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Fluorine in PDB 3oly: Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex

Protein crystallography data

The structure of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex, PDB code: 3oly 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) 26.72 / 2.05
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 (%) 18 / 21.2

Other elements in 3oly:

The structure of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex also contains other interesting chemical elements:

Manganese (Mn) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex (pdb code 3oly). 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: CHEYA88M-BEF3-Mn Complex, PDB code: 3oly:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3oly

Go back to Fluorine Binding Sites List in 3oly
Fluorine binding site 1 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-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: CHEYA88M-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F130

b:27.7
occ:1.00
 F1 A:BEF130 0.0 27.7 1.0
BE A:BEF130 1.4 34.9 1.0
F3 A:BEF130 2.3 27.3 1.0
F2 A:BEF130 2.4 32.7 1.0
OD1 A:ASP57 2.5 26.9 1.0
NZ A:LYS109 2.8 33.3 1.0
N A:MET88 3.0 26.2 1.0
CG A:MET88 3.3 37.9 1.0
CE A:LYS109 3.4 32.0 1.0
CA A:THR87 3.4 22.4 1.0
CD A:LYS109 3.5 30.3 1.0
CG A:ASP57 3.6 29.0 1.0
OG1 A:THR87 3.6 24.9 1.0
C A:THR87 3.7 25.9 1.0
CB A:MET88 3.9 35.3 1.0
O A:HOH138 4.0 27.2 1.0
CA A:MET88 4.0 31.1 1.0
CB A:THR87 4.0 26.0 1.0
OD2 A:ASP57 4.1 22.7 1.0
MN A:MN131 4.2 30.1 1.0
O A:HOH281 4.3 48.5 1.0
O A:VAL86 4.4 28.5 1.0
CG A:LYS109 4.6 31.4 1.0
N A:THR87 4.6 23.4 1.0
SD A:MET88 4.6 69.3 1.0
N A:TRP58 4.7 27.8 1.0
O A:HOH210 4.7 40.6 1.0
ND2 A:ASN59 4.8 36.8 1.0
CB A:ASP57 4.8 25.4 1.0
OD2 A:ASP12 4.8 29.4 1.0
N A:ASN59 4.9 29.7 1.0
O A:THR87 4.9 26.5 1.0
C A:VAL86 5.0 24.5 1.0

Fluorine binding site 2 out of 6 in 3oly

Go back to Fluorine Binding Sites List in 3oly
Fluorine binding site 2 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-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: CHEYA88M-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F130

b:32.7
occ:1.00
 F2 A:BEF130 0.0 32.7 1.0
BE A:BEF130 1.4 34.9 1.0
MN A:MN131 2.2 30.1 1.0
F3 A:BEF130 2.3 27.3 1.0
F1 A:BEF130 2.4 27.7 1.0
OD1 A:ASP57 2.5 26.9 1.0
OD2 A:ASP57 2.8 22.7 1.0
CG A:ASP57 3.0 29.0 1.0
O A:HOH137 3.1 27.9 1.0
O A:ASN59 3.2 26.2 1.0
O A:HOH138 3.2 27.2 1.0
O A:HOH281 3.3 48.5 1.0
N A:ASN59 3.4 29.7 1.0
CB A:ASN59 3.4 30.4 1.0
CA A:ASN59 3.7 29.9 1.0
ND2 A:ASN59 3.8 36.8 1.0
C A:ASN59 3.9 37.8 1.0
NZ A:LYS109 4.0 33.3 1.0
CG A:ASN59 4.1 42.9 1.0
N A:TRP58 4.4 27.8 1.0
OD1 A:ASP13 4.4 31.3 1.0
CG A:MET88 4.4 37.9 1.0
C A:TRP58 4.4 30.5 1.0
CB A:ASP57 4.5 25.4 1.0
OG1 A:THR87 4.8 24.9 1.0
CA A:TRP58 4.9 31.4 1.0

