Fluorine in PDB 2n89: Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH

The binding sites of Fluorine atom in the Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH (pdb code 2n89). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH, PDB code: 2n89:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:F4 b:0.0 occ:1.00 F A:CFL4 0.0 0.0 1.0 C2' A:CFL4 1.1 0.0 1.0 H2' A:CFL4 1.8 0.0 1.0 C3' A:CFL4 2.2 0.0 1.0 C1' A:CFL4 2.2 0.0 1.0 H6 A:CFL4 2.2 0.0 1.0 H3' A:CFL4 2.3 0.0 1.0 N1 A:CFL4 2.6 0.0 1.0 C6 A:CFL4 2.6 0.0 1.0 O4' A:CFL4 2.8 0.0 1.0 C4' A:CFL4 3.0 0.0 1.0 H1' A:CFL4 3.0 0.0 1.0 O3' A:CFL4 3.3 0.0 1.0 O5' A:CFL4 3.4 0.0 1.0 C5' A:CFL4 3.7 0.0 1.0 C2 A:CFL4 3.8 0.0 1.0 C5 A:CFL4 3.8 0.0 1.0 H4' A:CFL4 3.9 0.0 1.0 O2P A:CFL5 4.0 0.0 1.0 H5'2 A:CFL5 4.0 0.0 1.0 H5'2 A:CFL4 4.1 0.0 1.0 O5' A:CFL5 4.1 0.0 1.0 H42 B:DC9 4.1 0.0 1.0 P A:CFL5 4.1 0.0 1.0 H41 B:DC9 4.1 0.0 1.0 H5 A:CFL4 4.3 0.0 1.0 N4 B:DC9 4.4 0.0 1.0 O2 A:CFL4 4.4 0.0 1.0 H1' D:DC21 4.5 0.0 1.0 C5' A:CFL5 4.6 0.0 1.0 H5'1 A:CFL4 4.6 0.0 1.0 O2 D:DC21 4.7 0.0 1.0 N3 A:CFL4 4.7 0.0 1.0 C4 A:CFL4 4.7 0.0 1.0 P A:CFL4 4.8 0.0 1.0 H2'' D:DC21 4.8 0.0 1.0

Fluorine binding site 2 out of 8 in the Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:F5 b:0.0 occ:1.00 F A:CFL5 0.0 0.0 1.0 C2' A:CFL5 1.1 0.0 1.0 H2' A:CFL5 1.8 0.0 1.0 C3' A:CFL5 2.1 0.0 1.0 C1' A:CFL5 2.2 0.0 1.0 H3' A:CFL5 2.2 0.0 1.0 H6 A:CFL5 2.2 0.0 1.0 N1 A:CFL5 2.6 0.0 1.0 C6 A:CFL5 2.6 0.0 1.0 O4' A:CFL5 2.9 0.0 1.0 H1' A:CFL5 3.0 0.0 1.0 C4' A:CFL5 3.1 0.0 1.0 O3' A:CFL5 3.2 0.0 1.0 H5'' A:DC6 3.7 0.0 1.0 H5'2 A:CFL5 3.8 0.0 1.0 C5 A:CFL5 3.8 0.0 1.0 C2 A:CFL5 3.8 0.0 1.0 H4' A:CFL5 3.9 0.0 1.0 H41 B:DC8 3.9 0.0 1.0 C5' A:CFL5 4.0 0.0 1.0 H42 B:DC8 4.0 0.0 1.0 H1' D:DC20 4.0 0.0 1.0 O5' A:DC6 4.1 0.0 1.0 O2 D:DC20 4.2 0.0 1.0 P A:DC6 4.3 0.0 1.0 H5 A:CFL5 4.3 0.0 1.0 N4 B:DC8 4.3 0.0 1.0 O4' A:DC6 4.3 0.0 1.0 C5' A:DC6 4.4 0.0 1.0 H5'1 A:CFL5 4.4 0.0 1.0 O2 A:CFL5 4.5 0.0 1.0 H2'' D:DC20 4.6 0.0 1.0 N3 A:CFL5 4.7 0.0 1.0 C4 A:CFL5 4.7 0.0 1.0 OP1 A:DC6 4.7 0.0 1.0 H6 A:DC6 5.0 0.0 1.0 C4' A:DC6 5.0 0.0 1.0

