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Fluorine in PDB 3myy: Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride

Protein crystallography data

The structure of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride, PDB code: 3myy was solved by R.M.Immormino, L.R.Mcdonald, R.B.Bourret, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.59 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.445, 53.547, 161.082, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.2

Other elements in 3myy:

The structure of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride also contains other interesting chemical elements:

Manganese (Mn) 7 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride (pdb code 3myy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride, PDB code: 3myy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 3myy

Go back to Fluorine Binding Sites List in 3myy
Fluorine binding site 1 out of 12 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F130

b:27.8
occ:1.00
 F1 A:BEF130 0.0 27.8 1.0
BE A:BEF130 1.4 34.1 1.0
F2 A:BEF130 2.3 33.6 1.0
F3 A:BEF130 2.3 27.3 1.0
OD1 A:ASP57 2.6 26.6 1.0
NZ A:LYS109 2.9 30.7 1.0
N A:ALA88 2.9 25.7 1.0
O A:HOH252 3.0 42.1 1.0
O A:HOH243 3.1 53.1 1.0
CA A:THR87 3.5 25.4 1.0
CD A:LYS109 3.5 26.9 1.0
CE A:LYS109 3.5 27.5 1.0
OG1 A:THR87 3.5 24.1 1.0
C A:THR87 3.7 27.9 1.0
CG A:ASP57 3.7 27.1 1.0
CB A:ALA88 3.7 27.2 1.0
CA A:ALA88 3.9 26.3 1.0
CB A:THR87 4.0 29.2 1.0
O A:HOH139 4.1 28.0 1.0
MN A:MN131 4.2 36.6 1.0
OD2 A:ASP57 4.2 25.9 1.0
O A:HOH157 4.3 47.7 1.0
O A:HOH250 4.3 45.8 1.0
O A:VAL86 4.5 27.9 1.0
CG A:LYS109 4.6 25.7 1.0
N A:THR87 4.7 26.3 1.0
N A:TRP58 4.7 23.0 1.0
N A:GLU89 4.8 27.1 1.0
O A:THR87 4.8 28.8 1.0
C A:ALA88 4.9 31.9 1.0
N A:ASN59 4.9 26.2 1.0
CB A:ASP57 4.9 25.2 1.0
OD2 A:ASP12 4.9 26.9 1.0

Fluorine binding site 2 out of 12 in 3myy

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Fluorine binding site 2 out of 12 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F130

b:33.6
occ:1.00
 F2 A:BEF130 0.0 33.6 1.0
BE A:BEF130 1.4 34.1 1.0
F3 A:BEF130 2.3 27.3 1.0
F1 A:BEF130 2.3 27.8 1.0
MN A:MN131 2.3 36.6 1.0
OD1 A:ASP57 2.6 26.6 1.0
O A:HOH243 3.0 53.1 1.0
OD2 A:ASP57 3.1 25.9 1.0
CG A:ASP57 3.2 27.1 1.0
CB A:ASN59 3.3 31.7 0.5
O A:HOH250 3.3 45.8 1.0
O A:HOH139 3.3 28.0 1.0
O A:HOH174 3.3 35.1 1.0
O A:HOH252 3.3 42.1 1.0
CB A:ASN59 3.3 31.7 0.5
O A:ASN59 3.4 25.7 1.0
N A:ASN59 3.5 26.2 1.0
CA A:ASN59 3.7 31.3 0.5
CA A:ASN59 3.7 31.3 0.5
C A:ASN59 4.0 30.1 1.0
ND2 A:ASN59 4.1 40.0 0.5
CG A:ASN59 4.1 36.1 0.5
NZ A:LYS109 4.1 30.7 1.0
OD1 A:ASP13 4.5 29.9 1.0
CG A:ASN59 4.5 36.7 0.5
N A:TRP58 4.6 23.0 1.0
C A:TRP58 4.6 29.2 1.0
O A:HOH169 4.7 47.4 1.0
CB A:ASP57 4.7 25.2 1.0
OG1 A:THR87 4.7 24.1 1.0
ND2 A:ASN59 4.8 38.4 0.5
O A:HOH377 4.9 64.8 1.0
N A:ALA88 5.0 25.7 1.0

