Fluorine in PDB 3p4c: Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-R32

The structure of Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-R32, PDB code: 3p4c 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)	50.00 / 1.15
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	40.550, 40.550, 117.222, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 24.9

The structure of Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-R32 also contains other interesting chemical elements:

Strontium

(Sr)

3 atoms

The binding sites of Fluorine atom in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-R32 (pdb code 3p4c). 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/RA2U2-R32, PDB code: 3p4c:
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/RA2U2-R32


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/RA2U2-R32 within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:19.6 occ:1.00 F2' A:CFZ101 0.0 19.6 1.0 C2' A:CFZ101 1.4 14.8 1.0 C1' A:CFZ101 2.3 15.6 1.0 C3' A:CFZ101 2.3 15.5 1.0 C4' A:CFZ101 2.7 18.4 1.0 O3' A:CFZ101 2.7 18.3 1.0 O4' A:CFZ101 2.9 18.5 1.0 O A:HOH309 3.3 18.4 1.0 C5' A:G102 3.4 15.0 1.0 N1 A:CFZ101 3.6 12.7 1.0 O5' A:G102 3.6 15.0 1.0 O4' A:G102 3.7 14.2 1.0 O2 A:CFZ101 3.7 14.0 1.0 P A:G102 3.9 14.9 1.0 C2 A:CFZ101 4.1 12.7 1.0 C5' A:CFZ101 4.2 22.7 1.0 C4' A:G102 4.2 14.9 1.0 C8 A:G102 4.5 10.8 1.0 C6 A:CFZ101 4.6 15.2 1.0 OP2 A:G102 4.7 15.9 1.0 OP1 A:G102 4.8 17.8 1.0 O5' A:CFZ101 4.9 25.0 1.0 C1' A:G102 5.0 12.6 1.0

Fluorine binding site 2 out of 8 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-R32


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/RA2U2-R32 within 5.0Å range: probe atom residue distance (Å) B Occ A:F103 b:11.9 occ:1.00 F A:AF2103 0.0 11.9 1.0 C2' A:AF2103 1.4 10.2 1.0 C1' A:AF2103 2.3 10.6 1.0 C3' A:AF2103 2.4 10.9 1.0 O3' A:AF2103 2.7 11.9 1.0 C4' A:AF2103 2.8 10.8 1.0 O4' A:AF2103 2.9 11.9 1.0 C5' A:A104 3.5 9.4 1.0 O4' A:A104 3.5 9.7 1.0 N9 A:AF2103 3.6 8.8 1.0 O5' A:A104 3.7 9.5 1.0 P A:A104 4.0 11.1 1.0 C4' A:A104 4.1 9.6 1.0 C5' A:AF2103 4.3 11.8 1.0 N3 A:AF2103 4.3 9.0 1.0 C4 A:AF2103 4.4 8.5 1.0 C8 A:AF2103 4.7 10.5 1.0 OP1 A:A104 4.7 13.4 1.0 C8 A:A104 4.8 9.4 1.0 C1' A:A104 4.8 9.7 1.0 OP2 A:A104 4.9 13.6 1.0 O5' A:AF2103 5.0 10.7 1.0

Fluorine binding site 3 out of 8 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-R32


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/RA2U2-R32 within 5.0Å range: probe atom residue distance (Å) B Occ A:F105 b:13.8 occ:1.00 F2' A:UFT105 0.0 13.8 1.0 C2' A:UFT105 1.4 11.8 1.0 C3' A:UFT105 2.4 10.6 1.0 C1' A:UFT105 2.4 10.9 1.0 C4' A:UFT105 2.7 11.1 1.0 O3' A:UFT105 2.8 11.5 1.0 O4' A:UFT105 3.0 10.5 1.0 C5' A:U106 3.5 14.7 1.0 O4' A:U106 3.5 13.1 1.0 N1 A:UFT105 3.7 11.4 1.0 O5' A:U106 3.7 13.4 1.0 O2 A:UFT105 3.8 14.8 1.0 P A:U106 3.9 13.1 1.0 C4' A:U106 4.0 13.6 1.0 C2 A:UFT105 4.2 15.3 1.0 C5' A:UFT105 4.2 10.8 1.0 C6 A:UFT105 4.7 11.8 1.0 OP1 A:U106 4.8 14.5 1.0 C1' A:U106 4.8 13.3 1.0 OP2 A:U106 4.9 14.8 1.0 O5' A:UFT105 4.9 12.3 1.0 C6 A:U106 4.9 13.0 1.0

