Atomistry » Fluorine » PDB 3ohh-3oyj » 3oly
Atomistry »
  Fluorine »
    PDB 3ohh-3oyj »
      3oly »

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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy