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Fluorine in PDB 3olx: Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex

Protein crystallography data

The structure of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex, PDB code: 3olx was solved by R.M.Immormino, R.B.Bourret, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.88 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.687, 53.759, 160.013, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 23

Other elements in 3olx:

The structure of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Manganese (Mn) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex (pdb code 3olx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex, PDB code: 3olx:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 3olx

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Fluorine binding site 1 out of 9 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F130

b:29.9
occ:1.00
 F1 A:BEF130 0.0 29.9 1.0
BE A:BEF130 1.4 32.2 1.0
F2 A:BEF130 2.3 30.0 1.0
F3 A:BEF130 2.3 27.8 1.0
OD1 A:ASP57 2.6 27.2 1.0
NZ A:LYS109 2.8 31.8 1.0
N A:SER88 3.0 24.6 1.0
O A:HOH201 3.1 41.0 1.0
OG A:SER88 3.2 35.7 1.0
CE A:LYS109 3.4 27.4 1.0
CA A:THR87 3.6 23.0 1.0
OG1 A:THR87 3.6 22.2 1.0
CD A:LYS109 3.6 33.0 1.0
CG A:ASP57 3.7 25.8 1.0
CB A:SER88 3.7 30.3 1.0
C A:THR87 3.8 26.9 1.0
O A:HOH136 3.9 25.5 1.0
CA A:SER88 4.0 29.2 1.0
CB A:THR87 4.0 24.4 1.0
OD2 A:ASP57 4.1 17.9 1.0
MN A:MN131 4.1 30.1 1.0
O A:VAL86 4.5 28.0 1.0
ND2 A:ASN59 4.6 35.9 1.0
CG A:LYS109 4.6 35.1 1.0
N A:TRP58 4.7 31.4 1.0
N A:THR87 4.8 25.1 1.0
O1 A:GOL501 4.8 35.5 0.9
C1 A:GOL501 4.8 38.0 0.9
N A:ASN59 4.9 28.3 1.0
C2 A:GOL501 4.9 45.2 0.9
CB A:ASP57 4.9 24.1 1.0
OD2 A:ASP12 4.9 32.0 1.0
N A:GLU89 5.0 29.9 1.0
O A:THR87 5.0 30.9 1.0

Fluorine binding site 2 out of 9 in 3olx

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Fluorine binding site 2 out of 9 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F130

b:30.0
occ:1.00
 F2 A:BEF130 0.0 30.0 1.0
BE A:BEF130 1.4 32.2 1.0
MN A:MN131 2.1 30.1 1.0
F3 A:BEF130 2.3 27.8 1.0
F1 A:BEF130 2.3 29.9 1.0
OD1 A:ASP57 2.4 27.2 1.0
OD2 A:ASP57 2.7 17.9 1.0
CG A:ASP57 2.9 25.8 1.0
O A:HOH136 3.1 25.5 1.0
O A:HOH135 3.1 24.0 1.0
O A:ASN59 3.2 21.0 1.0
N A:ASN59 3.4 28.3 1.0
O A:HOH201 3.5 41.0 1.0
CB A:ASN59 3.5 25.6 1.0
CA A:ASN59 3.8 29.8 1.0
ND2 A:ASN59 3.8 35.9 1.0
C A:ASN59 3.9 37.5 1.0
NZ A:LYS109 4.0 31.8 1.0
CG A:ASN59 4.1 38.5 1.0
OD1 A:ASP13 4.2 29.8 1.0
N A:TRP58 4.3 31.4 1.0
O A:HOH217 4.4 44.0 1.0
OG A:SER88 4.4 35.7 1.0
CB A:ASP57 4.4 24.1 1.0
C A:TRP58 4.4 30.1 1.0
O3 A:GOL501 4.7 52.4 0.9
OG1 A:THR87 4.8 22.2 1.0
CA A:TRP58 4.9 29.8 1.0

Fluorine binding site 3 out of 9 in 3olx

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Fluorine binding site 3 out of 9 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F130

b:27.8
occ:1.00
 F3 A:BEF130 0.0 27.8 1.0
BE A:BEF130 1.4 32.2 1.0
F2 A:BEF130 2.3 30.0 1.0
F1 A:BEF130 2.3 29.9 1.0
OD1 A:ASP57 2.5 27.2 1.0
OG1 A:THR87 2.6 22.2 1.0
N A:ASN59 2.8 28.3 1.0
N A:TRP58 3.1 31.4 1.0
ND2 A:ASN59 3.3 35.9 1.0
CB A:TRP58 3.4 29.5 1.0
CB A:THR87 3.4 24.4 1.0
CA A:TRP58 3.5 29.8 1.0
CG A:ASP57 3.5 25.8 1.0
C A:TRP58 3.6 30.1 1.0
CG A:ASN59 3.7 38.5 1.0
CB A:ASN59 3.8 25.6 1.0
CA A:ASN59 3.9 29.8 1.0
N A:SER88 3.9 24.6 1.0
CA A:THR87 3.9 23.0 1.0
OG A:SER88 4.0 35.7 1.0
OD2 A:ASP57 4.0 17.9 1.0
MN A:MN131 4.2 30.1 1.0
C A:ASP57 4.3 30.5 1.0
OD1 A:ASN59 4.4 39.5 1.0
CG A:GLU89 4.4 29.2 1.0
C A:THR87 4.5 26.9 1.0
O A:ASN59 4.5 21.0 1.0
CG A:TRP58 4.6 30.7 1.0
CA A:ASP57 4.6 18.8 1.0
CB A:ASP57 4.7 24.1 1.0
C A:ASN59 4.7 37.5 1.0
O A:HOH201 4.7 41.0 1.0
N A:GLU89 4.7 29.9 1.0
NZ A:LYS109 4.8 31.8 1.0
CG2 A:THR87 4.8 22.7 1.0
O A:TRP58 4.8 28.6 1.0
CA A:SER88 4.9 29.2 1.0
O A:VAL86 4.9 28.0 1.0
CB A:SER88 5.0 30.3 1.0

