 23.2 0.5
O A:HOH216 3.5 33.2 1.0
O A:HOH335 3.5 39.7 1.0
N A:ARG59 3.6 22.7 1.0
CA A:ARG59 3.7 22.9 0.5
CA A:ARG59 3.7 22.9 0.5
C A:ARG59 3.8 22.8 1.0
CG A:ARG59 4.1 24.7 0.5
OD1 A:ASP13 4.1 20.3 1.0
NZ A:LYS109 4.3 18.1 1.0
CG A:ARG59 4.5 24.2 0.5
CD A:ARG59 4.6 26.0 0.5
C A:TRP58 4.7 21.5 1.0
OE1 A:GLU14 4.8 27.3 1.0
O A:HOH174 4.8 47.8 1.0
N A:TRP58 4.8 20.3 1.0
CB A:ASP57 4.8 19.7 1.0
NH1 A:ARG59 5.0 32.8 0.5

Fluorine binding site 2 out of 6 in 3ffx

Go back to Fluorine Binding Sites List in 3ffx
Fluorine binding site 2 out of 6 in the Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F130

b:23.5
occ:1.00
 F2 A:BEF130 0.0 23.5 1.0
BE A:BEF130 1.7 23.0 1.0
OG1 A:THR87 2.4 19.7 1.0
OD1 A:ASP57 2.7 18.9 1.0
O A:HOH335 2.7 39.7 1.0
F3 A:BEF130 2.8 21.2 1.0
N A:ARG59 2.8 22.7 1.0
F1 A:BEF130 2.9 26.1 1.0
N A:TRP58 3.1 20.3 1.0
CB A:TRP58 3.2 22.0 1.0
CB A:THR87 3.3 19.6 1.0
CA A:TRP58 3.4 21.6 1.0
C A:TRP58 3.6 21.5 1.0
CG A:ASP57 3.7 19.5 1.0
CB A:ARG59 3.7 23.4 0.5
CA A:THR87 3.8 20.5 1.0
CB A:ARG59 3.8 23.2 0.5
CA A:ARG59 3.8 22.9 0.5
CA A:ARG59 3.9 22.9 0.5
N A:ALA88 3.9 21.5 1.0
O A:HOH343 4.2 51.5 1.0
ND1 A:HIS89 4.2 35.9 1.0
OD2 A:ASP57 4.3 22.3 1.0
C A:ASP57 4.3 19.9 1.0
CG A:TRP58 4.3 22.2 1.0
C A:THR87 4.3 20.4 1.0
MN A:MN202 4.5 26.0 1.0
N A:HIS89 4.5 23.5 1.0
CE1 A:HIS89 4.5 36.6 1.0
CG2 A:THR87 4.7 22.1 1.0
CA A:ASP57 4.7 19.2 1.0
O A:ARG59 4.7 22.2 1.0
C A:ARG59 4.8 22.8 1.0
CG A:HIS89 4.8 29.2 1.0
CB A:ASP57 4.8 19.7 1.0
O A:TRP58 4.8 19.8 1.0
CA A:ALA88 4.9 22.3 1.0
O A:HOH216 4.9 33.2 1.0
O A:VAL86 5.0 19.6 1.0
CD1 A:TRP58 5.0 23.4 1.0
CB A:ALA88 5.0 22.6 1.0

Fluorine binding site 3 out of 6 in 3ffx

Go back to Fluorine Binding Sites List in 3ffx
Fluorine binding site 3 out of 6 in the Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F130