Fluorine binding site 3 out of 8 in the Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ B:F10 b:0.0 occ:1.00 F B:CFL10 0.0 0.0 1.0 C2' B:CFL10 1.1 0.0 1.0 H2' B:CFL10 1.8 0.0 1.0 C3' B:CFL10 2.2 0.0 1.0 C1' B:CFL10 2.2 0.0 1.0 H6 B:CFL10 2.2 0.0 1.0 H5'2 B:CFL10 2.3 0.0 1.0 H3' B:CFL10 2.4 0.0 1.0 N1 B:CFL10 2.6 0.0 1.0 C6 B:CFL10 2.7 0.0 1.0 C4' B:CFL10 2.7 0.0 1.0 O4' B:CFL10 2.8 0.0 1.0 C5' B:CFL10 3.0 0.0 1.0 H1' B:CFL10 3.0 0.0 1.0 O3' B:CFL10 3.4 0.0 1.0 H5'1 B:CFL10 3.5 0.0 1.0 H4' B:CFL10 3.8 0.0 1.0 C5 B:CFL10 3.9 0.0 1.0 C2 B:CFL10 3.9 0.0 1.0 H5'2 B:CFL11 4.0 0.0 1.0 O5' B:CFL11 4.1 0.0 1.0 H42 A:DC3 4.1 0.0 1.0 O5' B:CFL10 4.1 0.0 1.0 H41 A:DC3 4.2 0.0 1.0 P B:CFL11 4.3 0.0 1.0 H1' C:DC15 4.4 0.0 1.0 H5 B:CFL10 4.4 0.0 1.0 O2P B:CFL11 4.4 0.0 1.0 N4 A:DC3 4.4 0.0 1.0 O2 B:CFL10 4.5 0.0 1.0 C5' B:CFL11 4.6 0.0 1.0 O2 C:DC15 4.7 0.0 1.0 N3 B:CFL10 4.8 0.0 1.0 C4 B:CFL10 4.8 0.0 1.0 H2'' C:DC15 4.9 0.0 1.0 O4' B:CFL11 4.9 0.0 1.0

Fluorine binding site 4 out of 8 in the Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ B:F11 b:0.0 occ:1.00 F B:CFL11 0.0 0.0 1.0 C2' B:CFL11 1.1 0.0 1.0 H2' B:CFL11 1.8 0.0 1.0 H6 B:CFL11 2.1 0.0 1.0 C3' B:CFL11 2.1 0.0 1.0 C1' B:CFL11 2.2 0.0 1.0 H3' B:CFL11 2.3 0.0 1.0 C6 B:CFL11 2.6 0.0 1.0 N1 B:CFL11 2.7 0.0 1.0 O4' B:CFL11 2.7 0.0 1.0 C4' B:CFL11 2.9 0.0 1.0 H1' B:CFL11 3.0 0.0 1.0 O3' B:CFL11 3.3 0.0 1.0 H5'2 B:CFL11 3.6 0.0 1.0 C5' B:CFL11 3.8 0.0 1.0 H4' B:CFL11 3.8 0.0 1.0 OP2 B:DC12 3.8 0.0 1.0 C5 B:CFL11 3.9 0.0 1.0 C2 B:CFL11 4.0 0.0 1.0 O5' B:DC12 4.0 0.0 1.0 P B:DC12 4.0 0.0 1.0 H5'1 B:CFL11 4.2 0.0 1.0 H42 A:DC2 4.2 0.0 1.0 H1' C:DC14 4.3 0.0 1.0 H5 B:CFL11 4.3 0.0 1.0 H41 A:DC2 4.3 0.0 1.0 O2 C:DC14 4.5 0.0 1.0 N4 A:DC2 4.6 0.0 1.0 O2 B:CFL11 4.6 0.0 1.0 H5'' B:DC12 4.6 0.0 1.0 C4 B:CFL11 4.8 0.0 1.0 N3 B:CFL11 4.8 0.0 1.0 C5' B:DC12 4.9 0.0 1.0 H2'' C:DC14 5.0 0.0 1.0