Fluorine binding site 4 out of 8 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-R32


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/RA2U2-R32 within 5.0Å range: probe atom residue distance (Å) B Occ A:F107 b:16.8 occ:1.00 F2' A:CFZ107 0.0 16.8 1.0 C2' A:CFZ107 1.4 13.6 1.0 C3' A:CFZ107 2.3 13.2 1.0 C1' A:CFZ107 2.3 14.9 1.0 O3' A:CFZ107 2.7 12.9 1.0 C4' A:CFZ107 2.8 13.9 1.0 O4' A:CFZ107 2.9 15.7 1.0 O4' A:G108 3.5 13.3 0.2 O5' A:G108 3.6 15.6 0.2 OP1 A:G108 3.6 15.6 0.8 N1 A:CFZ107 3.6 16.2 1.0 O2 A:CFZ107 3.7 18.6 1.0 P A:G108 3.7 12.8 1.0 C2 A:CFZ107 4.1 18.9 1.0 C5' A:CFZ107 4.2 14.9 1.0 C1' A:G108 4.4 19.6 0.2 C8 A:G108 4.4 15.6 0.2 OP1 A:G108 4.6 14.7 0.2 OP2 A:G108 4.6 14.7 0.8 C4' A:G108 4.6 20.3 0.2 N9 A:G108 4.6 15.1 0.2 C6 A:CFZ107 4.6 17.6 1.0 C5' A:G108 4.7 23.7 0.2 OP2 A:G108 4.7 13.6 0.2 O5' A:G108 4.8 12.1 0.8 O5' A:CFZ107 4.9 14.1 1.0

Fluorine binding site 5 out of 8 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-R32


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/RA2U2-R32 within 5.0Å range: probe atom residue distance (Å) B Occ B:F209 b:21.9 occ:0.80 F2' B:CFZ209 0.0 21.9 0.8 C2' B:CFZ209 1.4 20.4 0.8 C3' B:CFZ209 2.3 16.0 0.8 C1' B:CFZ209 2.3 19.4 0.8 O3' B:CFZ209 2.6 20.6 0.8 C4' B:CFZ209 2.9 17.1 0.8 O4' B:CFZ209 3.0 18.9 0.8 O2 B:CFZ209 3.6 14.2 0.8 N1 B:CFZ209 3.6 15.5 0.8 O4' B:G210 3.8 20.8 1.0 O5' B:G210 3.8 18.9 1.0 P B:G210 3.9 16.4 1.0 C5' B:G210 4.1 21.5 1.0 C2 B:CFZ209 4.1 13.3 0.8 C5' B:CFZ209 4.4 20.8 0.8 C8 B:G210 4.4 18.6 1.0 C4' B:G210 4.6 21.0 1.0 OP1 B:G210 4.7 26.0 1.0 C6 B:CFZ209 4.7 14.4 0.8 OP2 B:G210 4.8 20.0 1.0 C1' B:G210 5.0 19.1 1.0 O5' B:CFZ209 5.0 17.7 0.8 N9 B:G210 5.0 19.2 1.0

Fluorine binding site 6 out of 8 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-R32


