Fluorine in PDB 3p4d: Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4

The structure of Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4, PDB code: 3p4d was solved by P.S.Pallan, E.M.Greene, P.A.Jicman, R.K.Pandey, M.Manoharan, E.Rozners, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.08 / 1.85
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	41.630, 41.630, 126.489, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 27.1

The binding sites of Fluorine atom in the Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4 (pdb code 3p4d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4, PDB code: 3p4d:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:38.0 occ:1.00 F2' A:CFZ101 0.0 38.0 1.0 C2' A:CFZ101 1.4 33.5 1.0 C1' A:CFZ101 2.4 35.1 1.0 C3' A:CFZ101 2.4 35.0 1.0 O3' A:CFZ101 2.8 37.0 1.0 C4' A:CFZ101 2.8 39.6 1.0 O4' A:CFZ101 3.0 35.1 1.0 O A:HOH22 3.1 22.7 1.0 O4' A:C102 3.4 33.0 1.0 C5' A:C102 3.6 33.5 1.0 N1 A:CFZ101 3.6 32.3 1.0 O5' A:C102 3.7 33.3 1.0 O2 A:CFZ101 3.8 32.8 1.0 P A:C102 3.9 38.7 1.0 C4' A:C102 4.1 32.6 1.0 C2 A:CFZ101 4.2 31.7 1.0 C5' A:CFZ101 4.2 41.2 1.0 C6 A:C102 4.5 28.1 1.0 C6 A:CFZ101 4.7 34.7 1.0 C1' A:C102 4.7 30.4 1.0 OP2 A:C102 4.7 34.4 1.0 OP1 A:C102 4.8 36.5 1.0 O5' A:CFZ101 5.0 40.8 1.0

Fluorine binding site 2 out of 8 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F103 b:32.3 occ:1.00 F2' A:CFZ103 0.0 32.3 1.0 C2' A:CFZ103 1.4 30.2 1.0 C1' A:CFZ103 2.3 26.7 1.0 C3' A:CFZ103 2.4 30.6 1.0 O3' A:CFZ103 2.8 33.0 1.0 C4' A:CFZ103 2.8 31.1 1.0 O4' A:CFZ103 2.9 31.1 1.0 C5' A:C104 3.5 30.5 1.0 N1 A:CFZ103 3.6 23.7 1.0 O4' A:C104 3.7 29.5 1.0 O2 A:CFZ103 3.7 21.9 1.0 O5' A:C104 3.7 30.2 1.0 P A:C104 4.0 31.6 1.0 C2 A:CFZ103 4.2 24.4 1.0 C4' A:C104 4.2 30.8 1.0 C5' A:CFZ103 4.3 31.2 1.0 C6 A:CFZ103 4.6 24.8 1.0 C6 A:C104 4.7 26.8 1.0 O A:HOH8 4.8 34.2 1.0 OP1 A:C104 4.8 35.5 1.0 OP2 A:C104 4.8 29.8 1.0 C1' A:C104 5.0 27.9 1.0

Fluorine binding site 3 out of 8 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F105 b:33.2 occ:1.00 F A:GF2105 0.0 33.2 1.0 C2' A:GF2105 1.4 31.9 1.0 C1' A:GF2105 2.4 29.5 1.0 C3' A:GF2105 2.4 32.5 1.0 O3' A:GF2105 2.8 36.6 1.0 C4' A:GF2105 2.9 31.4 1.0 O4' A:GF2105 3.1 29.9 1.0 O A:HOH18 3.1 33.1 1.0 O4' A:G106 3.5 37.2 1.0 C5' A:G106 3.6 36.9 1.0 O5' A:G106 3.6 37.4 1.0 N9 A:GF2105 3.6 28.2 1.0 P A:G106 3.9 39.0 1.0 C4' A:G106 4.1 36.9 1.0 N3 A:GF2105 4.1 31.3 1.0 C4 A:GF2105 4.2 28.9 1.0 C5' A:GF2105 4.4 34.0 1.0 C8 A:GF2105 4.7 26.4 1.0 C1' A:G106 4.8 34.0 1.0 OP1 A:G106 4.8 45.8 1.0 OP2 A:G106 4.8 38.2 1.0 C8 A:G106 5.0 35.7 1.0

Fluorine binding site 4 out of 8 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F107 b:48.6 occ:1.00 F A:GF2107 0.0 48.6 1.0 C2' A:GF2107 1.4 46.3 1.0 C1' A:GF2107 2.4 39.6 1.0 C3' A:GF2107 2.4 45.0 1.0 O3' A:GF2107 2.8 47.4 1.0 C4' A:GF2107 2.8 42.8 1.0 O4' A:GF2107 3.1 43.1 1.0 C5' A:G108 3.2 50.0 1.0 O4' A:G108 3.3 47.5 1.0 O5' A:G108 3.6 49.9 1.0 N9 A:GF2107 3.6 38.5 1.0 C4' A:G108 3.8 51.4 1.0 P A:G108 3.9 47.6 1.0 N3 A:GF2107 4.0 38.9 1.0 C4 A:GF2107 4.2 38.1 1.0 C5' A:GF2107 4.3 38.4 1.0 C8 A:G108 4.6 41.5 1.0 C1' A:G108 4.6 47.1 1.0 OP2 A:G108 4.7 48.2 1.0 C8 A:GF2107 4.7 40.1 1.0 OP1 A:G108 4.8 50.6 1.0 N9 A:G108 4.9 43.9 1.0