Fluorine binding site 3 out of 12 in 3myy

Go back to Fluorine Binding Sites List in 3myy
Fluorine binding site 3 out of 12 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F130

b:27.3
occ:1.00
 F3 A:BEF130 0.0 27.3 1.0
BE A:BEF130 1.4 34.1 1.0
F2 A:BEF130 2.3 33.6 1.0
F1 A:BEF130 2.3 27.8 1.0
OD1 A:ASP57 2.5 26.6 1.0
OG1 A:THR87 2.6 24.1 1.0
O A:HOH243 2.6 53.1 1.0
N A:ASN59 2.8 26.2 1.0
N A:TRP58 3.2 23.0 1.0
CB A:TRP58 3.3 26.9 1.0
CB A:THR87 3.4 29.2 1.0
CG A:ASP57 3.5 27.1 1.0
CA A:TRP58 3.5 26.1 1.0
C A:TRP58 3.6 29.2 1.0
CB A:ASN59 3.7 31.7 0.5
CB A:ASN59 3.7 31.7 0.5
CA A:ASN59 3.8 31.3 0.5
CA A:ASN59 3.8 31.3 0.5
ND2 A:ASN59 3.9 40.0 0.5
CG A:ASN59 3.9 36.1 0.5
N A:ALA88 3.9 25.7 1.0
CA A:THR87 3.9 25.4 1.0
OD2 A:ASP57 4.0 25.9 1.0
MN A:MN131 4.3 36.6 1.0
C A:ASP57 4.3 24.0 1.0
CG A:GLU89 4.4 39.2 1.0
C A:THR87 4.4 27.9 1.0
O A:HOH250 4.5 45.8 1.0
OD1 A:ASN59 4.6 38.8 0.5
CG A:TRP58 4.6 30.6 1.0
N A:GLU89 4.6 27.1 1.0
O A:ASN59 4.6 25.7 1.0
CA A:ASP57 4.6 22.1 1.0
CB A:ASP57 4.6 25.2 1.0
O A:HOH252 4.7 42.1 1.0
C A:ASN59 4.7 30.1 1.0
CG2 A:THR87 4.8 24.5 1.0
O A:TRP58 4.8 24.8 1.0
NZ A:LYS109 4.8 30.7 1.0
CA A:ALA88 4.9 26.3 1.0
CB A:ALA88 5.0 27.2 1.0
O A:VAL86 5.0 27.9 1.0

Fluorine binding site 4 out of 12 in 3myy

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Fluorine binding site 4 out of 12 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F132

b:67.8
occ:1.00
 F1 A:BEF132 0.0 67.8 1.0
BE A:BEF132 1.4 55.8 1.0
F2 A:BEF132 2.2 55.8 1.0
F3 A:BEF132 2.3 47.0 1.0
O A:HOH270 2.9 56.1 1.0
O A:HOH363 3.2 64.8 1.0
O A:HOH247 3.5 55.1 1.0
NZ A:LYS45 3.5 47.4 1.0
O A:GLU35 3.7 36.8 1.0
O A:HOH221 4.3 41.4 1.0
C A:GLU35 4.4 33.1 1.0
CE A:LYS45 4.5 36.8 1.0
OD2 A:ASP41 4.5 32.5 1.0
O A:HOH290 4.8 57.1 1.0
CB A:GLU35 4.8 38.4 1.0

Fluorine binding site 5 out of 12 in 3myy

Go back to Fluorine Binding Sites List in 3myy
Fluorine binding site 5 out of 12 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F132

b:55.8
occ:1.00
 F2 A:BEF132 0.0 55.8 1.0
BE A:BEF132 1.4 55.8 1.0
F1 A:BEF132 2.2 67.8 1.0
F3 A:BEF132 2.3 47.0 1.0
O A:HOH247 2.9 55.1 1.0
O A:HOH290 2.9 57.1 1.0
OD2 A:ASP41 4.1 32.5 1.0
NH2 A:ARG18 4.1 37.0 1.0
O A:GLU35 4.1 36.8 1.0
CZ A:ARG18 4.3 35.7 1.0
N A:GLU37 4.3 27.3 1.0
CB A:GLU37 4.3 30.4 1.0
CA A:ALA36 4.4 32.2 1.0
C A:GLU35 4.4 33.1 1.0
C A:ALA36 4.4 36.9 1.0
NE A:ARG18 4.4 32.8 1.0
N A:ALA36 4.6 27.0 1.0
CB A:GLU35 4.6 38.4 1.0
OE1 A:GLU37 4.6 39.8 1.0
CG A:GLU37 4.7 34.7 1.0
CA A:GLU37 4.8 26.0 1.0
CD A:GLU37 4.9 45.7 1.0
NH1 A:ARG18 5.0 32.9 1.0

