Fluorine in PDB 2kp4: Structure of 2'F-Ana/Rna Hybrid Duplex

The binding sites of Fluorine atom in the Structure of 2'F-Ana/Rna Hybrid Duplex (pdb code 2kp4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the Structure of 2'F-Ana/Rna Hybrid Duplex, PDB code: 2kp4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in the Structure of 2'F-Ana/Rna Hybrid Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of 2'F-Ana/Rna Hybrid Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:0.0 occ:1.00 F A:GFL1 0.0 0.0 1.0 C2' A:GFL1 1.4 0.0 1.0 H2' A:GFL1 2.0 0.0 1.0 H8 A:GFL1 2.3 0.0 1.0 C1' A:GFL1 2.4 0.0 1.0 C3' A:GFL1 2.4 0.0 1.0 H3' A:GFL1 2.4 0.0 1.0 HO5' A:GFL1 2.6 0.0 1.0 C8 A:GFL1 2.8 0.0 1.0 N9 A:GFL1 2.8 0.0 1.0 O4' A:GFL1 2.9 0.0 1.0 C4' A:GFL1 3.0 0.0 1.0 O5' A:GFL1 3.0 0.0 1.0 H1' A:GFL1 3.3 0.0 1.0 C5' A:GFL1 3.6 0.0 1.0 O3' A:GFL1 3.7 0.0 1.0 H5 A:CFL2 3.7 0.0 1.0 H6 A:CFL2 3.8 0.0 1.0 O2P A:CFL2 4.0 0.0 1.0 H4' A:GFL1 4.0 0.0 1.0 N7 A:GFL1 4.1 0.0 1.0 C4 A:GFL1 4.2 0.0 1.0 H5'1 A:GFL1 4.2 0.0 1.0 C5 A:CFL2 4.4 0.0 1.0 H5'2 A:GFL1 4.4 0.0 1.0 C6 A:CFL2 4.4 0.0 1.0 P A:CFL2 4.4 0.0 1.0 C5 A:GFL1 4.7 0.0 1.0 O5' A:CFL2 4.8 0.0 1.0

Fluorine binding site 2 out of 10 in the Structure of 2'F-Ana/Rna Hybrid Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of 2'F-Ana/Rna Hybrid Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:F2 b:0.0 occ:1.00 F A:CFL2 0.0 0.0 1.0 C2' A:CFL2 1.4 0.0 1.0 H2' A:CFL2 2.0 0.0 1.0 H6 A:CFL2 2.4 0.0 1.0 C3' A:CFL2 2.4 0.0 1.0 C1' A:CFL2 2.4 0.0 1.0 H3' A:CFL2 2.4 0.0 1.0 H73 A:TAF3 2.6 0.0 1.0 C6 A:CFL2 2.8 0.0 1.0 N1 A:CFL2 2.8 0.0 1.0 O4' A:CFL2 3.0 0.0 1.0 H71 A:TAF3 3.0 0.0 1.0 C4' A:CFL2 3.1 0.0 1.0 O5' A:CFL2 3.3 0.0 1.0 C5M A:TAF3 3.3 0.0 1.0 H1' A:CFL2 3.3 0.0 1.0 H6 A:TAF3 3.6 0.0 1.0 O3' A:CFL2 3.6 0.0 1.0 C5' A:CFL2 3.7 0.0 1.0 OP2 A:TAF3 3.8 0.0 1.0 H2' A:GFL1 3.9 0.0 1.0 C5 A:CFL2 3.9 0.0 1.0 C5 A:TAF3 4.0 0.0 1.0 C6 A:TAF3 4.0 0.0 1.0 C2 A:CFL2 4.1 0.0 1.0 H4' A:CFL2 4.1 0.0 1.0 H72 A:TAF3 4.2 0.0 1.0 P A:TAF3 4.3 0.0 1.0 H5'1 A:CFL2 4.4 0.0 1.0 H5 A:CFL2 4.4 0.0 1.0 O5' A:TAF3 4.4 0.0 1.0 H5'2 A:CFL2 4.5 0.0 1.0 P A:CFL2 4.6 0.0 1.0 O2 A:CFL2 4.7 0.0 1.0 O2P A:CFL2 4.7 0.0 1.0 C4 A:CFL2 4.9 0.0 1.0 N3 A:CFL2 4.9 0.0 1.0 C2' A:GFL1 4.9 0.0 1.0

