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Fluorine in PDB 3olw: Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88T-BEF3-Mn Complex

Protein crystallography data

The structure of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88T-BEF3-Mn Complex, PDB code: 3olw 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) 44.93 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.033, 53.731, 161.804, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.2

Other elements in 3olw:

The structure of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88T-BEF3-Mn Complex also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88T-BEF3-Mn Complex (pdb code 3olw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88T-BEF3-Mn Complex, PDB code: 3olw:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3olw

Go back to Fluorine Binding Sites List in 3olw
Fluorine binding site 1 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88T-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: CHEYA88T-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F130

b:36.2
occ:1.00
 F1 A:BEF130 0.0 36.2 1.0
BE A:BEF130 1.4 39.8 1.0
F2 A:BEF130 2.3 31.1 1.0
F3 A:BEF130 2.4 36.6 1.0
OD1 A:ASP57 2.6 30.1 1.0
NZ A:LYS109 2.9 33.1 1.0
N A:THR88 3.0 29.9 1.0
O A:HOH209 3.1 47.7 1.0
OG1 A:THR88 3.3 38.3 1.0
CA A:THR87 3.5 26.7 1.0
CE A:LYS109 3.6 39.2 1.0
OG1 A:THR87 3.6 28.9 1.0
O A:HOH216 3.6 48.5 1.0
C A:THR87 3.7 32.6 1.0
CD A:LYS109 3.7 34.0 1.0
CG A:ASP57 3.8 33.0 1.0
CB A:THR88 3.9 38.8 1.0
CG2 A:THR88 3.9 34.6 1.0
CB A:THR87 4.0 30.0 1.0
CA A:THR88 4.0 30.5 1.0
O2 A:GOL135 4.1 45.9 0.8
O A:HOH157 4.1 39.7 1.0
MN A:MN131 4.2 39.4 1.0
OD2 A:ASP57 4.2 27.4 1.0
O A:VAL86 4.5 32.1 1.0
N A:THR87 4.7 30.4 1.0
ND2 A:ASN59 4.7 41.4 1.0
CG A:LYS109 4.7 35.4 1.0
N A:TRP58 4.7 33.2 1.0
O A:THR87 4.8 32.8 1.0
N A:ASN59 4.9 32.3 1.0
O1 A:GOL135 5.0 41.0 0.8

Fluorine binding site 2 out of 6 in 3olw

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Fluorine binding site 2 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88T-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: CHEYA88T-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F130

b:31.1
occ:1.00
 F2 A:BEF130 0.0 31.1 1.0
BE A:BEF130 1.4 39.8 1.0
MN A:MN131 2.2 39.4 1.0
F1 A:BEF130 2.3 36.2 1.0
F3 A:BEF130 2.3 36.6 1.0
OD1 A:ASP57 2.6 30.1 1.0
O A:HOH216 2.6 48.5 1.0
OD2 A:ASP57 2.9 27.4 1.0
CG A:ASP57 3.1 33.0 1.0
O A:HOH209 3.2 47.7 1.0
O A:ASN59 3.3 36.3 1.0
O A:HOH146 3.3 38.5 1.0
O A:HOH157 3.3 39.7 1.0
N A:ASN59 3.4 32.3 1.0
CB A:ASN59 3.4 33.0 1.0
CA A:ASN59 3.8 33.9 1.0
ND2 A:ASN59 3.8 41.4 1.0
C A:ASN59 3.9 40.1 1.0
CG A:ASN59 4.1 46.6 1.0
NZ A:LYS109 4.1 33.1 1.0
N A:TRP58 4.4 33.2 1.0
OG1 A:THR88 4.4 38.3 1.0
OD1 A:ASP13 4.5 40.5 1.0
C A:TRP58 4.5 30.6 1.0
CB A:ASP57 4.6 26.5 1.0
O2 A:GOL135 4.7 45.9 0.8
OG1 A:THR87 4.8 28.9 1.0
O A:HOH175 4.8 44.1 1.0
O3 A:GOL135 4.8 58.5 0.8
CA A:TRP58 4.9 31.0 1.0