Fluorine binding site 6 out of 12 in 3myy

Go back to Fluorine Binding Sites List in 3myy
Fluorine binding site 6 out of 12 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F132

b:47.0
occ:1.00
 F3 A:BEF132 0.0 47.0 1.0
BE A:BEF132 1.4 55.8 1.0
F2 A:BEF132 2.3 55.8 1.0
F1 A:BEF132 2.3 67.8 1.0
OD2 A:ASP41 2.5 32.5 1.0
CG A:ASP41 3.4 32.7 1.0
OD1 A:ASP41 3.7 38.5 1.0
O A:HOH270 3.8 56.1 1.0
O A:GLU35 3.9 36.8 1.0
CA A:ALA36 4.1 32.2 1.0
NZ A:LYS45 4.2 47.4 1.0
N A:GLU37 4.2 27.3 1.0
O A:HOH290 4.3 57.1 1.0
CE A:LYS45 4.4 36.8 1.0
CG A:GLU37 4.4 34.7 1.0
C A:ALA36 4.6 36.9 1.0
O A:HOH216 4.6 54.4 1.0
CD A:GLU37 4.6 45.7 1.0
C A:GLU35 4.6 33.1 1.0
CB A:GLU37 4.6 30.4 1.0
CB A:ASP41 4.8 29.6 1.0
N A:ALA36 4.8 27.0 1.0
OE1 A:GLU37 4.8 39.8 1.0
O A:HOH247 5.0 55.1 1.0

Fluorine binding site 7 out of 12 in 3myy

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Fluorine binding site 7 out of 12 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F130

b:31.0
occ:1.00
 F1 B:BEF130 0.0 31.0 1.0
BE B:BEF130 1.4 35.4 1.0
F2 B:BEF130 2.3 31.3 1.0
F3 B:BEF130 2.3 29.7 1.0
OD1 B:ASP57 2.6 29.2 1.0
NZ B:LYS109 2.9 29.0 1.0
N B:ALA88 2.9 29.6 1.0
O B:HOH153 3.0 46.5 1.0
OG1 B:THR87 3.5 27.6 1.0
CA B:THR87 3.5 27.8 1.0
CE B:LYS109 3.5 30.1 1.0
O B:HOH241 3.6 44.5 1.0
CD B:LYS109 3.6 26.8 1.0
C B:THR87 3.7 26.0 1.0
CB B:ALA88 3.7 35.6 1.0
CG B:ASP57 3.8 27.4 1.0
CA B:ALA88 3.9 32.5 1.0
CB B:THR87 4.0 25.5 1.0
O B:HOH254 4.0 46.0 1.0
O B:HOH137 4.0 27.5 1.0
MN B:MN131 4.2 38.1 1.0
OD2 B:ASP57 4.2 28.4 1.0
O B:VAL86 4.5 30.9 1.0
CG B:LYS109 4.6 30.4 1.0
O B:HOH228 4.7 43.9 1.0
N B:THR87 4.7 26.0 1.0
N B:TRP58 4.7 29.6 1.0
N B:GLU89 4.7 33.2 1.0
C B:ALA88 4.8 34.0 1.0
O B:THR87 4.8 28.4 1.0
N B:ASN59 4.9 28.5 1.0
OD2 B:ASP12 4.9 30.9 1.0
CB B:ASP57 5.0 24.3 1.0

Fluorine binding site 8 out of 12 in 3myy

Go back to Fluorine Binding Sites List in 3myy
Fluorine binding site 8 out of 12 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F130

b:31.3
occ:1.00
 F2 B:BEF130 0.0 31.3 1.0
BE B:BEF130 1.4 35.4 1.0
MN B:MN131 2.3 38.1 1.0
F1 B:BEF130 2.3 31.0 1.0
F3 B:BEF130 2.3 29.7 1.0
OD1 B:ASP57 2.6 29.2 1.0
OD2 B:ASP57 3.0 28.4 1.0
CG B:ASP57 3.2 27.4 1.0
O B:ASN59 3.2 31.6 1.0
O B:HOH137 3.3 27.5 1.0
O B:HOH142 3.3 28.7 1.0
O B:HOH153 3.3 46.5 1.0
O B:HOH241 3.4 44.5 1.0
CB B:ASN59 3.5 31.9 1.0
N B:ASN59 3.5 28.5 1.0
O B:HOH228 3.7 43.9 1.0
CA B:ASN59 3.8 30.1 1.0
C B:ASN59 3.9 32.7 1.0
NZ B:LYS109 4.0 29.0 1.0
N B:TRP58 4.5 29.6 1.0
OD1 B:ASP13 4.5 26.5 1.0
C B:TRP58 4.5 28.9 1.0
CG B:ASN59 4.5 43.5 1.0
OG1 B:THR87 4.6 27.6 1.0
O B:HOH254 4.6 46.0 1.0
CB B:ASP57 4.6 24.3 1.0
ND2 B:ASN59 4.8 37.8 1.0
CA B:TRP58 5.0 25.9 1.0
N B:ALA88 5.0 29.6 1.0