Fluorine binding site 3 out of 10 in the Structure of 2'F-Ana/Rna Hybrid Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of 2'F-Ana/Rna Hybrid Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:F3 b:0.0 occ:1.00 F2' A:TAF3 0.0 0.0 1.0 C2' A:TAF3 1.4 0.0 1.0 H2' A:TAF3 2.0 0.0 1.0 C1' A:TAF3 2.4 0.0 1.0 C3' A:TAF3 2.4 0.0 1.0 H3' A:TAF3 2.4 0.0 1.0 H6 A:TAF3 2.5 0.0 1.0 H8 A:A5L4 2.5 0.0 1.0 N1 A:TAF3 2.8 0.0 1.0 C6 A:TAF3 2.9 0.0 1.0 O4' A:TAF3 3.0 0.0 1.0 C4' A:TAF3 3.2 0.0 1.0 H1' A:TAF3 3.3 0.0 1.0 C8 A:A5L4 3.3 0.0 1.0 O5' A:TAF3 3.5 0.0 1.0 O3' A:TAF3 3.6 0.0 1.0 N7 A:A5L4 3.8 0.0 1.0 C5' A:TAF3 3.9 0.0 1.0 C2 A:TAF3 3.9 0.0 1.0 F A:A5L4 4.0 0.0 1.0 C5 A:TAF3 4.1 0.0 1.0 H2' A:CFL2 4.1 0.0 1.0 O5' A:A5L4 4.1 0.0 1.0 OP2 A:A5L4 4.1 0.0 1.0 H4' A:TAF3 4.1 0.0 1.0 P A:A5L4 4.3 0.0 1.0 N9 A:A5L4 4.4 0.0 1.0 H73 A:TAF3 4.4 0.0 1.0 H5' A:TAF3 4.4 0.0 1.0 O2 A:TAF3 4.5 0.0 1.0 H71 A:TAF5 4.5 0.0 1.0 H5'' A:TAF3 4.7 0.0 1.0 C5M A:TAF3 4.8 0.0 1.0 O4' A:A5L4 4.9 0.0 1.0 P A:TAF3 4.9 0.0 1.0 N3 A:TAF3 4.9 0.0 1.0 H5'A A:A5L4 4.9 0.0 1.0 OP2 A:TAF3 4.9 0.0 1.0

Fluorine binding site 4 out of 10 in the Structure of 2'F-Ana/Rna Hybrid Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of 2'F-Ana/Rna Hybrid Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:F4 b:0.0 occ:1.00 F A:A5L4 0.0 0.0 1.0 C2' A:A5L4 1.4 0.0 1.0 H2' A:A5L4 2.0 0.0 1.0 H8 A:A5L4 2.3 0.0 1.0 C3' A:A5L4 2.4 0.0 1.0 C1' A:A5L4 2.4 0.0 1.0 H3' A:A5L4 2.4 0.0 1.0 C8 A:A5L4 2.8 0.0 1.0 N9 A:A5L4 2.9 0.0 1.0 O4' A:A5L4 3.0 0.0 1.0 C4' A:A5L4 3.1 0.0 1.0 O5' A:A5L4 3.1 0.0 1.0 H2' A:TAF3 3.1 0.0 1.0 H1' A:A5L4 3.3 0.0 1.0 H71 A:TAF5 3.4 0.0 1.0 C5' A:A5L4 3.6 0.0 1.0 O3' A:A5L4 3.6 0.0 1.0 H73 A:TAF5 3.7 0.0 1.0 H6 A:TAF5 3.7 0.0 1.0 OP2 A:TAF5 3.8 0.0 1.0 C5M A:TAF5 4.0 0.0 1.0 F2' A:TAF3 4.0 0.0 1.0 C2' A:TAF3 4.0 0.0 1.0 N7 A:A5L4 4.1 0.0 1.0 H4' A:A5L4 4.1 0.0 1.0 C4 A:A5L4 4.2 0.0 1.0 H5'A A:A5L4 4.3 0.0 1.0 P A:TAF5 4.3 0.0 1.0 C6 A:TAF5 4.3 0.0 1.0 P A:A5L4 4.4 0.0 1.0 H5' A:A5L4 4.4 0.0 1.0 OP2 A:A5L4 4.5 0.0 1.0 O5' A:TAF5 4.5 0.0 1.0 C5 A:TAF5 4.5 0.0 1.0 C5 A:A5L4 4.7 0.0 1.0 O4' A:TAF5 4.9 0.0 1.0 C3' A:TAF3 4.9 0.0 1.0 H72 A:TAF5 4.9 0.0 1.0 O3' A:TAF3 5.0 0.0 1.0 H3' A:TAF3 5.0 0.0 1.0