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/RA2U2-R32 within 5.0Å range: probe atom residue distance (Å) B Occ B:F211 b:14.1 occ:1.00 F B:AF2211 0.0 14.1 1.0 C2' B:AF2211 1.4 12.4 1.0 C3' B:AF2211 2.4 12.1 1.0 C1' B:AF2211 2.4 11.8 1.0 O3' B:AF2211 2.7 14.8 1.0 C4' B:AF2211 2.8 14.3 1.0 O4' B:AF2211 3.0 14.6 1.0 O5' B:A212 3.6 11.3 1.0 C5' B:A212 3.6 9.8 1.0 N9 B:AF2211 3.6 10.7 1.0 O4' B:A212 3.6 12.2 1.0 O B:HOH321 3.7 27.4 1.0 P B:A212 3.8 14.2 1.0 C4' B:A212 4.2 9.3 1.0 N3 B:AF2211 4.2 10.4 1.0 C4 B:AF2211 4.3 9.6 1.0 C5' B:AF2211 4.3 17.5 1.0 C8 B:AF2211 4.7 12.2 1.0 OP2 B:A212 4.7 18.9 1.0 OP1 B:A212 4.7 16.4 1.0 C8 B:A212 4.8 11.2 1.0 C1' B:A212 4.9 11.2 1.0 O5' B:AF2211 5.0 16.8 1.0

Fluorine binding site 7 out of 8 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-R32


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/RA2U2-R32 within 5.0Å range: probe atom residue distance (Å) B Occ B:F213 b:12.3 occ:1.00 F2' B:UFT213 0.0 12.3 1.0 C2' B:UFT213 1.4 11.5 1.0 C1' B:UFT213 2.3 11.9 1.0 C3' B:UFT213 2.3 10.1 1.0 C4' B:UFT213 2.8 11.1 1.0 O3' B:UFT213 2.8 9.6 1.0 O4' B:UFT213 2.9 13.4 1.0 O4' B:U214 3.3 7.7 1.0 C5' B:U214 3.5 8.7 1.0 O5' B:U214 3.6 8.2 1.0 N1 B:UFT213 3.6 12.6 1.0 O2 B:UFT213 3.8 14.5 1.0 P B:U214 3.9 9.5 1.0 C4' B:U214 3.9 7.3 1.0 C2 B:UFT213 4.2 12.6 1.0 C5' B:UFT213 4.3 10.4 1.0 C6 B:U214 4.4 8.9 1.0 C1' B:U214 4.5 7.4 1.0 C6 B:UFT213 4.7 13.5 1.0 SR B:SR303 4.7 77.1 0.3 OP2 B:U214 4.7 11.1 1.0 OP1 B:U214 4.8 11.4 1.0 N1 B:U214 4.8 7.7 1.0 O5' B:UFT213 5.0 10.8 1.0

Fluorine binding site 8 out of 8 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-R32


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/RA2U2-R32 within 5.0Å range: probe atom residue distance (Å) B Occ B:F215 b:11.0 occ:1.00 F2' B:CFZ215 0.0 11.0 1.0 C2' B:CFZ215 1.4 8.4 1.0 C1' B:CFZ215 2.3 9.2 1.0 C3' B:CFZ215 2.3 10.3 1.0 O3' B:CFZ215 2.7 15.4 1.0 C4' B:CFZ215 2.8 10.7 1.0 O4' B:CFZ215 2.9 9.4 1.0 C5' B:G216 3.4 9.1 1.0 N1 B:CFZ215 3.6 8.7 1.0 O B:HOH347 3.6 30.2 1.0 O5' B:G216 3.7 10.8 1.0 O4' B:G216 3.7 8.9 1.0 O2 B:CFZ215 3.7 7.9 1.0 P B:G216 3.9 17.5 1.0 O B:HOH385 4.0 31.1 1.0 C4' B:G216 4.1 8.3 1.0 C2 B:CFZ215 4.1 8.2 1.0 C5' B:CFZ215 4.3 11.3 1.0 C6 B:CFZ215 4.6 9.2 1.0 OP1 B:G216 4.7 24.6 1.0 O B:HOH365 4.8 21.5 1.0 OP2 B:G216 4.9 23.1 1.0 O5' B:CFZ215 5.0 9.9 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