Fluorine in PDB 6ywa: Human Ref Sting in Complex with 3',3'-C-[2'Fdamp-2'Fdam(Ps)]

Protein crystallography data

The structure of Human Ref Sting in Complex with 3',3'-C-[2'Fdamp-2'Fdam(Ps)], PDB code: 6ywa was solved by E.Boura, M.Smola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.96 / 2.31
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 35.959, 94.244, 116.826, 90, 90, 90
R / Rfree (%) 19.4 / 24.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Ref Sting in Complex with 3',3'-C-[2'Fdamp-2'Fdam(Ps)] (pdb code 6ywa). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human Ref Sting in Complex with 3',3'-C-[2'Fdamp-2'Fdam(Ps)], PDB code: 6ywa:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6ywa

Go back to Fluorine Binding Sites List in 6ywa
Fluorine binding site 1 out of 4 in the Human Ref Sting in Complex with 3',3'-C-[2'Fdamp-2'Fdam(Ps)]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Ref Sting in Complex with 3',3'-C-[2'Fdamp-2'Fdam(Ps)] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:24.5
occ:0.50
F1 B:PWB401 0.0 24.5 0.5
F2 B:PWB401 0.0 24.5 0.5
C6 B:PWB401 1.3 23.6 0.5
C16 B:PWB401 1.3 23.6 0.5
H6 B:PWB401 2.0 28.4 0.5
H16 B:PWB401 2.0 28.4 0.5
HD3 B:PRO264 2.3 29.8 1.0
C7 B:PWB401 2.3 23.0 0.5
C17 B:PWB401 2.3 23.2 0.5
HB B:THR263 2.3 40.4 1.0
C15 B:PWB401 2.4 20.7 0.5
C5 B:PWB401 2.4 21.1 0.5
H7 B:PWB401 2.4 27.7 0.5
H17 B:PWB401 2.4 27.9 0.5
HD1 B:TYR163 2.7 35.5 1.0
H18 B:PWB401 2.7 35.0 0.5
O7 B:PWB401 2.7 24.6 0.5
O10 B:PWB401 2.7 24.6 0.5
