Fluorine in PDB 7nbl: Solution Structure of Dna:Rna Hybrid Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification

The binding sites of Fluorine atom in the Solution Structure of Dna:Rna Hybrid Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification (pdb code 7nbl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Solution Structure of Dna:Rna Hybrid Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification, PDB code: 7nbl:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Solution Structure of Dna:Rna Hybrid Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Solution Structure of Dna:Rna Hybrid Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification within 5.0Å range: probe atom residue distance (Å) B Occ A:F4 b:0.0 occ:1.00 F1 A:U7B4 0.0 0.0 1.0 C2' A:U7B4 1.4 0.0 1.0 F2 A:U7B4 2.2 0.0 1.0 H8 A:DA5 2.3 0.0 1.0 C1' A:U7B4 2.4 0.0 1.0 C3' A:U7B4 2.5 0.0 1.0 H1' A:U7B4 2.5 0.0 1.0 O5' A:DA5 2.8 0.0 1.0 O3' A:U7B4 2.8 0.0 1.0 H3' A:U7B4 3.0 0.0 1.0 OP2 A:DA5 3.0 0.0 1.0 C8 A:DA5 3.1 0.0 1.0 P A:DA5 3.1 0.0 1.0 N1 A:U7B4 3.2 0.0 1.0 H2' A:DA5 3.4 0.0 1.0 O4' A:DA5 3.5 0.0 1.0 O4' A:U7B4 3.5 0.0 1.0 C4' A:U7B4 3.6 0.0 1.0 H5' A:DA5 3.6 0.0 1.0 C5' A:DA5 3.7 0.0 1.0 C2 A:U7B4 3.8 0.0 1.0 N9 A:DA5 3.8 0.0 1.0 O2 A:U7B4 3.8 0.0 1.0 N7 A:DA5 3.9 0.0 1.0 C6 A:U7B4 3.9 0.0 1.0 C1' A:DA5 4.0 0.0 1.0 H6 A:U7B4 4.1 0.0 1.0 C4' A:DA5 4.1 0.0 1.0 C2' A:DA5 4.2 0.0 1.0 H4' A:U7B4 4.2 0.0 1.0 H3' A:DA5 4.6 0.0 1.0 OP1 A:DA5 4.6 0.0 1.0 C3' A:DA5 4.6 0.0 1.0 H5'' A:DA5 4.6 0.0 1.0 O5' A:U7B4 4.8 0.0 1.0 C5' A:U7B4 4.8 0.0 1.0 N3 A:U7B4 4.9 0.0 1.0 C4 A:DA5 4.9 0.0 1.0 C5 A:DA5 5.0 0.0 1.0 C5 A:U7B4 5.0 0.0 1.0

Fluorine binding site 2 out of 2 in the Solution Structure of Dna:Rna Hybrid Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Solution Structure of Dna:Rna Hybrid Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification within 5.0Å range: probe atom residue distance (Å) B Occ A:F4 b:0.0 occ:1.00 F2 A:U7B4 0.0 0.0 1.0 C2' A:U7B4 1.4 0.0 1.0 F1 A:U7B4 2.2 0.0 1.0 C3' A:U7B4 2.4 0.0 1.0 H6 A:U7B4 2.4 0.0 1.0 C1' A:U7B4 2.4 0.0 1.0 H3' A:U7B4 2.5 0.0 1.0 C6 A:U7B4 2.9 0.0 1.0 N1 A:U7B4 2.9 0.0 1.0 O4' A:U7B4 3.0 0.0 1.0 O5' A:U7B4 3.0 0.0 1.0 C4' A:U7B4 3.1 0.0 1.0 H1' A:U7B4 3.3 0.0 1.0 C5' A:U7B4 3.6 0.0 1.0 O3' A:U7B4 3.6 0.0 1.0 H2'' A:DA3 3.7 0.0 1.0 H8 A:DA5 3.8 0.0 1.0 OP2 A:DA5 3.9 0.0 1.0 C5 A:U7B4 4.0 0.0 1.0 H4' A:U7B4 4.1 0.0 1.0 C2 A:U7B4 4.1 0.0 1.0 OP2 A:U7B4 4.3 0.0 1.0 H5' A:U7B4 4.3 0.0 1.0 P A:U7B4 4.3 0.0 1.0 H5'' A:U7B4 4.4 0.0 1.0 P A:DA5 4.4 0.0 1.0 H5 A:U7B4 4.5 0.0 1.0 C8 A:DA5 4.5 0.0 1.0 O5' A:DA5 4.7 0.0 1.0 O2 A:U7B4 4.7 0.0 1.0 N7 A:DA5 4.8 0.0 1.0 C2' A:DA3 4.8 0.0 1.0 C4 A:U7B4 4.9 0.0 1.0

C.Cabrero, N.Martin-Pintado, S.Mazzini, R.Gargallo, R.Eritja, A.Avino, C.Gonzalez. Structural Effects of Incorporation of 2 -Deoxy-2 2 -Difluorodeoxycytidine (Gemcitabine) in A- and B-Form Duplexes. Chemistry 2021.
ISSN: ISSN 0947-6539
PubMed: 33772916
DOI: 10.1002/CHEM.202100503