Fluorine in PDB 3p4a: 2'Fluoro Modified Rna Octamer FA2U2

The structure of 2'Fluoro Modified Rna Octamer FA2U2, PDB code: 3p4a was solved by M.Manoharan, A.Akinc, R.K.Pandey, J.Qin, P.Hadwiger, M.John, K.Mills, K.Charisse, M.A.Maier, L.Nechev, E.M.Greene, P.S.Pallan, E.Rozners, K.G.Rajeev, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.20
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	43.245, 43.245, 60.791, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 23.4

The structure of 2'Fluoro Modified Rna Octamer FA2U2 also contains other interesting chemical elements:

Strontium	(Sr)	9 atoms
Magnesium	(Mg)	2 atoms

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 52;

Binding sites:

The binding sites of Fluorine atom in the 2'Fluoro Modified Rna Octamer FA2U2 (pdb code 3p4a). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 52 binding sites of Fluorine where determined in the 2'Fluoro Modified Rna Octamer FA2U2, PDB code: 3p4a:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 52 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:26.3 occ:1.00 F2' A:CFZ101 0.0 26.3 1.0 C2' A:CFZ101 1.4 24.6 1.0 C1' A:CFZ101 2.3 25.1 1.0 C3' A:CFZ101 2.4 25.1 1.0 O3' A:CFZ101 2.8 26.1 1.0 C4' A:CFZ101 2.8 30.2 1.0 O4' A:CFZ101 3.0 28.9 1.0 O A:HOH926 3.2 35.2 1.0 C5' A:GF2102 3.4 19.6 1.0 O5' A:GF2102 3.5 22.1 1.0 N1 A:CFZ101 3.6 23.2 1.0 O4' A:GF2102 3.7 18.1 1.0 O2 A:CFZ101 3.8 20.9 1.0 P A:GF2102 3.9 24.1 1.0 O A:HOH1009 3.9 73.1 1.0 C4' A:GF2102 4.1 18.9 1.0 C2 A:CFZ101 4.2 21.7 1.0 C5' A:CFZ101 4.3 33.8 1.0 C6 A:CFZ101 4.7 23.7 1.0 C8 A:GF2102 4.7 15.7 1.0 OP1 A:GF2102 4.8 27.9 1.0 OP2 A:GF2102 4.8 27.7 1.0 O5' A:CFZ101 4.8 51.8 1.0 C1' A:GF2102 5.0 15.9 1.0

Fluorine binding site 2 out of 52 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F102 b:17.4 occ:1.00 F A:GF2102 0.0 17.4 1.0 C2' A:GF2102 1.4 16.9 1.0 C1' A:GF2102 2.3 15.9 1.0 C3' A:GF2102 2.3 17.2 1.0 O3' A:GF2102 2.6 19.2 1.0 C4' A:GF2102 2.8 18.9 1.0 O4' A:GF2102 3.0 18.1 1.0 C5' A:AF2103 3.5 15.5 1.0 O4' A:AF2103 3.5 15.9 1.0 N9 A:GF2102 3.6 16.2 1.0 O5' A:AF2103 3.7 16.2 1.0 P A:AF2103 3.9 18.9 1.0 C4' A:AF2103 4.0 14.8 1.0 N3 A:GF2102 4.2 15.5 1.0 C4 A:GF2102 4.3 14.6 1.0 C5' A:GF2102 4.3 19.6 1.0 O A:HOH990 4.5 53.4 1.0 C8 A:GF2102 4.7 15.7 1.0 OP2 A:AF2103 4.7 23.8 1.0 OP1 A:AF2103 4.7 23.6 1.0 C1' A:AF2103 4.8 14.8 1.0 C8 A:AF2103 5.0 15.8 1.0 O5' A:GF2102 5.0 22.1 1.0

Fluorine binding site 3 out of 52 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F103 b:15.7 occ:1.00 F A:AF2103 0.0 15.7 1.0 C2' A:AF2103 1.4 16.0 1.0 C3' A:AF2103 2.4 13.8 1.0 C1' A:AF2103 2.4 14.8 1.0 O3' A:AF2103 2.8 15.0 1.0 C4' A:AF2103 2.8 14.8 1.0 O4' A:AF2103 3.1 15.9 1.0 C5' A:AF2104 3.5 15.8 1.0 N9 A:AF2103 3.6 15.2 1.0 O4' A:AF2104 3.6 13.7 1.0 O5' A:AF2104 3.8 15.5 1.0 P A:AF2104 4.0 17.0 1.0 C4' A:AF2104 4.0 15.8 1.0 N3 A:AF2103 4.2 15.7 1.0 C4 A:AF2103 4.2 13.7 1.0 C5' A:AF2103 4.3 15.5 1.0 C8 A:AF2103 4.7 15.8 1.0 OP1 A:AF2104 4.8 21.2 1.0 OP2 A:AF2104 4.9 21.6 1.0 C1' A:AF2104 4.9 13.0 1.0