Fluorine binding site 9 out of 12 in 3myy

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Fluorine binding site 9 out of 12 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F130

b:29.7
occ:1.00
 F3 B:BEF130 0.0 29.7 1.0
BE B:BEF130 1.4 35.4 1.0
F2 B:BEF130 2.3 31.3 1.0
F1 B:BEF130 2.3 31.0 1.0
OG1 B:THR87 2.5 27.6 1.0
OD1 B:ASP57 2.6 29.2 1.0
N B:ASN59 2.8 28.5 1.0
O B:HOH241 2.8 44.5 1.0
N B:TRP58 3.2 29.6 1.0
CB B:TRP58 3.3 29.9 1.0
CB B:THR87 3.4 25.5 1.0
CA B:TRP58 3.5 25.9 1.0
CG B:ASP57 3.6 27.4 1.0
C B:TRP58 3.6 28.9 1.0
CB B:ASN59 3.7 31.9 1.0
CA B:ASN59 3.8 30.1 1.0
N B:ALA88 3.9 29.6 1.0
CA B:THR87 3.9 27.8 1.0
OD2 B:ASP57 4.1 28.4 1.0
MN B:MN131 4.3 38.1 1.0
C B:ASP57 4.3 28.6 1.0
C B:THR87 4.4 26.0 1.0
O B:ASN59 4.5 31.6 1.0
N B:GLU89 4.5 33.2 1.0
CG B:TRP58 4.5 36.6 1.0
C B:ASN59 4.6 32.7 1.0
O B:HOH153 4.6 46.5 1.0
CA B:ASP57 4.7 21.3 1.0
CB B:ASP57 4.7 24.3 1.0
O B:HOH228 4.7 43.9 1.0
CG2 B:THR87 4.8 30.7 1.0
O B:TRP58 4.8 27.6 1.0
NZ B:LYS109 4.8 29.0 1.0
CB B:GLU89 4.9 31.6 1.0
CA B:ALA88 4.9 32.5 1.0
O1 B:GOL502 4.9 57.0 1.0
O B:VAL86 5.0 30.9 1.0

Fluorine binding site 10 out of 12 in 3myy

Go back to Fluorine Binding Sites List in 3myy
Fluorine binding site 10 out of 12 in the Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Structure of E. Coli Chey Mutant A113P Bound to Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:49.4
occ:1.00
 F1 B:BEF1 0.0 49.4 1.0
BE B:BEF1 1.4 59.7 1.0
F2 B:BEF1 2.2 73.1 1.0
F3 B:BEF1 2.3 51.6 1.0
O B:HOH343 2.6 56.1 1.0
O B:HOH360 2.6 60.5 1.0
NH2 B:ARG18 4.0 32.1 1.0
CZ B:ARG18 4.2 33.3 1.0
O B:GLU35 4.2 33.2 1.0
NE B:ARG18 4.3 30.1 1.0
CB B:GLU35 4.3 26.2 1.0
OD2 B:ASP41 4.4 31.0 1.0
C B:GLU35 4.4 38.6 1.0
CA B:ALA36 4.5 31.1 1.0
N B:GLU37 4.5 24.4 1.0
N B:ALA36 4.6 28.2 1.0
C B:ALA36 4.6 27.0 1.0
CB B:GLU37 4.6 29.5 1.0
OE1 B:GLU37 4.7 48.5 1.0
OE1 B:GLU35 4.7 33.7 1.0
O B:HOH285 4.8 53.8 1.0
NH1 B:ARG18 4.9 28.1 1.0

Reference:

R.M.Immormino, L.R.Mcdonald, A.L.Lee, R.B.Bourret. Activation of Chey By Mutation at An Allosteric Site To Be Published.
Page generated: Mon Jul 14 17:57:47 2025

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