Fluorine binding site 3 out of 6 in 3oly

Go back to Fluorine Binding Sites List in 3oly
Fluorine binding site 3 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-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: CHEYA88M-BEF3-Mn Complex 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 34.9 1.0
F2 A:BEF130 2.3 32.7 1.0
F1 A:BEF130 2.3 27.7 1.0
OD1 A:ASP57 2.5 26.9 1.0
OG1 A:THR87 2.6 24.9 1.0
N A:ASN59 2.8 29.7 1.0
N A:TRP58 3.1 27.8 1.0
CB A:TRP58 3.2 26.8 1.0
CB A:THR87 3.4 26.0 1.0
ND2 A:ASN59 3.4 36.8 1.0
CA A:TRP58 3.4 31.4 1.0
CG A:ASP57 3.5 29.0 1.0
C A:TRP58 3.6 30.5 1.0
CG A:ASN59 3.8 42.9 1.0
CA A:THR87 3.8 22.4 1.0
CB A:ASN59 3.8 30.4 1.0
N A:MET88 3.9 26.2 1.0
CA A:ASN59 3.9 29.9 1.0
OD2 A:ASP57 4.1 22.7 1.0
CG A:MET88 4.2 37.9 1.0
C A:ASP57 4.2 28.4 1.0
MN A:MN131 4.3 30.1 1.0
C A:THR87 4.3 25.9 1.0
O A:HOH281 4.5 48.5 1.0
CG A:TRP58 4.5 30.5 1.0
CG A:GLU89 4.5 33.6 1.0
CA A:ASP57 4.6 21.0 1.0
O A:ASN59 4.6 26.2 1.0
OD1 A:ASN59 4.6 40.8 1.0
CB A:ASP57 4.6 25.4 1.0
SD A:MET88 4.6 69.3 1.0
C A:ASN59 4.7 37.8 1.0
N A:GLU89 4.7 29.4 1.0
NZ A:LYS109 4.7 33.3 1.0
CG2 A:THR87 4.8 24.0 1.0
O A:TRP58 4.8 29.1 1.0
CA A:MET88 4.9 31.1 1.0
O A:VAL86 4.9 28.5 1.0

Fluorine binding site 4 out of 6 in 3oly

Go back to Fluorine Binding Sites List in 3oly
Fluorine binding site 4 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-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: CHEYA88M-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F130

b:31.2
occ:1.00
 F1 B:BEF130 0.0 31.2 1.0
BE B:BEF130 1.4 35.0 1.0
F2 B:BEF130 2.3 30.1 1.0
F3 B:BEF130 2.3 30.4 1.0
OD1 B:ASP57 2.7 25.8 1.0
N B:MET88 2.8 30.8 1.0
NZ B:LYS109 3.0 32.4 1.0
CB B:MET88 3.5 38.2 1.0
CG B:MET88 3.5 54.9 1.0
OG1 B:THR87 3.5 29.6 1.0
CA B:THR87 3.6 27.2 1.0
CE B:LYS109 3.6 32.5 1.0
C B:THR87 3.6 26.9 1.0
CA B:MET88 3.7 32.6 1.0
CD B:LYS109 3.7 30.5 1.0
CG B:ASP57 3.8 30.4 1.0
O B:HOH227 4.0 48.3 1.0
CB B:THR87 4.1 28.6 1.0
O B:HOH142 4.1 30.5 1.0
OD2 B:ASP57 4.2 26.1 1.0
MN B:MN131 4.2 33.7 1.0
O B:HOH212 4.5 44.4 1.0
O B:VAL86 4.6 33.2 1.0
N B:GLU89 4.7 34.2 1.0
N B:TRP58 4.7 34.0 1.0
CG B:LYS109 4.8 33.4 1.0
C B:MET88 4.8 36.6 1.0
N B:THR87 4.8 28.1 1.0
O B:THR87 4.8 31.8 1.0
N B:ASN59 4.9 30.7 1.0
ND2 B:ASN59 4.9 41.4 0.5
CB B:ASP57 5.0 26.1 1.0