Fluorine binding site 5 out of 8 in the Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ C:F16 b:0.0 occ:1.00 F C:CFL16 0.0 0.0 1.0 C2' C:CFL16 1.4 0.0 1.0 H2' C:CFL16 2.0 0.0 1.0 H3' C:CFL16 2.3 0.0 1.0 C3' C:CFL16 2.4 0.0 1.0 C1' C:CFL16 2.4 0.0 1.0 H6 C:CFL16 2.5 0.0 1.0 N1 C:CFL16 2.7 0.0 1.0 C6 C:CFL16 2.7 0.0 1.0 H42 D:DC21 3.0 0.0 1.0 H5'2 C:CFL16 3.2 0.0 1.0 O4' C:CFL16 3.2 0.0 1.0 C4' C:CFL16 3.2 0.0 1.0 H1' C:CFL16 3.3 0.0 1.0 H41 D:DC21 3.3 0.0 1.0 O3' C:CFL16 3.5 0.0 1.0 N4 D:DC21 3.5 0.0 1.0 C5 C:CFL16 3.7 0.0 1.0 C5' C:CFL16 3.7 0.0 1.0 C2 C:CFL16 3.8 0.0 1.0 O2 B:DC9 4.1 0.0 1.0 H6 C:CFL17 4.1 0.0 1.0 H1' B:DC9 4.1 0.0 1.0 H5'2 C:CFL17 4.2 0.0 1.0 H4' C:CFL16 4.2 0.0 1.0 H5 C:CFL16 4.2 0.0 1.0 H5'1 C:CFL16 4.2 0.0 1.0 O4' C:CFL17 4.3 0.0 1.0 O5' C:CFL17 4.4 0.0 1.0 C6 C:CFL17 4.4 0.0 1.0 O2 C:CFL16 4.5 0.0 1.0 C4 C:CFL16 4.5 0.0 1.0 N3 C:CFL16 4.5 0.0 1.0 P C:CFL17 4.5 0.0 1.0 O1P C:CFL17 4.7 0.0 1.0 C4 D:DC21 4.7 0.0 1.0 C5' C:CFL17 4.7 0.0 1.0 H5 C:CFL17 4.8 0.0 1.0 C5 C:CFL17 4.8 0.0 1.0 H2'' B:DC9 4.9 0.0 1.0 O5' C:CFL16 4.9 0.0 1.0

Fluorine binding site 6 out of 8 in the Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ C:F17 b:0.0 occ:1.00 F C:CFL17 0.0 0.0 1.0 C2' C:CFL17 1.4 0.0 1.0 H2' C:CFL17 2.0 0.0 1.0 H3' C:CFL17 2.4 0.0 1.0 C3' C:CFL17 2.4 0.0 1.0 C1' C:CFL17 2.4 0.0 1.0 H6 C:CFL17 2.4 0.0 1.0 N1 C:CFL17 2.8 0.0 1.0 C6 C:CFL17 2.8 0.0 1.0 O4' C:CFL17 3.1 0.0 1.0 H1' C:CFL17 3.3 0.0 1.0 C4' C:CFL17 3.4 0.0 1.0 O3' C:CFL17 3.5 0.0 1.0 H5'' C:DC18 3.6 0.0 1.0 O5' C:DC18 3.7 0.0 1.0 H1' B:DC8 3.8 0.0 1.0 OP2 C:DC18 3.8 0.0 1.0 C5 C:CFL17 3.9 0.0 1.0 C2 C:CFL17 4.0 0.0 1.0 P C:DC18 4.0 0.0 1.0 H5'2 C:CFL17 4.1 0.0 1.0 H4' C:CFL17 4.1 0.0 1.0 H41 D:DC20 4.1 0.0 1.0 C5' C:DC18 4.2 0.0 1.0 H42 D:DC20 4.2 0.0 1.0 O4' C:DC18 4.3 0.0 1.0 C5' C:CFL17 4.3 0.0 1.0 O2 B:DC8 4.3 0.0 1.0 H2'' B:DC8 4.4 0.0 1.0 H5 C:CFL17 4.4 0.0 1.0 N4 D:DC20 4.6 0.0 1.0 O2 C:CFL17 4.6 0.0 1.0 C4 C:CFL17 4.8 0.0 1.0 C1' B:DC8 4.8 0.0 1.0 H5'1 C:CFL17 4.8 0.0 1.0 N3 C:CFL17 4.8 0.0 1.0 C4' C:DC18 4.9 0.0 1.0