Fluorine binding site 4 out of 52 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F104 b:17.3 occ:1.00 F A:AF2104 0.0 17.3 1.0 C2' A:AF2104 1.4 14.0 1.0 C3' A:AF2104 2.3 14.1 1.0 C1' A:AF2104 2.4 13.0 1.0 O3' A:AF2104 2.7 15.9 1.0 C4' A:AF2104 2.8 15.8 1.0 O4' A:AF2104 3.0 13.7 1.0 C5' A:UFT105 3.4 15.8 1.0 O5' A:UFT105 3.4 15.2 1.0 O4' A:UFT105 3.5 11.9 1.0 N9 A:AF2104 3.6 13.4 1.0 P A:UFT105 3.7 18.4 1.0 O A:HOH753 3.8 20.1 1.0 O B:HOH779 3.9 15.7 0.6 O B:HOH925 4.0 37.7 1.0 C4' A:UFT105 4.1 13.6 1.0 N3 A:AF2104 4.1 12.5 1.0 C4 A:AF2104 4.3 11.8 1.0 C5' A:AF2104 4.3 15.8 1.0 C6 A:UFT105 4.3 11.1 1.0 OP2 A:UFT105 4.6 21.6 1.0 OP1 A:UFT105 4.7 20.6 1.0 C8 A:AF2104 4.7 15.2 1.0 C1' A:UFT105 4.7 10.1 1.0 N1 A:UFT105 4.9 10.8 1.0

Fluorine binding site 5 out of 52 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F105 b:11.8 occ:1.00 F2' A:UFT105 0.0 11.8 1.0 C2' A:UFT105 1.4 10.0 1.0 C1' A:UFT105 2.3 10.1 1.0 C3' A:UFT105 2.4 11.2 1.0 O3' A:UFT105 2.8 12.2 1.0 C4' A:UFT105 2.8 13.6 1.0 O4' A:UFT105 2.9 11.9 1.0 C5' A:UFT106 3.3 13.6 1.0 O4' A:UFT106 3.3 12.3 1.0 O5' A:UFT106 3.5 12.9 1.0 N1 A:UFT105 3.6 10.8 1.0 C4' A:UFT106 3.8 12.8 1.0 P A:UFT106 3.8 14.6 1.0 O2 A:UFT105 3.9 11.6 1.0 C2 A:UFT105 4.2 10.5 1.0 C5' A:UFT105 4.3 15.8 1.0 C6 A:UFT106 4.6 11.8 1.0 C1' A:UFT106 4.6 12.4 1.0 C6 A:UFT105 4.7 11.1 1.0 OP1 A:UFT106 4.7 19.6 1.0 OP2 A:UFT106 4.7 18.1 1.0 O5' A:UFT105 4.9 15.2 1.0 N1 A:UFT106 4.9 10.9 1.0

Fluorine binding site 6 out of 52 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F106 b:15.9 occ:1.00 F2' A:UFT106 0.0 15.9 1.0 C2' A:UFT106 1.4 13.1 1.0 C1' A:UFT106 2.3 12.4 1.0 C3' A:UFT106 2.4 12.5 1.0 O3' A:UFT106 2.7 14.3 1.0 C4' A:UFT106 2.8 12.8 1.0 O4' A:UFT106 2.9 12.3 1.0 O4' A:CFZ107 3.4 12.7 1.0 O A:HOH954 3.5 47.1 1.0 N1 A:UFT106 3.6 10.9 1.0 C5' A:CFZ107 3.6 15.2 1.0 O5' A:CFZ107 3.7 13.5 1.0 O2 A:UFT106 3.8 14.1 1.0 P A:CFZ107 3.9 14.1 1.0 C4' A:CFZ107 4.0 13.4 1.0 C2 A:UFT106 4.2 11.6 1.0 C5' A:UFT106 4.2 13.6 1.0 C6 A:UFT106 4.6 11.8 1.0 C6 A:CFZ107 4.6 12.1 1.0 C1' A:CFZ107 4.6 11.1 1.0 O1P A:CFZ107 4.7 17.6 1.0 O2P A:CFZ107 4.8 14.7 1.0 O5' A:UFT106 4.9 12.9 1.0 N1 A:CFZ107 5.0 10.9 1.0

Fluorine binding site 7 out of 52 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F107 b:13.4 occ:1.00 F2' A:CFZ107 0.0 13.4 1.0 C2' A:CFZ107 1.4 11.3 1.0 C1' A:CFZ107 2.3 11.1 1.0 C3' A:CFZ107 2.4 12.6 1.0 O3' A:CFZ107 2.7 12.8 1.0 C4' A:CFZ107 2.8 13.4 1.0 O4' A:CFZ107 3.0 12.7 1.0 C5' A:GF2108 3.2 10.9 1.0 O5' A:GF2108 3.6 10.9 1.0 O4' A:GF2108 3.6 9.1 1.0 N1 A:CFZ107 3.6 10.9 1.0 O2 A:CFZ107 3.7 10.8 1.0 P A:GF2108 3.9 13.0 1.0 C4' A:GF2108 4.0 10.0 1.0 C2 A:CFZ107 4.2 10.4 1.0 C5' A:CFZ107 4.3 15.2 1.0 C6 A:CFZ107 4.7 12.1 1.0 OP1 A:GF2108 4.7 13.9 1.0 O A:HOH954 4.8 47.1 1.0 OP2 A:GF2108 4.8 14.5 1.0 C1' A:GF2108 4.9 8.9 1.0 C8 A:GF2108 5.0 9.7 1.0 O5' A:CFZ107 5.0 13.5 1.0