Fluorine binding site 5 out of 10 in the Structure of 2'F-Ana/Rna Hybrid Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of 2'F-Ana/Rna Hybrid Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:F5 b:0.0 occ:1.00 F2' A:TAF5 0.0 0.0 1.0 C2' A:TAF5 1.4 0.0 1.0 H2' A:TAF5 2.0 0.0 1.0 H3' A:TAF5 2.3 0.0 1.0 C3' A:TAF5 2.4 0.0 1.0 H8 A:A5L6 2.4 0.0 1.0 C1' A:TAF5 2.4 0.0 1.0 N1 A:TAF5 2.7 0.0 1.0 H6 A:TAF5 2.8 0.0 1.0 C6 A:TAF5 3.0 0.0 1.0 O4' A:TAF5 3.1 0.0 1.0 H1' A:TAF5 3.3 0.0 1.0 C4' A:TAF5 3.3 0.0 1.0 C8 A:A5L6 3.4 0.0 1.0 O3' A:TAF5 3.4 0.0 1.0 C2 A:TAF5 3.7 0.0 1.0 OP2 A:A5L6 3.7 0.0 1.0 O5' A:A5L6 3.8 0.0 1.0 P A:A5L6 3.9 0.0 1.0 N7 A:A5L6 4.0 0.0 1.0 C5 A:TAF5 4.0 0.0 1.0 O5' A:TAF5 4.1 0.0 1.0 H4' A:TAF5 4.1 0.0 1.0 O2 A:TAF5 4.2 0.0 1.0 O4' A:A5L6 4.2 0.0 1.0 C5' A:TAF5 4.3 0.0 1.0 N9 A:A5L6 4.5 0.0 1.0 H73 A:TAF5 4.5 0.0 1.0 H2' A:A5L4 4.5 0.0 1.0 H5'A A:A5L6 4.6 0.0 1.0 N3 A:TAF5 4.6 0.0 1.0 C5' A:A5L6 4.6 0.0 1.0 F A:A5L6 4.7 0.0 1.0 H5' A:TAF5 4.8 0.0 1.0 C4 A:TAF5 4.8 0.0 1.0 C5M A:TAF5 4.9 0.0 1.0 C1' A:A5L6 4.9 0.0 1.0

Fluorine binding site 6 out of 10 in the Structure of 2'F-Ana/Rna Hybrid Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of 2'F-Ana/Rna Hybrid Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:F6 b:0.0 occ:1.00 F A:A5L6 0.0 0.0 1.0 C2' A:A5L6 1.4 0.0 1.0 H2' A:A5L6 2.1 0.0 1.0 C1' A:A5L6 2.4 0.0 1.0 H3' A:A5L6 2.4 0.0 1.0 C3' A:A5L6 2.4 0.0 1.0 N9 A:A5L6 2.7 0.0 1.0 H8 A:A5L7 2.8 0.0 1.0 H8 A:A5L6 3.0 0.0 1.0 O4' A:A5L6 3.0 0.0 1.0 C8 A:A5L6 3.1 0.0 1.0 H1' A:A5L6 3.2 0.0 1.0 C4' A:A5L6 3.2 0.0 1.0 C8 A:A5L7 3.5 0.0 1.0 O3' A:A5L6 3.6 0.0 1.0 C4 A:A5L6 3.7 0.0 1.0 O5' A:A5L6 3.7 0.0 1.0 OP2 A:A5L7 3.9 0.0 1.0 N7 A:A5L7 4.0 0.0 1.0 O5' A:A5L7 4.0 0.0 1.0 C5' A:A5L6 4.1 0.0 1.0 H4' A:A5L6 4.1 0.0 1.0 N7 A:A5L6 4.1 0.0 1.0 P A:A5L7 4.1 0.0 1.0 H2' A:TAF5 4.3 0.0 1.0 N3 A:A5L6 4.4 0.0 1.0 C5 A:A5L6 4.4 0.0 1.0 N9 A:A5L7 4.6 0.0 1.0 F A:A5L7 4.6 0.0 1.0 O4' A:A5L7 4.6 0.0 1.0 H5' A:A5L6 4.7 0.0 1.0 F2' A:TAF5 4.7 0.0 1.0 H5'A A:A5L6 4.9 0.0 1.0 H5'A A:A5L7 4.9 0.0 1.0 C5' A:A5L7 5.0 0.0 1.0