b:21.2
occ:1.00
 F3 A:BEF130 0.0 21.2 1.0
BE A:BEF130 1.7 23.0 1.0
NZ A:LYS109 2.6 18.1 1.0
OD1 A:ASP57 2.7 18.9 1.0
F2 A:BEF130 2.8 23.5 1.0
O A:HOH216 2.8 33.2 1.0
N A:ALA88 2.9 21.5 1.0
F1 A:BEF130 2.9 26.1 1.0
CE A:LYS109 3.2 21.4 1.0
CD A:LYS109 3.2 21.9 1.0
CA A:THR87 3.5 20.5 1.0
O A:HOH335 3.6 39.7 1.0
C A:THR87 3.6 20.4 1.0
CB A:ALA88 3.6 22.6 1.0
CG A:ASP57 3.8 19.5 1.0
CA A:ALA88 3.8 22.3 1.0
OG1 A:THR87 3.8 19.7 1.0
O A:HOH343 3.9 51.5 1.0
O A:HOH223 3.9 20.0 1.0
CB A:THR87 4.2 19.6 1.0
MN A:MN202 4.3 26.0 1.0
OD2 A:ASP57 4.4 22.3 1.0
O A:VAL86 4.4 19.6 1.0
CG A:LYS109 4.4 20.5 1.0
O A:HOH219 4.6 26.9 1.0
N A:THR87 4.6 20.3 1.0
O A:THR87 4.8 21.3 1.0
OD2 A:ASP12 4.9 19.8 1.0
C A:ALA88 4.9 22.8 1.0
C A:VAL86 4.9 19.5 1.0
N A:TRP58 5.0 20.3 1.0
CB A:ASP57 5.0 19.7 1.0
O A:HOH308 5.0 47.9 1.0
N A:HIS89 5.0 23.5 1.0

Fluorine binding site 4 out of 6 in 3ffx

Go back to Fluorine Binding Sites List in 3ffx
Fluorine binding site 4 out of 6 in the Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F130

b:27.2
occ:1.00
 F1 B:BEF130 0.0 27.2 1.0
BE B:BEF130 1.7 24.8 1.0
MN B:MN202 2.0 30.0 1.0
O B:HOH331 2.6 42.6 1.0
O B:HOH319 2.7 28.8 1.0
F3 B:BEF130 2.8 23.3 1.0
F2 B:BEF130 2.9 26.9 1.0
OD1 B:ASP57 3.0 22.3 1.0
O B:HOH199 3.1 22.9 1.0
OD2 B:ASP57 3.1 22.1 1.0
O B:ARG59 3.1 24.8 1.0
O B:HOH332 3.2 42.6 1.0
CB B:ARG59 3.4 24.4 0.5
CG B:ASP57 3.4 22.0 1.0
CB B:ARG59 3.5 24.8 0.5
N B:ARG59 3.7 24.2 1.0
CA B:ARG59 3.8 24.4 0.5
CA B:ARG59 3.8 24.9 0.5
C B:ARG59 3.9 24.7 1.0
NZ B:LYS109 4.2 23.3 1.0
NE2 B:HIS89 4.2 40.9 1.0
CG B:ARG59 4.2 25.5 0.5
OD1 B:ASP13 4.3 29.9 1.0
CD2 B:HIS89 4.3 40.0 1.0
CG B:ARG59 4.6 24.4 0.5
NE B:ARG59 4.8 30.7 0.5
C B:TRP58 4.8 23.7 1.0
OE1 B:GLU14 4.9 31.2 1.0
CB B:ASP57 4.9 21.2 1.0
N B:TRP58 4.9 23.2 1.0
CD B:ARG59 5.0 24.9 0.5
O B:HOH161 5.0 28.6 1.0
CZ B:ARG59 5.0 31.5 0.5

Fluorine binding site 5 out of 6 in 3ffx

Go back to Fluorine Binding Sites List in 3ffx
Fluorine binding site 5 out of 6 in the Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F130