Fluorine binding site 4 out of 9 in 3olx

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Fluorine binding site 4 out of 9 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F132

b:69.3
occ:1.00
 F1 A:BEF132 0.0 69.3 1.0
BE A:BEF132 1.4 60.2 1.0
F3 A:BEF132 2.2 61.5 1.0
F2 A:BEF132 2.3 73.7 1.0
O A:HOH157 3.0 52.6 1.0
O A:HOH184 3.1 39.7 1.0
O A:HOH138 3.2 50.4 1.0
CB A:ARG73 4.1 32.1 1.0
O A:ALA101 4.3 33.6 1.0
O A:HOH174 4.3 37.9 1.0
CD A:ARG73 4.5 46.5 1.0
CG A:ARG73 4.6 40.8 1.0
O A:ARG73 4.7 38.2 1.0
C A:ALA101 4.8 34.2 1.0
O A:HOH264 5.0 60.6 1.0

Fluorine binding site 5 out of 9 in 3olx

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Fluorine binding site 5 out of 9 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F132

b:73.7
occ:1.00
 F2 A:BEF132 0.0 73.7 1.0
BE A:BEF132 1.4 60.2 1.0
F1 A:BEF132 2.3 69.3 1.0
F3 A:BEF132 2.3 61.5 1.0
O A:HOH207 3.7 55.7 1.0
O A:HOH184 4.0 39.7 1.0
O A:GLN100 4.1 38.4 1.0
O A:HOH214 4.1 43.4 1.0
O A:HOH157 4.4 52.6 1.0
NZ B:LYS126 4.5 63.6 1.0
O A:HOH246 4.5 47.1 1.0
O A:HOH192 4.7 40.7 1.0
O B:HOH222 4.8 57.2 1.0

Fluorine binding site 6 out of 9 in 3olx

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Fluorine binding site 6 out of 9 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F132

b:61.5
occ:1.00
 F3 A:BEF132 0.0 61.5 1.0
BE A:BEF132 1.4 60.2 1.0
F1 A:BEF132 2.2 69.3 1.0
F2 A:BEF132 2.3 73.7 1.0
O A:HOH214 3.1 43.4 1.0
O A:GLN100 3.8 38.4 1.0
CA A:GLY102 3.8 36.5 1.0
O A:ALA101 3.9 33.6 1.0
C A:ALA101 4.0 34.2 1.0
N A:GLY102 4.0 33.6 1.0
O A:HOH184 4.0 39.7 1.0
O A:HOH162 4.1 51.3 1.0
O A:HOH138 4.3 50.4 1.0
O B:HOH198 4.5 43.4 1.0
CD A:ARG73 4.6 46.5 1.0
O A:HOH264 4.7 60.6 1.0
CA A:ALA101 4.8 31.4 1.0
O B:HOH177 4.8 53.7 1.0
C A:GLN100 4.8 36.0 1.0

Fluorine binding site 7 out of 9 in 3olx

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Fluorine binding site 7 out of 9 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F130

b:37.3
occ:1.00
 F1 B:BEF130 0.0 37.3 1.0
BE B:BEF130 1.4 35.7 1.0
F2 B:BEF130 2.3 31.9 1.0
F3 B:BEF130 2.3 35.0 1.0
OD1 B:ASP57 2.6 28.1 1.0
O B:HOH243 2.8 48.3 1.0
NZ B:LYS109 2.8 40.4 1.0
N B:SER88 3.0 32.3 1.0
OG B:SER88 3.3 44.0 1.0
CE B:LYS109 3.4 38.5 1.0
CD B:LYS109 3.6 35.3 1.0
CA B:THR87 3.6 28.6 1.0
OG1 B:THR87 3.7 25.4 1.0
CG B:ASP57 3.7 30.7 1.0
CB B:SER88 3.8 33.5 1.0
C B:THR87 3.8 31.0 1.0
O B:HOH137 4.0 28.3 1.0
CA B:SER88 4.0 36.2 1.0
CB B:THR87 4.1 30.3 1.0
MN B:MN131 4.1 37.8 1.0
OD2 B:ASP57 4.2 28.7 1.0
O B:HOH225 4.4 45.0 1.0
O B:VAL86 4.5 29.2 1.0
CG B:LYS109 4.7 38.4 1.0
N B:THR87 4.8 28.8 1.0
N B:TRP58 4.8 36.4 1.0
N B:GLU89 4.8 41.0 1.0
CB B:ASP57 4.9 29.8 1.0
O B:HOH147 4.9 51.6 1.0
OD2 B:ASP12 4.9 31.9 1.0
C B:SER88 5.0 36.5 1.0
N B:ASN59 5.0 36.9 1.0
O B:THR87 5.0 33.0 1.0