Fluorine binding site 8 out of 52 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F108 b:9.5 occ:1.00 F A:GF2108 0.0 9.5 1.0 C2' A:GF2108 1.4 9.2 1.0 C1' A:GF2108 2.3 8.9 1.0 C3' A:GF2108 2.3 9.3 1.0 O3' A:GF2108 2.7 9.8 1.0 C4' A:GF2108 2.8 10.0 1.0 O4' A:GF2108 3.0 9.1 1.0 O A:HOH716 3.1 13.6 1.0 N9 A:GF2108 3.6 8.9 1.0 N3 A:GF2108 4.3 9.3 1.0 C5' A:GF2108 4.3 10.9 1.0 F2' C:CFZ301 4.3 10.3 1.0 C4 A:GF2108 4.4 8.3 1.0 O4' C:CFZ301 4.4 11.3 1.0 C8 A:GF2108 4.7 9.7 1.0 C1' C:CFZ301 4.7 10.4 1.0 C4' C:CFZ301 4.8 11.4 1.0 O5' A:GF2108 4.9 10.9 1.0

Fluorine binding site 9 out of 52 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range: probe atom residue distance (Å) B Occ B:F209 b:13.4 occ:1.00 F2' B:CFZ209 0.0 13.4 1.0 C2' B:CFZ209 1.4 11.2 1.0 C1' B:CFZ209 2.3 11.9 1.0 C3' B:CFZ209 2.4 13.2 1.0 C4' B:CFZ209 2.8 13.9 1.0 O3' B:CFZ209 2.8 14.0 1.0 O4' B:CFZ209 2.9 12.7 1.0 O B:HOH980 3.4 12.6 1.0 C5' B:GF2210 3.5 13.4 1.0 N1 B:CFZ209 3.6 12.2 1.0 O4' B:GF2210 3.6 12.2 1.0 O5' B:GF2210 3.6 13.6 1.0 O2 B:CFZ209 3.6 10.6 1.0 O D:HOH738 3.8 14.7 1.0 C2' D:GF2416 3.9 11.4 1.0 P B:GF2210 3.9 14.6 1.0 C2 B:CFZ209 4.1 10.8 1.0 C4' B:GF2210 4.1 12.7 1.0 C5' B:CFZ209 4.2 16.2 1.0 F D:GF2416 4.3 11.1 1.0 C8 B:GF2210 4.5 12.7 1.0 O3' D:GF2416 4.6 12.7 1.0 C3' D:GF2416 4.6 11.3 1.0 C6 B:CFZ209 4.6 13.5 1.0 OP2 B:GF2210 4.7 15.0 1.0 OP1 B:GF2210 4.8 16.7 1.0 C1' B:GF2210 4.9 12.6 1.0 O5' B:CFZ209 5.0 19.9 1.0

Fluorine binding site 10 out of 52 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range: probe atom residue distance (Å) B Occ B:F210 b:13.1 occ:1.00 F B:GF2210 0.0 13.1 1.0 C2' B:GF2210 1.4 11.7 1.0 C1' B:GF2210 2.3 12.6 1.0 C3' B:GF2210 2.4 13.6 1.0 O3' B:GF2210 2.7 13.8 1.0 C4' B:GF2210 2.8 12.7 1.0 O4' B:GF2210 2.9 12.2 1.0 O C:HOH724 3.1 15.0 1.0 C5' B:AF2211 3.4 13.3 1.0 O4' B:AF2211 3.6 12.9 1.0 N9 B:GF2210 3.7 11.7 1.0 O5' B:AF2211 3.7 13.0 1.0 O B:HOH737 3.7 15.7 1.0 O B:HOH723 3.7 13.4 0.3 P B:AF2211 3.9 14.6 1.0 O B:HOH736 4.0 18.7 0.3 C4' B:AF2211 4.0 13.1 1.0 C5' B:GF2210 4.3 13.4 1.0 N3 B:GF2210 4.3 11.4 1.0 C4 B:GF2210 4.4 10.8 1.0 C8 B:AF2211 4.7 11.6 1.0 OP1 B:AF2211 4.7 16.5 1.0 C8 B:GF2210 4.8 12.7 1.0 OP2 B:AF2211 4.8 16.7 1.0 C1' B:AF2211 4.9 13.1 1.0 O5' B:GF2210 4.9 13.6 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