Fluorine binding site 3 out of 6 in 3olw

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Fluorine binding site 3 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88T-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: CHEYA88T-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F130

b:36.6
occ:1.00
 F3 A:BEF130 0.0 36.6 1.0
BE A:BEF130 1.4 39.8 1.0
F2 A:BEF130 2.3 31.1 1.0
F1 A:BEF130 2.4 36.2 1.0
OD1 A:ASP57 2.5 30.1 1.0
OG1 A:THR87 2.6 28.9 1.0
N A:ASN59 2.9 32.3 1.0
N A:TRP58 3.0 33.2 1.0
CB A:TRP58 3.2 30.7 1.0
CB A:THR87 3.3 30.0 1.0
CA A:TRP58 3.4 31.0 1.0
ND2 A:ASN59 3.4 41.4 1.0
CG A:ASP57 3.5 33.0 1.0
C A:TRP58 3.6 30.6 1.0
O A:HOH216 3.8 48.5 1.0
CG A:ASN59 3.8 46.6 1.0
CA A:THR87 3.8 26.7 1.0
CB A:ASN59 3.9 33.0 1.0
CA A:ASN59 3.9 33.9 1.0
N A:THR88 3.9 29.9 1.0
OD2 A:ASP57 4.0 27.4 1.0
OG1 A:THR88 4.1 38.3 1.0
C A:ASP57 4.2 32.3 1.0
MN A:MN131 4.3 39.4 1.0
C A:THR87 4.4 32.6 1.0
CG A:TRP58 4.4 37.9 1.0
CG A:GLU89 4.5 38.9 1.0
CA A:ASP57 4.6 25.8 1.0
OD1 A:ASN59 4.6 47.7 1.0
O A:ASN59 4.6 36.3 1.0
CB A:ASP57 4.6 26.5 1.0
O A:HOH209 4.7 47.7 1.0
CG2 A:THR87 4.7 26.8 1.0
C A:ASN59 4.7 40.1 1.0
O A:TRP58 4.8 34.6 1.0
NZ A:LYS109 4.8 33.1 1.0
N A:GLU89 4.9 30.2 1.0
O A:VAL86 5.0 32.1 1.0
CA A:THR88 5.0 30.5 1.0

Fluorine binding site 4 out of 6 in 3olw

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Fluorine binding site 4 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88T-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: CHEYA88T-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F130

b:33.1
occ:1.00
 F1 B:BEF130 0.0 33.1 1.0
BE B:BEF130 1.4 40.0 1.0
F2 B:BEF130 2.3 35.4 1.0
F3 B:BEF130 2.4 35.0 1.0
OD1 B:ASP57 2.6 33.3 1.0
N B:THR88 2.9 35.9 1.0
NZ B:LYS109 3.0 41.9 1.0
CA B:THR87 3.4 32.2 1.0
OG1 B:THR88 3.4 46.6 1.0
OG1 B:THR87 3.5 35.4 1.0
CD B:LYS109 3.6 37.5 1.0
C B:THR87 3.6 36.7 1.0
CE B:LYS109 3.6 38.9 1.0
CG B:ASP57 3.7 34.9 1.0
CG2 B:THR88 3.8 44.4 1.0
CB B:THR88 3.9 40.6 1.0
CB B:THR87 3.9 32.5 1.0
CA B:THR88 4.0 39.7 1.0
O2 B:GOL135 4.0 43.5 0.8
O B:HOH147 4.1 36.9 1.0
OD2 B:ASP57 4.2 33.6 1.0
MN B:MN131 4.3 36.9 1.0
O B:VAL86 4.4 33.7 1.0
N B:THR87 4.6 30.3 1.0
N B:TRP58 4.7 34.7 1.0
CG B:LYS109 4.7 40.0 1.0
O B:THR87 4.8 37.7 1.0
OD2 B:ASP12 4.9 37.8 1.0
C B:VAL86 4.9 35.4 1.0
N B:GLU89 4.9 40.9 1.0
CB B:ASP57 4.9 30.0 1.0