Fluorine binding site 8 out of 9 in 3olx

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Fluorine binding site 8 out of 9 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F130

b:31.9
occ:1.00
 F2 B:BEF130 0.0 31.9 1.0
BE B:BEF130 1.4 35.7 1.0
MN B:MN131 2.2 37.8 1.0
F3 B:BEF130 2.2 35.0 1.0
F1 B:BEF130 2.3 37.3 1.0
OD1 B:ASP57 2.5 28.1 1.0
OD2 B:ASP57 2.8 28.7 1.0
CG B:ASP57 3.0 30.7 1.0
O B:HOH145 3.1 34.6 1.0
O B:ASN59 3.2 27.8 1.0
O B:HOH243 3.2 48.3 1.0
O B:HOH137 3.3 28.3 1.0
CB B:ASN59 3.4 36.6 0.4
N B:ASN59 3.5 36.9 1.0
CB B:ASN59 3.5 36.6 0.6
CA B:ASN59 3.7 33.8 0.4
CA B:ASN59 3.8 33.7 0.6
C B:ASN59 3.9 36.2 1.0
O B:HOH147 4.0 51.6 1.0
NZ B:LYS109 4.1 40.4 1.0
ND2 B:ASN59 4.1 41.3 0.6
CG B:ASN59 4.2 43.0 0.6
N B:TRP58 4.3 36.4 1.0
OG B:SER88 4.5 44.0 1.0
C B:TRP58 4.5 34.5 1.0
OD1 B:ASP13 4.5 33.6 1.0
CB B:ASP57 4.5 29.8 1.0
CG B:ASN59 4.5 38.4 0.4
OG1 B:THR87 4.7 25.4 1.0
O B:HOH221 4.8 57.4 1.0
ND2 B:ASN59 4.8 40.2 0.4
CA B:TRP58 4.9 31.5 1.0

Fluorine binding site 9 out of 9 in 3olx

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Fluorine binding site 9 out of 9 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88S-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F130

b:35.0
occ:1.00
 F3 B:BEF130 0.0 35.0 1.0
BE B:BEF130 1.4 35.7 1.0
F2 B:BEF130 2.2 31.9 1.0
F1 B:BEF130 2.3 37.3 1.0
OD1 B:ASP57 2.5 28.1 1.0
OG1 B:THR87 2.6 25.4 1.0
N B:ASN59 2.9 36.9 1.0
N B:TRP58 3.2 36.4 1.0
CB B:THR87 3.4 30.3 1.0
CB B:TRP58 3.5 34.4 1.0
CG B:ASP57 3.6 30.7 1.0
CA B:TRP58 3.6 31.5 1.0
ND2 B:ASN59 3.7 41.3 0.6
CB B:ASN59 3.7 36.6 0.4
C B:TRP58 3.8 34.5 1.0
CG B:ASN59 3.8 43.0 0.6
CB B:ASN59 3.8 36.6 0.6
N B:SER88 3.8 32.3 1.0
CA B:ASN59 3.9 33.8 0.4
CA B:THR87 3.9 28.6 1.0
CA B:ASN59 3.9 33.7 0.6
OD2 B:ASP57 4.1 28.7 1.0
OG B:SER88 4.1 44.0 1.0
MN B:MN131 4.3 37.8 1.0
O B:HOH243 4.3 48.3 1.0
C B:THR87 4.4 31.0 1.0
C B:ASP57 4.4 32.8 1.0
N B:GLU89 4.5 41.0 1.0
OD1 B:ASN59 4.5 37.7 0.6
O B:ASN59 4.6 27.8 1.0
CG B:TRP58 4.6 36.9 1.0
C B:ASN59 4.7 36.2 1.0
CA B:ASP57 4.7 27.9 1.0
CB B:ASP57 4.7 29.8 1.0
NZ B:LYS109 4.8 40.4 1.0
CG2 B:THR87 4.8 30.4 1.0
O B:HOH147 4.8 51.6 1.0
CA B:SER88 4.9 36.2 1.0
CB B:GLU89 4.9 39.6 1.0
O B:TRP58 4.9 33.1 1.0
O B:VAL86 5.0 29.2 1.0
CB B:SER88 5.0 33.5 1.0

Reference:

R.M.Immormino, R.E.Silversmith, R.B.Bourret. A Variable Active Site Residue Influences the Kinetics of Response Regulator Phosphorylation and Dephosphorylation. Biochemistry V. 55 5595 2016.
ISSN: ISSN 0006-2960
PubMed: 27589219
DOI: 10.1021/ACS.BIOCHEM.6B00645
Page generated: Wed Jul 31 21:15:26 2024

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