Fluorine binding site 5 out of 6 in 3oly

Go back to Fluorine Binding Sites List in 3oly
Fluorine binding site 5 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-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: CHEYA88M-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F130

b:30.1
occ:1.00
 F2 B:BEF130 0.0 30.1 1.0
BE B:BEF130 1.4 35.0 1.0
MN B:MN131 2.2 33.7 1.0
F3 B:BEF130 2.3 30.4 1.0
F1 B:BEF130 2.3 31.2 1.0
OD1 B:ASP57 2.5 25.8 1.0
OD2 B:ASP57 2.9 26.1 1.0
CG B:ASP57 3.0 30.4 1.0
O B:HOH227 3.1 48.3 1.0
O B:HOH139 3.1 30.7 1.0
O B:ASN59 3.3 31.3 1.0
O B:HOH142 3.3 30.5 1.0
CB B:ASN59 3.4 34.7 0.5
CB B:ASN59 3.4 34.8 0.5
N B:ASN59 3.5 30.7 1.0
CA B:ASN59 3.7 34.1 0.5
CA B:ASN59 3.8 34.1 0.5
C B:ASN59 3.9 37.5 1.0
NZ B:LYS109 4.1 32.4 1.0
ND2 B:ASN59 4.1 41.4 0.5
CG B:ASN59 4.2 40.3 0.5
N B:TRP58 4.4 34.0 1.0
OD1 B:ASP13 4.4 32.1 1.0
C B:TRP58 4.5 32.8 1.0
CB B:ASP57 4.5 26.1 1.0
CG B:ASN59 4.6 38.2 0.5
OG1 B:THR87 4.8 29.6 1.0
O B:HOH271 4.8 57.8 1.0
ND2 B:ASN59 4.8 39.5 0.5
CA B:TRP58 4.9 33.5 1.0
N B:MET88 4.9 30.8 1.0

Fluorine binding site 6 out of 6 in 3oly

Go back to Fluorine Binding Sites List in 3oly
Fluorine binding site 6 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-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: CHEYA88M-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F130

b:30.4
occ:1.00
 F3 B:BEF130 0.0 30.4 1.0
BE B:BEF130 1.4 35.0 1.0
F2 B:BEF130 2.3 30.1 1.0
F1 B:BEF130 2.3 31.2 1.0
OD1 B:ASP57 2.5 25.8 1.0
OG1 B:THR87 2.6 29.6 1.0
N B:ASN59 2.8 30.7 1.0
N B:TRP58 3.1 34.0 1.0
CB B:TRP58 3.3 32.0 1.0
CA B:TRP58 3.5 33.5 1.0
CG B:ASP57 3.5 30.4 1.0
ND2 B:ASN59 3.6 41.4 0.5
CB B:THR87 3.6 28.6 1.0
C B:TRP58 3.6 32.8 1.0
CB B:ASN59 3.7 34.7 0.5
CB B:ASN59 3.7 34.8 0.5
CA B:ASN59 3.8 34.1 0.5
CA B:ASN59 3.8 34.1 0.5
CG B:ASN59 3.8 40.3 0.5
N B:MET88 3.9 30.8 1.0
CA B:THR87 4.0 27.2 1.0
OD2 B:ASP57 4.1 26.1 1.0
O B:HOH227 4.1 48.3 1.0
MN B:MN131 4.3 33.7 1.0
C B:ASP57 4.3 34.0 1.0
C B:THR87 4.5 26.9 1.0
N B:GLU89 4.5 34.2 1.0
O B:ASN59 4.5 31.3 1.0
CG B:TRP58 4.5 38.4 1.0
C B:ASN59 4.6 37.5 1.0
CA B:ASP57 4.7 24.9 1.0
CB B:ASP57 4.7 26.1 1.0
OD1 B:ASN59 4.7 40.3 0.5
CB B:MET88 4.7 38.2 1.0
O B:TRP58 4.8 32.0 1.0
CA B:MET88 4.8 32.6 1.0
NZ B:LYS109 4.9 32.4 1.0
CG2 B:THR87 4.9 29.8 1.0
CB B:GLU89 5.0 36.2 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: Mon Jul 14 18:20:46 2025

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