Fluorine in PDB 1fc8: uc(Nmr) Solution Structure of A Chimeric Oligonucleotide Hairpin R(Ggac)D(Ttcg)2'F-A(Gtcc)

The binding sites of Fluorine atom in the uc(Nmr) Solution Structure of A Chimeric Oligonucleotide Hairpin R(Ggac)D(Ttcg)2'F-A(Gtcc) (pdb code 1fc8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the uc(Nmr) Solution Structure of A Chimeric Oligonucleotide Hairpin R(Ggac)D(Ttcg)2'F-A(Gtcc), PDB code: 1fc8:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the uc(Nmr) Solution Structure of A Chimeric Oligonucleotide Hairpin R(Ggac)D(Ttcg)2'F-A(Gtcc)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of uc(Nmr) Solution Structure of A Chimeric Oligonucleotide Hairpin R(Ggac)D(Ttcg)2'F-A(Gtcc) within 5.0Å range: probe atom residue distance (Å) B Occ A:F9 b:0.0 occ:1.00 F A:GFL9 0.0 0.0 1.0 C2' A:GFL9 1.4 0.0 1.0 H2' A:GFL9 2.0 0.0 1.0 H71 A:TAF10 2.3 0.0 1.0 C3' A:GFL9 2.4 0.0 1.0 C1' A:GFL9 2.4 0.0 1.0 H3' A:GFL9 2.4 0.0 1.0 N9 A:GFL9 2.7 0.0 1.0 O4' A:GFL9 3.0 0.0 1.0 H73 A:TAF10 3.1 0.0 1.0 C5M A:TAF10 3.1 0.0 1.0 C8 A:GFL9 3.2 0.0 1.0 H6 A:TAF10 3.2 0.0 1.0 C4' A:GFL9 3.2 0.0 1.0 H1' A:GFL9 3.3 0.0 1.0 H8 A:GFL9 3.3 0.0 1.0 O3' A:GFL9 3.5 0.0 1.0 C4 A:GFL9 3.5 0.0 1.0 O2P A:GFL9 3.6 0.0 1.0 OP2 A:TAF10 3.6 0.0 1.0 O5' A:GFL9 3.7 0.0 1.0 H72 A:TAF10 3.9 0.0 1.0 C6 A:TAF10 4.0 0.0 1.0 C5 A:TAF10 4.0 0.0 1.0 N3 A:GFL9 4.1 0.0 1.0 P A:TAF10 4.1 0.0 1.0 C5' A:GFL9 4.1 0.0 1.0 H4' A:GFL9 4.1 0.0 1.0 N7 A:GFL9 4.1 0.0 1.0 O5' A:TAF10 4.2 0.0 1.0 C5 A:GFL9 4.3 0.0 1.0 P A:GFL9 4.4 0.0 1.0 H5'2 A:GFL9 4.6 0.0 1.0 H5'1 A:GFL9 4.9 0.0 1.0

Fluorine binding site 2 out of 4 in the uc(Nmr) Solution Structure of A Chimeric Oligonucleotide Hairpin R(Ggac)D(Ttcg)2'F-A(Gtcc)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of uc(Nmr) Solution Structure of A Chimeric Oligonucleotide Hairpin R(Ggac)D(Ttcg)2'F-A(Gtcc) within 5.0Å range: probe atom residue distance (Å) B Occ A:F10 b:0.0 occ:1.00 F2' A:TAF10 0.0 0.0 1.0 C2' A:TAF10 1.4 0.0 1.0 H2' A:TAF10 2.0 0.0 1.0 C3' A:TAF10 2.4 0.0 1.0 C1' A:TAF10 2.4 0.0 1.0 H3' A:TAF10 2.4 0.0 1.0 N1 A:TAF10 2.7 0.0 1.0 H6 A:TAF10 2.7 0.0 1.0 H5 A:CFL11 2.8 0.0 1.0 C6 A:TAF10 2.8 0.0 1.0 O4' A:TAF10 3.0 0.0 1.0 C4' A:TAF10 3.3 0.0 1.0 H1' A:TAF10 3.3 0.0 1.0 H6 A:CFL11 3.3 0.0 1.0 C5 A:CFL11 3.5 0.0 1.0 O3' A:TAF10 3.5 0.0 1.0 C2 A:TAF10 3.7 0.0 1.0 O2P A:CFL11 3.7 0.0 1.0 C6 A:CFL11 3.7 0.0 1.0 C5 A:TAF10 3.9 0.0 1.0 O5' A:TAF10 4.0 0.0 1.0 C5' A:TAF10 4.1 0.0 1.0 P A:CFL11 4.1 0.0 1.0 H4' A:TAF10 4.1 0.0 1.0 H5'' A:TAF10 4.2 0.0 1.0 O2 A:TAF10 4.2 0.0 1.0 O5' A:CFL11 4.3 0.0 1.0 H73 A:TAF10 4.4 0.0 1.0 N3 A:TAF10 4.5 0.0 1.0 C4 A:CFL11 4.6 0.0 1.0 HN42 A:CFL11 4.6 0.0 1.0 C4 A:TAF10 4.7 0.0 1.0 C5M A:TAF10 4.7 0.0 1.0 H2' A:GFL9 4.7 0.0 1.0 OP2 A:TAF10 4.8 0.0 1.0 N1 A:CFL11 4.9 0.0 1.0