Fluorine binding site 7 out of 8 in the Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ D:F22 b:0.0 occ:1.00 F D:CFL22 0.0 0.0 1.0 C2' D:CFL22 1.4 0.0 1.0 H2' D:CFL22 2.0 0.0 1.0 C3' D:CFL22 2.4 0.0 1.0 H6 D:CFL22 2.4 0.0 1.0 H3' D:CFL22 2.4 0.0 1.0 C1' D:CFL22 2.4 0.0 1.0 C6 D:CFL22 2.8 0.0 1.0 N1 D:CFL22 2.8 0.0 1.0 H5'2 D:CFL22 2.9 0.0 1.0 H42 C:DC15 2.9 0.0 1.0 O4' D:CFL22 3.1 0.0 1.0 C4' D:CFL22 3.1 0.0 1.0 H41 C:DC15 3.2 0.0 1.0 H1' D:CFL22 3.3 0.0 1.0 N4 C:DC15 3.4 0.0 1.0 C5' D:CFL22 3.5 0.0 1.0 O3' D:CFL22 3.6 0.0 1.0 C5 D:CFL22 3.8 0.0 1.0 C2 D:CFL22 4.0 0.0 1.0 H5'1 D:CFL22 4.0 0.0 1.0 O2 A:DC3 4.0 0.0 1.0 H6 D:CFL23 4.1 0.0 1.0 H4' D:CFL22 4.1 0.0 1.0 H1' A:DC3 4.2 0.0 1.0 H5 D:CFL22 4.3 0.0 1.0 O5' D:CFL23 4.3 0.0 1.0 C6 D:CFL23 4.3 0.0 1.0 O4' D:CFL23 4.4 0.0 1.0 H5 D:CFL23 4.4 0.0 1.0 C5 D:CFL23 4.5 0.0 1.0 O2 D:CFL22 4.6 0.0 1.0 C4 C:DC15 4.6 0.0 1.0 O5' D:CFL22 4.6 0.0 1.0 C4 D:CFL22 4.7 0.0 1.0 P D:CFL23 4.7 0.0 1.0 N3 D:CFL22 4.8 0.0 1.0 N1 D:CFL23 5.0 0.0 1.0

Fluorine binding site 8 out of 8 in the Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Tetrameric I-Motif Structure of Dt-Dc-Dc-Cfl-Cfl-Dc at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ D:F23 b:0.0 occ:1.00 F D:CFL23 0.0 0.0 1.0 C2' D:CFL23 1.4 0.0 1.0 H2' D:CFL23 2.0 0.0 1.0 C1' D:CFL23 2.4 0.0 1.0 C3' D:CFL23 2.4 0.0 1.0 H3' D:CFL23 2.5 0.0 1.0 H6 D:CFL23 2.5 0.0 1.0 N1 D:CFL23 2.8 0.0 1.0 H5'2 D:CFL23 2.9 0.0 1.0 C6 D:CFL23 2.9 0.0 1.0 O4' D:CFL23 2.9 0.0 1.0 C4' D:CFL23 3.1 0.0 1.0 H5'' D:DC24 3.3 0.0 1.0 H1' D:CFL23 3.3 0.0 1.0 C5' D:CFL23 3.5 0.0 1.0 O3' D:CFL23 3.6 0.0 1.0 H1' A:DC2 3.9 0.0 1.0 C2 D:CFL23 4.0 0.0 1.0 H42 C:DC14 4.0 0.0 1.0 C5 D:CFL23 4.0 0.0 1.0 H4' D:CFL23 4.1 0.0 1.0 H5'1 D:CFL23 4.1 0.0 1.0 H41 C:DC14 4.1 0.0 1.0 O4' D:DC24 4.1 0.0 1.0 C5' D:DC24 4.2 0.0 1.0 O2 A:DC2 4.3 0.0 1.0 O5' D:DC24 4.4 0.0 1.0 N4 C:DC14 4.4 0.0 1.0 O2 D:CFL23 4.5 0.0 1.0 H5 D:CFL23 4.6 0.0 1.0 P D:DC24 4.6 0.0 1.0 O5' D:CFL23 4.6 0.0 1.0 H2'' A:DC2 4.6 0.0 1.0 H6 D:DC24 4.7 0.0 1.0 OP2 D:DC24 4.7 0.0 1.0 C4' D:DC24 4.8 0.0 1.0 N3 D:CFL23 4.9 0.0 1.0 C4 D:CFL23 4.9 0.0 1.0 C1' A:DC2 5.0 0.0 1.0 C6 D:DC24 5.0 0.0 1.0

H.A.Assi, R.W.Harkness, N.Martin-Pintado, C.J.Wilds, R.Campos-Olivas, A.K.Mittermaier, C.Gonzalez, M.J.Damha. Stabilization of I-Motif Structures By 2'-Beta-Fluorination of Dna. Nucleic Acids Res. V. 44 4998 2016.
ISSN: ISSN 0305-1048
PubMed: 27166371
DOI: 10.1093/NAR/GKW402