H8 B:PWB401 2.7 35.0 0.5
C8 B:PWB401 2.9 29.1 0.5
C18 B:PWB401 2.9 29.1 0.5
O1 B:PWB401 3.0 23.0 0.5
O5 B:PWB401 3.0 23.0 0.5
HG3 B:PRO264 3.1 32.0 1.0
CD B:PRO264 3.1 24.8 1.0
HE1 B:TYR163 3.2 30.2 1.0
H5 B:PWB401 3.3 25.5 0.5
H15 B:PWB401 3.3 24.9 0.5
CB B:THR263 3.3 33.6 1.0
CD1 B:TYR163 3.4 29.5 1.0
O B:HOH526 3.5 26.1 1.0
N2 B:PWB401 3.5 30.9 0.5
N6 B:PWB401 3.5 30.9 0.5
CG B:PRO264 3.6 26.6 1.0
CE1 B:TYR163 3.7 25.1 1.0
O22 B:PWB401 3.7 24.6 0.5
O B:PWB401 3.7 24.7 0.5
HG1 B:THR263 3.8 38.2 1.0
HD2 B:PRO264 3.8 29.8 1.0
P B:PWB401 3.8 28.0 0.5
P1 B:PWB401 3.8 28.0 0.5
H B:THR263 3.9 39.3 1.0
OG1 B:THR263 3.9 31.7 1.0
HG2 B:PRO264 3.9 32.0 1.0
N B:PRO264 3.9 23.6 1.0
HG22 B:THR263 4.0 33.4 1.0
N1 B:PWB401 4.1 31.4 0.5
C1 B:PWB401 4.1 30.9 0.5
N5 B:PWB401 4.1 31.4 0.5
C11 B:PWB401 4.1 30.9 0.5
CG2 B:THR263 4.1 27.7 1.0
HG21 B:THR263 4.1 33.4 1.0
CA B:THR263 4.1 25.6 1.0
HH12 A:ARG238 4.2 42.0 1.0
N B:THR263 4.3 32.6 1.0
C B:THR263 4.3 18.2 1.0
C9 B:PWB401 4.3 20.9 0.5
C19 B:PWB401 4.3 20.8 0.5
HA B:TYR163 4.4 19.5 1.0
O B:HOH504 4.4 33.8 1.0
HH22 A:ARG238 4.5 41.0 1.0
O4 B:PWB401 4.6 26.8 0.5
C4 B:PWB401 4.6 30.4 0.5
C14 B:PWB401 4.6 30.4 0.5
CG B:TYR163 4.6 11.9 1.0
H192 B:PWB401 4.6 25.1 0.5
H92 B:PWB401 4.7 25.1 0.5
HB2 B:TYR163 4.8 22.7 1.0
CB B:PRO264 4.8 24.0 1.0
HA B:PRO264 4.9 40.0 1.0
CA B:PRO264 4.9 33.2 1.0
H191 B:PWB401 4.9 25.1 0.5
H91 B:PWB401 4.9 25.1 0.5
H4 B:PWB401 4.9 36.5 0.5
H14 B:PWB401 4.9 36.5 0.5
NH1 A:ARG238 4.9 34.9 1.0
HB2 B:TYR167 5.0 29.2 1.0
O2 B:PWB401 5.0 23.4 0.5