Fluorine binding site 3 out of 4 in the uc(Nmr) Solution Structure of A Chimeric Oligonucleotide Hairpin R(Ggac)D(Ttcg)2'F-A(Gtcc)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of uc(Nmr) Solution Structure of A Chimeric Oligonucleotide Hairpin R(Ggac)D(Ttcg)2'F-A(Gtcc) within 5.0Å range: probe atom residue distance (Å) B Occ A:F11 b:0.0 occ:1.00 F A:CFL11 0.0 0.0 1.0 C2' A:CFL11 1.4 0.0 1.0 H2' A:CFL11 2.0 0.0 1.0 C3' A:CFL11 2.4 0.0 1.0 H3' A:CFL11 2.4 0.0 1.0 C1' A:CFL11 2.4 0.0 1.0 N1 A:CFL11 2.6 0.0 1.0 H5 A:CFL12 2.7 0.0 1.0 H6 A:CFL11 2.8 0.0 1.0 H6 A:CFL12 2.8 0.0 1.0 C6 A:CFL11 2.9 0.0 1.0 O4' A:CFL11 3.2 0.0 1.0 H1' A:CFL11 3.2 0.0 1.0 C5 A:CFL12 3.3 0.0 1.0 C6 A:CFL12 3.3 0.0 1.0 C4' A:CFL11 3.4 0.0 1.0 O3' A:CFL11 3.4 0.0 1.0 O2P A:CFL12 3.4 0.0 1.0 C2 A:CFL11 3.5 0.0 1.0 O5' A:CFL12 3.8 0.0 1.0 P A:CFL12 3.8 0.0 1.0 C5 A:CFL11 3.9 0.0 1.0 O2 A:CFL11 4.0 0.0 1.0 H4' A:CFL11 4.2 0.0 1.0 O5' A:CFL11 4.2 0.0 1.0 C5' A:CFL11 4.2 0.0 1.0 H5'2 A:CFL11 4.3 0.0 1.0 N3 A:CFL11 4.4 0.0 1.0 C4 A:CFL12 4.5 0.0 1.0 N1 A:CFL12 4.5 0.0 1.0 H5 A:CFL11 4.6 0.0 1.0 C4 A:CFL11 4.6 0.0 1.0 O4' A:CFL12 4.6 0.0 1.0 HN42 A:CFL12 4.7 0.0 1.0 H21 A:G2 5.0 0.0 1.0

Fluorine binding site 4 out of 4 in the uc(Nmr) Solution Structure of A Chimeric Oligonucleotide Hairpin R(Ggac)D(Ttcg)2'F-A(Gtcc)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of uc(Nmr) Solution Structure of A Chimeric Oligonucleotide Hairpin R(Ggac)D(Ttcg)2'F-A(Gtcc) within 5.0Å range: probe atom residue distance (Å) B Occ A:F12 b:0.0 occ:1.00 F A:CFL12 0.0 0.0 1.0 C2' A:CFL12 1.4 0.0 1.0 H2' A:CFL12 2.0 0.0 1.0 H3' A:CFL12 2.3 0.0 1.0 C3' A:CFL12 2.4 0.0 1.0 C1' A:CFL12 2.4 0.0 1.0 N1 A:CFL12 2.6 0.0 1.0 H6 A:CFL12 2.7 0.0 1.0 C6 A:CFL12 2.8 0.0 1.0 O4' A:CFL12 3.2 0.0 1.0 H1' A:CFL12 3.2 0.0 1.0 C4' A:CFL12 3.3 0.0 1.0 O3' A:CFL12 3.4 0.0 1.0 C2 A:CFL12 3.6 0.0 1.0 C5 A:CFL12 3.8 0.0 1.0 HO3' A:CFL12 3.9 0.0 1.0 O5' A:CFL12 4.0 0.0 1.0 O2 A:CFL12 4.1 0.0 1.0 H4' A:CFL12 4.2 0.0 1.0 C5' A:CFL12 4.2 0.0 1.0 N3 A:CFL12 4.4 0.0 1.0 H5 A:CFL12 4.4 0.0 1.0 C4 A:CFL12 4.5 0.0 1.0 H5'2 A:CFL12 4.5 0.0 1.0 H2' A:CFL11 4.9 0.0 1.0

J.F.Trempe, C.J.Wilds, A.Y.Denisov, R.T.Pon, M.J.Damha, K.Gehring. uc(Nmr) Solution Structure of An Oligonucleotide Hairpin with A 2'F-Ana/Rna Stem: Implications For Rnase H Specificity Toward Dna/Rna Hybrid Duplexes. J.Am.Chem.Soc. V. 123 4896 2001.
ISSN: ISSN 0002-7863
PubMed: 11457316
DOI: 10.1021/JA003859P