Fluorine binding site 7 out of 10 in the Structure of 2'F-Ana/Rna Hybrid Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of 2'F-Ana/Rna Hybrid Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:F7 b:0.0 occ:1.00 F A:A5L7 0.0 0.0 1.0 C2' A:A5L7 1.4 0.0 1.0 H2' A:A5L7 2.0 0.0 1.0 H8 A:A5L7 2.3 0.0 1.0 C1' A:A5L7 2.4 0.0 1.0 C3' A:A5L7 2.4 0.0 1.0 H3' A:A5L7 2.4 0.0 1.0 H72 A:TAF8 2.7 0.0 1.0 N9 A:A5L7 2.8 0.0 1.0 C8 A:A5L7 2.8 0.0 1.0 O4' A:A5L7 3.0 0.0 1.0 C4' A:A5L7 3.1 0.0 1.0 H1' A:A5L7 3.3 0.0 1.0 O5' A:A5L7 3.3 0.0 1.0 H6 A:TAF8 3.6 0.0 1.0 O3' A:A5L7 3.6 0.0 1.0 H2' A:A5L6 3.8 0.0 1.0 C5' A:A5L7 3.8 0.0 1.0 C5M A:TAF8 3.8 0.0 1.0 OP2 A:TAF8 3.8 0.0 1.0 N7 A:A5L7 4.0 0.0 1.0 C4 A:A5L7 4.1 0.0 1.0 H4' A:A5L7 4.1 0.0 1.0 C6 A:TAF8 4.2 0.0 1.0 P A:TAF8 4.3 0.0 1.0 H71 A:TAF8 4.3 0.0 1.0 H73 A:TAF8 4.4 0.0 1.0 C5 A:TAF8 4.4 0.0 1.0 H5' A:A5L7 4.4 0.0 1.0 O5' A:TAF8 4.4 0.0 1.0 F A:A5L6 4.6 0.0 1.0 H5'A A:A5L7 4.6 0.0 1.0 C2' A:A5L6 4.6 0.0 1.0 C5 A:A5L7 4.6 0.0 1.0 P A:A5L7 4.7 0.0 1.0 OP2 A:A5L7 4.7 0.0 1.0 O4' A:TAF8 4.8 0.0 1.0 N3 A:A5L7 5.0 0.0 1.0

Fluorine binding site 8 out of 10 in the Structure of 2'F-Ana/Rna Hybrid Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of 2'F-Ana/Rna Hybrid Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:F8 b:0.0 occ:1.00 F2' A:TAF8 0.0 0.0 1.0 C2' A:TAF8 1.4 0.0 1.0 H2' A:TAF8 2.0 0.0 1.0 H3' A:TAF8 2.3 0.0 1.0 C3' A:TAF8 2.4 0.0 1.0 C1' A:TAF8 2.4 0.0 1.0 H8 A:GFL9 2.4 0.0 1.0 H6 A:TAF8 2.6 0.0 1.0 N1 A:TAF8 2.7 0.0 1.0 C6 A:TAF8 2.9 0.0 1.0 O4' A:TAF8 3.0 0.0 1.0 H1' A:TAF8 3.3 0.0 1.0 C4' A:TAF8 3.3 0.0 1.0 C8 A:GFL9 3.3 0.0 1.0 O3' A:TAF8 3.5 0.0 1.0 C2 A:TAF8 3.8 0.0 1.0 O5' A:GFL9 3.8 0.0 1.0 F A:GFL9 3.9 0.0 1.0 O2P A:GFL9 3.9 0.0 1.0 O5' A:TAF8 3.9 0.0 1.0 N7 A:GFL9 4.0 0.0 1.0 C5 A:TAF8 4.0 0.0 1.0 P A:GFL9 4.0 0.0 1.0 H4' A:TAF8 4.1 0.0 1.0 C5' A:TAF8 4.2 0.0 1.0 O2 A:TAF8 4.3 0.0 1.0 N9 A:GFL9 4.3 0.0 1.0 H2' A:A5L7 4.3 0.0 1.0 O4' A:GFL9 4.5 0.0 1.0 H71 A:TAF8 4.5 0.0 1.0 H5'2 A:GFL9 4.6 0.0 1.0 N3 A:TAF8 4.6 0.0 1.0 C5' A:GFL9 4.7 0.0 1.0 C1' A:GFL9 4.7 0.0 1.0 H5' A:TAF8 4.7 0.0 1.0 C5M A:TAF8 4.8 0.0 1.0 C4 A:TAF8 4.8 0.0 1.0 C2' A:GFL9 4.9 0.0 1.0 H72 A:TAF8 5.0 0.0 1.0