Fluorine binding site 2 out of 4 in 6ywa

Go back to Fluorine Binding Sites List in 6ywa
Fluorine binding site 2 out of 4 in the Human Ref Sting in Complex with 3',3'-C-[2'Fdamp-2'Fdam(Ps)]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Ref Sting in Complex with 3',3'-C-[2'Fdamp-2'Fdam(Ps)] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:24.1
occ:0.50
F1 B:PWB401 0.0 24.1 0.5
F2 B:PWB401 0.0 24.1 0.5
C6 B:PWB401 1.3 22.2 0.5
C16 B:PWB401 1.3 22.1 0.5
H6 B:PWB401 2.0 26.8 0.5
H16 B:PWB401 2.0 26.7 0.5
HB A:THR263 2.3 40.6 1.0
HD3 A:PRO264 2.3 36.6 1.0
C7 B:PWB401 2.3 23.3 0.5
C17 B:PWB401 2.3 23.3 0.5
C5 B:PWB401 2.3 24.6 0.5
C15 B:PWB401 2.3 24.2 0.5
H7 B:PWB401 2.4 28.1 0.5
H17 B:PWB401 2.4 28.1 0.5
O7 B:PWB401 2.7 24.9 0.5
O10 B:PWB401 2.7 24.9 0.5
H8 B:PWB401 2.7 26.3 0.5
H18 B:PWB401 2.7 24.1 0.5
C8 B:PWB401 2.9 21.8 0.5
C18 B:PWB401 2.9 20.0 0.5
HD1 A:TYR163 2.9 21.5 1.0
O1 B:PWB401 3.0 20.7 0.5
O5 B:PWB401 3.0 19.5 0.5
HE1 A:TYR163 3.1 32.3 1.0
CB A:THR263 3.2 33.8 1.0
CD A:PRO264 3.2 30.4 1.0
H5 B:PWB401 3.3 29.6 0.5
H15 B:PWB401 3.3 29.1 0.5
HG3 A:PRO264 3.3 29.5 1.0
O A:HOH631 3.4 29.4 1.0
N2 B:PWB401 3.5 30.1 0.5
N6 B:PWB401 3.5 30.1 0.5
CD1 A:TYR163 3.5 17.8 1.0
HG1 A:THR263 3.6 25.9 1.0
CE1 A:TYR163 3.7 26.8 1.0
O B:PWB401 3.7 18.2 0.5
O22 B:PWB401 3.7 17.1 0.5
OG1 A:THR263 3.7 21.5 1.0
P B:PWB401 3.7 24.4 0.5
CG A:PRO264 3.8 24.5 1.0
P1 B:PWB401 3.8 24.4 0.5
HD2 A:PRO264 3.8 36.6 1.0
H A:THR263 3.8 26.7 1.0
HH12 B:ARG238 4.0 45.2 1.0
C1 B:PWB401 4.0 32.2 0.5
N1 B:PWB401 4.0 36.4 0.5
N5 B:PWB401 4.0 36.4 0.5
C11 B:PWB401 4.0 32.2 0.5
HG21 A:THR263 4.0 30.1 1.0
N A:PRO264 4.0 26.1 1.0
CG2 A:THR263 4.1 25.0 1.0
HG22 A:THR263 4.1 30.1 1.0
HG2 A:PRO264 4.1 29.5 1.0
CA A:THR263 4.1 32.8 1.0
HH22 B:ARG238 4.3 52.5 1.0
N A:THR263 4.3 22.2 1.0
C9 B:PWB401 4.3 23.4 0.5
C19 B:PWB401 4.3 23.4 0.5
C A:THR263 4.4 20.5 1.0
HA A:TYR163 4.5 34.0 1.0
O A:HOH610 4.5 40.3 1.0
O4 B:PWB401 4.6 18.4 0.5
C4 B:PWB401 4.6 29.5 0.5
C14 B:PWB401 4.6 29.5 0.5
H192 B:PWB401 4.7 28.2 0.5
H92 B:PWB401 4.7 28.2 0.5
O B:HOH520 4.7 34.8 1.0
NH1 B:ARG238 4.8 37.5 1.0
CG A:TYR163 4.8 21.0 1.0
S1 B:PWB401 4.9 21.0 0.5
HB2 A:TYR167 4.9 31.8 1.0
H4 B:PWB401 4.9 35.5 0.5
H14 B:PWB401 4.9 35.5 0.5
H91 B:PWB401 4.9 28.2 0.5
H191 B:PWB401 4.9 28.2 0.5
HG23 A:THR263 5.0 30.1 1.0
HA A:PRO264 5.0 32.2 1.0
CZ A:TYR163 5.0 17.3 1.0
O2 B:PWB401 5.0 21.4 0.5
NH2 B:ARG238 5.0 43.7 1.0
O8 B:PWB401 5.0 21.3 0.5