Fluorine binding site 5 out of 8 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4 within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:58.8 occ:1.00 F2' B:CFZ201 0.0 58.8 1.0 C2' B:CFZ201 1.4 56.1 1.0 C1' B:CFZ201 2.4 55.9 1.0 C3' B:CFZ201 2.4 56.1 1.0 O3' B:CFZ201 2.8 57.0 1.0 C4' B:CFZ201 2.8 57.7 1.0 O4' B:CFZ201 3.0 57.5 1.0 O4' B:C202 3.4 46.3 1.0 C5' B:C202 3.7 47.7 1.0 N1 B:CFZ201 3.7 51.9 1.0 O2 B:CFZ201 3.8 55.3 1.0 O5' B:C202 3.9 49.5 1.0 C4' B:C202 4.1 47.1 1.0 P B:C202 4.1 53.8 1.0 C2 B:CFZ201 4.2 52.0 1.0 C5' B:CFZ201 4.3 56.8 1.0 C6 B:C202 4.6 40.5 1.0 C1' B:C202 4.7 41.4 1.0 C6 B:CFZ201 4.7 48.0 1.0 OP2 B:C202 5.0 54.3 1.0 N1 B:C202 5.0 39.1 1.0 OP1 B:C202 5.0 54.8 1.0

Fluorine binding site 6 out of 8 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4 within 5.0Å range: probe atom residue distance (Å) B Occ B:F203 b:34.8 occ:1.00 F2' B:CFZ203 0.0 34.8 1.0 C2' B:CFZ203 1.4 33.6 1.0 C1' B:CFZ203 2.3 33.9 1.0 C3' B:CFZ203 2.4 35.8 1.0 O3' B:CFZ203 2.7 32.7 1.0 C4' B:CFZ203 2.7 37.4 1.0 O4' B:CFZ203 2.9 41.1 1.0 C5' B:C204 3.4 27.3 1.0 N1 B:CFZ203 3.6 31.2 1.0 O5' B:C204 3.6 27.3 1.0 O2 B:CFZ203 3.8 33.9 1.0 P B:C204 3.8 30.9 1.0 O4' B:C204 3.8 25.9 1.0 C2 B:CFZ203 4.2 28.1 1.0 C5' B:CFZ203 4.2 42.0 1.0 C4' B:C204 4.2 24.1 1.0 C6 B:CFZ203 4.6 31.3 1.0 OP1 B:C204 4.7 33.5 1.0 OP2 B:C204 4.8 28.8 1.0 C6 B:C204 4.8 29.7 1.0 O5' B:CFZ203 4.9 42.9 1.0

Fluorine binding site 7 out of 8 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4 within 5.0Å range: probe atom residue distance (Å) B Occ B:F205 b:20.3 occ:1.00 F B:GF2205 0.0 20.3 1.0 C2' B:GF2205 1.4 19.4 1.0 C1' B:GF2205 2.4 21.2 1.0 C3' B:GF2205 2.4 20.4 1.0 O3' B:GF2205 2.8 20.6 1.0 C4' B:GF2205 3.0 25.2 1.0 O4' B:GF2205 3.1 24.1 1.0 O B:HOH13 3.3 27.9 0.3 O4' B:G206 3.5 22.0 1.0 C5' B:G206 3.5 20.2 1.0 N9 B:GF2205 3.6 23.3 1.0 O5' B:G206 3.7 23.9 1.0 P B:G206 3.9 25.2 1.0 C4' B:G206 4.0 21.3 1.0 N3 B:GF2205 4.2 27.2 1.0 C4 B:GF2205 4.3 24.4 1.0 C5' B:GF2205 4.3 34.2 1.0 OP1 B:G206 4.6 23.4 1.0 C8 B:GF2205 4.7 23.6 1.0 C1' B:G206 4.7 19.6 1.0 OP2 B:G206 4.9 23.4 1.0 C8 B:G206 5.0 22.9 1.0

Fluorine binding site 8 out of 8 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Alternatingly Modified 2'Fluoro Rna Octamer F/RC4G4 within 5.0Å range: probe atom residue distance (Å) B Occ B:F207 b:23.6 occ:1.00 F B:GF2207 0.0 23.6 1.0 C2' B:GF2207 1.4 23.3 1.0 C1' B:GF2207 2.3 24.6 1.0 C3' B:GF2207 2.4 26.1 1.0 O3' B:GF2207 2.7 27.5 1.0 C4' B:GF2207 2.8 24.8 1.0 O4' B:GF2207 3.0 24.8 1.0 C5' B:G208 3.4 25.1 1.0 N9 B:GF2207 3.6 22.7 1.0 O5' B:G208 3.7 26.8 1.0 O4' B:G208 3.9 21.1 1.0 P B:G208 3.9 29.3 1.0 N3 B:GF2207 4.2 25.5 1.0 C4' B:G208 4.2 25.0 1.0 C4 B:GF2207 4.2 24.6 1.0 C5' B:GF2207 4.3 23.9 1.0 OP1 B:G208 4.7 31.7 1.0 C8 B:GF2207 4.7 24.3 1.0 OP2 B:G208 4.8 31.0 1.0 O5' B:GF2207 4.9 26.2 1.0

P.S.Pallan, E.M.Greene, P.A.Jicman, R.K.Pandey, M.Manoharan, E.Rozners, M.Egli. Unexpected Origins of the Enhanced Pairing Affinity of 2'-Fluoro-Modified Rna. Nucleic Acids Res. V. 39 3482 2011.
ISSN: ISSN 0305-1048
PubMed: 21183463
DOI: 10.1093/NAR/GKQ1270