b:26.9
occ:1.00
 F2 B:BEF130 0.0 26.9 1.0
BE B:BEF130 1.7 24.8 1.0
OG1 B:THR87 2.5 23.1 1.0
OD1 B:ASP57 2.7 22.3 1.0
F3 B:BEF130 2.7 23.3 1.0
N B:ARG59 2.8 24.2 1.0
F1 B:BEF130 2.9 27.2 1.0
N B:TRP58 3.1 23.2 1.0
CB B:TRP58 3.2 24.0 1.0
CD2 B:HIS89 3.3 40.0 1.0
CB B:THR87 3.3 23.9 1.0
CA B:TRP58 3.4 23.7 1.0
C B:TRP58 3.5 23.7 1.0
CG B:ASP57 3.7 22.0 1.0
CB B:ARG59 3.8 24.4 0.5
CA B:ARG59 3.9 24.4 0.5
CA B:THR87 3.9 24.8 1.0
CA B:ARG59 3.9 24.9 0.5
CB B:ARG59 3.9 24.8 0.5
N B:ALA88 4.0 27.3 1.0
NE2 B:HIS89 4.1 40.9 1.0
OD2 B:ASP57 4.2 22.1 1.0
O B:HOH331 4.3 42.6 1.0
C B:ASP57 4.3 21.9 1.0
CG B:HIS89 4.3 37.1 1.0
CG B:TRP58 4.4 24.7 1.0
C B:THR87 4.5 25.5 1.0
MN B:MN202 4.5 30.0 1.0
N B:HIS89 4.6 31.4 1.0
O B:ARG59 4.6 24.8 1.0
CG2 B:THR87 4.7 24.6 1.0
CA B:ASP57 4.7 22.0 1.0
C B:ARG59 4.7 24.7 1.0
O B:TRP58 4.8 23.4 1.0
CB B:ASP57 4.8 21.2 1.0
CB B:HIS89 4.8 34.3 1.0
O B:VAL86 4.9 23.4 1.0
O B:HOH332 4.9 42.6 1.0

Fluorine binding site 6 out of 6 in 3ffx

Go back to Fluorine Binding Sites List in 3ffx
Fluorine binding site 6 out of 6 in the Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Chey Triple Mutant F14E, N59R, E89H Complexed with BEF3- and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F130

b:23.3
occ:1.00
 F3 B:BEF130 0.0 23.3 1.0
BE B:BEF130 1.7 24.8 1.0
F2 B:BEF130 2.7 26.9 1.0
N B:ALA88 2.8 27.3 1.0
NZ B:LYS109 2.8 23.3 1.0
OD1 B:ASP57 2.8 22.3 1.0
F1 B:BEF130 2.8 27.2 1.0
O B:HOH332 3.0 42.6 1.0
CE B:LYS109 3.2 25.2 1.0
CD B:LYS109 3.3 25.1 1.0
CA B:THR87 3.4 24.8 1.0
CB B:ALA88 3.5 29.0 1.0
C B:THR87 3.6 25.5 1.0
OG1 B:THR87 3.6 23.1 1.0
CA B:ALA88 3.7 28.9 1.0
O B:HOH331 3.9 42.6 1.0
CG B:ASP57 4.0 22.0 1.0
CB B:THR87 4.0 23.9 1.0
O B:HOH199 4.0 22.9 1.0
O B:HOH161 4.1 28.6 1.0
CD2 B:HIS89 4.2 40.0 1.0
O B:VAL86 4.4 23.4 1.0
MN B:MN202 4.4 30.0 1.0
CG B:LYS109 4.4 24.9 1.0
OD2 B:ASP57 4.4 22.1 1.0
NE2 B:HIS89 4.5 40.9 1.0
N B:THR87 4.6 23.2 1.0
N B:HIS89 4.7 31.4 1.0
C B:ALA88 4.7 29.8 1.0
O B:THR87 4.8 24.6 1.0
C B:VAL86 4.9 23.1 1.0

Reference:

Y.Pazy, A.C.Wollish, S.A.Thomas, P.J.Miller, E.J.Collins, R.B.Bourret, R.E.Silversmith. Matching Biochemical Reaction Kinetics to the Timescales of Life: Structural Determinants That Influence the Autodephosphorylation Rate of Response Regulator Proteins. J.Mol.Biol. V. 392 1205 2009.
ISSN: ISSN 0022-2836
PubMed: 19646451
DOI: 10.1016/J.JMB.2009.07.064
Page generated: Wed Jul 31 18:31:12 2024

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