Fluorine binding site 3 out of 4 in 6ywa

Go back to Fluorine Binding Sites List in 6ywa
Fluorine binding site 3 out of 4 in the Human Ref Sting in Complex with 3',3'-C-[2'Fdamp-2'Fdam(Ps)]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Ref Sting in Complex with 3',3'-C-[2'Fdamp-2'Fdam(Ps)] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:24.1
occ:0.50
F2 B:PWB401 0.0 24.1 0.5
F1 B:PWB401 0.0 24.1 0.5
C6 B:PWB401 1.3 22.2 0.5
C16 B:PWB401 1.3 22.1 0.5
H6 B:PWB401 2.0 26.8 0.5
H16 B:PWB401 2.0 26.7 0.5
HB A:THR263 2.3 40.6 1.0
HD3 A:PRO264 2.3 36.6 1.0
C7 B:PWB401 2.3 23.3 0.5
C17 B:PWB401 2.3 23.3 0.5
C5 B:PWB401 2.4 24.6 0.5
C15 B:PWB401 2.4 24.2 0.5
H7 B:PWB401 2.4 28.1 0.5
H17 B:PWB401 2.4 28.1 0.5
O7 B:PWB401 2.7 24.9 0.5
O10 B:PWB401 2.7 24.9 0.5
H8 B:PWB401 2.7 26.3 0.5
H18 B:PWB401 2.7 24.1 0.5
C8 B:PWB401 2.9 21.8 0.5
C18 B:PWB401 2.9 20.0 0.5
HD1 A:TYR163 2.9 21.5 1.0
O1 B:PWB401 3.0 20.7 0.5
O5 B:PWB401 3.0 19.5 0.5
HE1 A:TYR163 3.1 32.3 1.0
CB A:THR263 3.2 33.8 1.0
CD A:PRO264 3.2 30.4 1.0
H5 B:PWB401 3.3 29.6 0.5
H15 B:PWB401 3.3 29.1 0.5
HG3 A:PRO264 3.3 29.5 1.0
O A:HOH631 3.4 29.4 1.0
N2 B:PWB401 3.5 30.1 0.5
N6 B:PWB401 3.5 30.1 0.5
CD1 A:TYR163 3.5 17.8 1.0
HG1 A:THR263 3.6 25.9 1.0
CE1 A:TYR163 3.7 26.8 1.0
O B:PWB401 3.7 18.2 0.5
O22 B:PWB401 3.7 17.1 0.5
OG1 A:THR263 3.7 21.5 1.0
P B:PWB401 3.7 24.4 0.5
CG A:PRO264 3.8 24.5 1.0
P1 B:PWB401 3.8 24.4 0.5
HD2 A:PRO264 3.8 36.6 1.0
H A:THR263 3.8 26.7 1.0
HH12 B:ARG238 4.0 45.2 1.0
HG21 A:THR263 4.0 30.1 1.0
N1 B:PWB401 4.0 36.4 0.5
N5 B:PWB401 4.0 36.4 0.5
C1 B:PWB401 4.0 32.2 0.5
C11 B:PWB401 4.0 32.2 0.5
N A:PRO264 4.0 26.1 1.0
CG2 A:THR263 4.0 25.0 1.0
HG22 A:THR263 4.1 30.1 1.0
HG2 A:PRO264 4.1 29.5 1.0
CA A:THR263 4.1 32.8 1.0
HH22 B:ARG238 4.3 52.5 1.0
N A:THR263 4.3 22.2 1.0
C9 B:PWB401 4.3 23.4 0.5
C19 B:PWB401 4.3 23.4 0.5
C A:THR263 4.4 20.5 1.0
O A:HOH610 4.5 40.3 1.0
HA A:TYR163 4.5 34.0 1.0
O4 B:PWB401 4.6 18.4 0.5
C4 B:PWB401 4.6 29.5 0.5
C14 B:PWB401 4.6 29.5 0.5
H192 B:PWB401 4.7 28.2 0.5
H92 B:PWB401 4.7 28.2 0.5
O B:HOH520 4.7 34.8 1.0
NH1 B:ARG238 4.8 37.5 1.0
CG A:TYR163 4.8 21.0 1.0
S1 B:PWB401 4.9 21.0 0.5
HB2 A:TYR167 4.9 31.8 1.0
H4 B:PWB401 4.9 35.5 0.5
H14 B:PWB401 4.9 35.5 0.5
H91 B:PWB401 4.9 28.2 0.5
H191 B:PWB401 4.9 28.2 0.5
HG23 A:THR263 5.0 30.1 1.0
HA A:PRO264 5.0 32.2 1.0
CZ A:TYR163 5.0 17.3 1.0
O2 B:PWB401 5.0 21.4 0.5
NH2 B:ARG238 5.0 43.7 1.0
O8 B:PWB401 5.0 21.3 0.5
CA A:PRO264 5.0 26.8 1.0