Fluorine binding site 9 out of 10 in the Structure of 2'F-Ana/Rna Hybrid Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of 2'F-Ana/Rna Hybrid Duplex 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 C1' A:GFL9 2.4 0.0 1.0 H8 A:GFL9 2.4 0.0 1.0 C3' A:GFL9 2.4 0.0 1.0 H3' A:GFL9 2.6 0.0 1.0 N9 A:GFL9 2.9 0.0 1.0 C8 A:GFL9 2.9 0.0 1.0 O4' A:GFL9 3.0 0.0 1.0 O5' A:GFL9 3.0 0.0 1.0 C4' A:GFL9 3.1 0.0 1.0 H1' A:GFL9 3.2 0.0 1.0 H2' A:TAF8 3.5 0.0 1.0 C5' A:GFL9 3.5 0.0 1.0 O3' A:GFL9 3.7 0.0 1.0 F2' A:TAF8 3.9 0.0 1.0 O2P A:GFL10 4.0 0.0 1.0 H4' A:GFL9 4.1 0.0 1.0 N7 A:GFL9 4.1 0.0 1.0 C4 A:GFL9 4.1 0.0 1.0 H8 A:GFL10 4.1 0.0 1.0 C2' A:TAF8 4.2 0.0 1.0 H5'2 A:GFL9 4.3 0.0 1.0 H5'1 A:GFL9 4.3 0.0 1.0 P A:GFL9 4.3 0.0 1.0 O2P A:GFL9 4.4 0.0 1.0 P A:GFL10 4.4 0.0 1.0 C5 A:GFL9 4.7 0.0 1.0 O5' A:GFL10 4.8 0.0 1.0 N3 A:GFL9 5.0 0.0 1.0 C8 A:GFL10 5.0 0.0 1.0

Fluorine binding site 10 out of 10 in the Structure of 2'F-Ana/Rna Hybrid Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Structure of 2'F-Ana/Rna Hybrid Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:F10 b:0.0 occ:1.00 F A:GFL10 0.0 0.0 1.0 C2' A:GFL10 1.4 0.0 1.0 H2' A:GFL10 2.0 0.0 1.0 C1' A:GFL10 2.4 0.0 1.0 C3' A:GFL10 2.4 0.0 1.0 H3' A:GFL10 2.5 0.0 1.0 H8 A:GFL10 2.6 0.0 1.0 N9 A:GFL10 2.8 0.0 1.0 O5' A:GFL10 2.9 0.0 1.0 C8 A:GFL10 2.9 0.0 1.0 O4' A:GFL10 3.0 0.0 1.0 C4' A:GFL10 3.0 0.0 1.0 H1' A:GFL10 3.3 0.0 1.0 C5' A:GFL10 3.5 0.0 1.0 O3' A:GFL10 3.6 0.0 1.0 C4 A:GFL10 3.9 0.0 1.0 N7 A:GFL10 4.1 0.0 1.0 HO3' A:GFL10 4.1 0.0 1.0 H4' A:GFL10 4.1 0.0 1.0 H2' A:GFL9 4.1 0.0 1.0 H5'1 A:GFL10 4.2 0.0 1.0 P A:GFL10 4.2 0.0 1.0 H5'2 A:GFL10 4.2 0.0 1.0 O2P A:GFL10 4.3 0.0 1.0 C5 A:GFL10 4.6 0.0 1.0 N3 A:GFL10 4.7 0.0 1.0 H1' A:GFL9 5.0 0.0 1.0

J.K.Watts, N.Martin-Pintado, I.Gomez-Pinto, J.Schwartzentruber, G.Portella, M.Orozco, C.Gonzalez, M.J.Damha. Differential Stability of 2'F-Ana*Rna and Ana*Rna Hybrid Duplexes: Roles of Structure, Pseudohydrogen Bonding, Hydration, Ion Uptake and Flexibility. Nucleic Acids Res. V. 38 2498 2010.
ISSN: ISSN 0305-1048
PubMed: 20071751
DOI: 10.1093/NAR/GKP1225