Fluorine binding site 5 out of 6 in 3olw

Go back to Fluorine Binding Sites List in 3olw
Fluorine binding site 5 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88T-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: CHEYA88T-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F130

b:35.4
occ:1.00
 F2 B:BEF130 0.0 35.4 1.0
BE B:BEF130 1.4 40.0 1.0
MN B:MN131 2.3 36.9 1.0
F3 B:BEF130 2.3 35.0 1.0
F1 B:BEF130 2.3 33.1 1.0
OD1 B:ASP57 2.6 33.3 1.0
OD2 B:ASP57 2.9 33.6 1.0
CG B:ASP57 3.1 34.9 1.0
O B:HOH147 3.1 36.9 1.0
O B:HOH154 3.3 41.3 1.0
O B:ASN59 3.5 38.8 1.0
CB B:ASN59 3.6 38.1 0.3
N B:ASN59 3.7 29.8 1.0
CB B:ASN59 3.7 38.0 0.7
CA B:ASN59 4.0 36.5 0.3
CA B:ASN59 4.0 36.5 0.7
C B:ASN59 4.1 40.9 1.0
ND2 B:ASN59 4.1 38.3 0.7
NZ B:LYS109 4.1 41.9 1.0
CG B:ASN59 4.3 42.5 0.7
N B:TRP58 4.4 34.7 1.0
OG1 B:THR88 4.4 46.6 1.0
OD1 B:ASP13 4.5 40.1 1.0
O2 B:GOL135 4.6 43.5 0.8
CB B:ASP57 4.6 30.0 1.0
OG1 B:THR87 4.6 35.4 1.0
CG B:ASN59 4.7 40.5 0.3
C B:TRP58 4.7 37.8 1.0
ND2 B:ASN59 4.8 43.0 0.3
O B:HOH239 4.9 55.2 1.0
N B:THR88 5.0 35.9 1.0
OD2 B:ASP12 5.0 37.8 1.0

Fluorine binding site 6 out of 6 in 3olw

Go back to Fluorine Binding Sites List in 3olw
Fluorine binding site 6 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88T-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: CHEYA88T-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 40.0 1.0
F2 B:BEF130 2.3 35.4 1.0
F1 B:BEF130 2.4 33.1 1.0
OG1 B:THR87 2.5 35.4 1.0
OD1 B:ASP57 2.7 33.3 1.0
N B:ASN59 2.9 29.8 1.0
N B:TRP58 3.1 34.7 1.0
CB B:TRP58 3.4 37.6 1.0
CB B:THR87 3.5 32.5 1.0
CA B:TRP58 3.5 34.9 1.0
ND2 B:ASN59 3.5 38.3 0.7
CG B:ASP57 3.5 34.9 1.0
C B:TRP58 3.7 37.8 1.0
CB B:ASN59 3.7 38.1 0.3
CG B:ASN59 3.8 42.5 0.7
CB B:ASN59 3.8 38.0 0.7
CA B:ASN59 3.8 36.5 0.3
CA B:ASN59 3.8 36.5 0.7
CA B:THR87 3.9 32.2 1.0
N B:THR88 3.9 35.9 1.0
OD2 B:ASP57 3.9 33.6 1.0
OG1 B:THR88 4.1 46.6 1.0
MN B:MN131 4.3 36.9 1.0
C B:ASP57 4.3 36.2 1.0
C B:THR87 4.4 36.7 1.0
OD1 B:ASN59 4.5 39.4 0.7
O B:ASN59 4.6 38.8 1.0
CG B:TRP58 4.6 41.5 1.0
C B:ASN59 4.6 40.9 1.0
CA B:ASP57 4.7 30.8 1.0
N B:GLU89 4.7 40.9 1.0
CB B:ASP57 4.7 30.0 1.0
CG2 B:THR87 4.8 30.5 1.0
O B:TRP58 4.9 40.8 1.0
CA B:THR88 5.0 39.7 1.0
NZ B:LYS109 5.0 41.9 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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