Fluorine binding site 4 out of 4 in 6ywa

Go back to Fluorine Binding Sites List in 6ywa
Fluorine binding site 4 out of 4 in the Human Ref Sting in Complex with 3',3'-C-[2'Fdamp-2'Fdam(Ps)]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Ref Sting in Complex with 3',3'-C-[2'Fdamp-2'Fdam(Ps)] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:24.5
occ:0.50
F2 B:PWB401 0.0 24.5 0.5
F1 B:PWB401 0.0 24.5 0.5
C6 B:PWB401 1.3 23.6 0.5
C16 B:PWB401 1.3 23.6 0.5
H6 B:PWB401 2.0 28.4 0.5
H16 B:PWB401 2.0 28.4 0.5
HD3 B:PRO264 2.3 29.8 1.0
C7 B:PWB401 2.3 23.0 0.5
C17 B:PWB401 2.3 23.2 0.5
HB B:THR263 2.3 40.4 1.0
C15 B:PWB401 2.4 20.7 0.5
C5 B:PWB401 2.4 21.1 0.5
H7 B:PWB401 2.4 27.7 0.5
H17 B:PWB401 2.4 27.9 0.5
HD1 B:TYR163 2.7 35.5 1.0
O7 B:PWB401 2.7 24.6 0.5
H18 B:PWB401 2.7 35.0 0.5
O10 B:PWB401 2.7 24.6 0.5
H8 B:PWB401 2.7 35.0 0.5
C8 B:PWB401 2.9 29.1 0.5
C18 B:PWB401 2.9 29.1 0.5
O1 B:PWB401 3.0 23.0 0.5
O5 B:PWB401 3.0 23.0 0.5
HG3 B:PRO264 3.1 32.0 1.0
CD B:PRO264 3.1 24.8 1.0
HE1 B:TYR163 3.2 30.2 1.0
H5 B:PWB401 3.3 25.5 0.5
H15 B:PWB401 3.3 24.9 0.5
CB B:THR263 3.3 33.6 1.0
CD1 B:TYR163 3.4 29.5 1.0
O B:HOH526 3.5 26.1 1.0
N2 B:PWB401 3.5 30.9 0.5
N6 B:PWB401 3.5 30.9 0.5
CG B:PRO264 3.6 26.6 1.0
CE1 B:TYR163 3.7 25.1 1.0
O22 B:PWB401 3.7 24.6 0.5
O B:PWB401 3.7 24.7 0.5
HG1 B:THR263 3.8 38.2 1.0
HD2 B:PRO264 3.8 29.8 1.0
P B:PWB401 3.8 28.0 0.5
P1 B:PWB401 3.8 28.0 0.5
H B:THR263 3.9 39.3 1.0
OG1 B:THR263 3.9 31.7 1.0
HG2 B:PRO264 3.9 32.0 1.0
N B:PRO264 3.9 23.6 1.0
HG22 B:THR263 4.0 33.4 1.0
N1 B:PWB401 4.1 31.4 0.5
N5 B:PWB401 4.1 31.4 0.5
C1 B:PWB401 4.1 30.9 0.5
C11 B:PWB401 4.1 30.9 0.5
CG2 B:THR263 4.1 27.7 1.0
HG21 B:THR263 4.1 33.4 1.0
CA B:THR263 4.1 25.6 1.0
HH12 A:ARG238 4.2 42.0 1.0
N B:THR263 4.3 32.6 1.0
C B:THR263 4.3 18.2 1.0
C9 B:PWB401 4.3 20.9 0.5
C19 B:PWB401 4.3 20.8 0.5
HA B:TYR163 4.4 19.5 1.0
O B:HOH504 4.4 33.8 1.0
HH22 A:ARG238 4.5 41.0 1.0
O4 B:PWB401 4.6 26.8 0.5
C4 B:PWB401 4.6 30.4 0.5
C14 B:PWB401 4.6 30.4 0.5
CG B:TYR163 4.6 11.9 1.0
H192 B:PWB401 4.6 25.1 0.5
H92 B:PWB401 4.7 25.1 0.5
HB2 B:TYR163 4.8 22.7 1.0
CB B:PRO264 4.8 24.0 1.0
HA B:PRO264 4.8 40.0 1.0
CA B:PRO264 4.9 33.2 1.0
H191 B:PWB401 4.9 25.1 0.5
H91 B:PWB401 4.9 25.1 0.5
H4 B:PWB401 4.9 36.5 0.5
H14 B:PWB401 4.9 36.5 0.5
NH1 A:ARG238 4.9 34.9 1.0
HB2 B:TYR167 5.0 29.2 1.0
O2 B:PWB401 5.0 23.4 0.5
HG23 B:THR263 5.0 33.4 1.0

Reference:

E.Boura, M.Smola. Human Ref Sting in Complex with 3',3'-C-[2'Fdamp-2'Fdam(Ps)] To Be Published.
Page generated: Sat Jul 10 13:56:31 2021

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