Fluorine in PDB 2g92: Crystal Structure Analysis of the Rna Dodecamer Cgc-(NF2)-Aauuagcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2)

The structure of Crystal Structure Analysis of the Rna Dodecamer Cgc-(NF2)-Aauuagcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2), PDB code: 2g92 was solved by M.Egli, F.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.78 / 1.61
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	28.614, 28.614, 63.171, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 23.1

The binding sites of Fluorine atom in the Crystal Structure Analysis of the Rna Dodecamer Cgc-(NF2)-Aauuagcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2) (pdb code 2g92). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure Analysis of the Rna Dodecamer Cgc-(NF2)-Aauuagcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2), PDB code: 2g92:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure Analysis of the Rna Dodecamer Cgc-(NF2)-Aauuagcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure Analysis of the Rna Dodecamer Cgc-(NF2)-Aauuagcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2) within 5.0Å range: probe atom residue distance (Å) B Occ A:F4 b:31.4 occ:1.00 F2 A:NF24 0.0 31.4 1.0 C2 A:NF24 1.3 29.3 1.0 C3 A:NF24 2.2 25.7 1.0 C1 A:NF24 2.3 27.0 1.0 C1' A:NF24 2.7 25.2 1.0 C2' A:NF24 3.3 27.2 1.0 N2 B:G22 3.3 28.9 1.0 C4 A:NF24 3.4 29.7 1.0 C2 B:G22 3.4 30.0 1.0 C6 A:NF24 3.4 28.5 1.0 N1 B:G22 3.6 27.9 1.0 C8 A:A5 3.8 30.6 1.0 C2 B:A21 3.8 30.6 1.0 C5 A:NF24 3.9 28.7 1.0 N1 B:A21 3.9 28.7 1.0 N3 B:G22 4.0 30.6 1.0 N9 A:A5 4.0 29.3 1.0 O2' A:NF24 4.0 31.0 1.0 N7 A:A5 4.1 28.6 1.0 O4' A:NF24 4.1 29.2 1.0 O4' A:A5 4.2 30.1 1.0 C4 A:A5 4.4 30.0 1.0 C5 A:A5 4.4 30.2 1.0 C6 B:G22 4.5 30.9 1.0 C1' A:A5 4.5 30.4 1.0 N3 A:C3 4.5 27.7 1.0 F4 A:NF24 4.5 32.0 1.0 C3' A:NF24 4.5 27.3 1.0 O2 A:C3 4.6 27.6 1.0 C4 B:G22 4.6 31.4 1.0 C2 A:C3 4.8 25.8 1.0 C5 B:G22 4.9 29.3 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure Analysis of the Rna Dodecamer Cgc-(NF2)-Aauuagcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure Analysis of the Rna Dodecamer Cgc-(NF2)-Aauuagcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2) within 5.0Å range: probe atom residue distance (Å) B Occ A:F4 b:32.0 occ:1.00 F4 A:NF24 0.0 32.0 1.0 C4 A:NF24 1.3 29.7 1.0 C3 A:NF24 2.3 25.7 1.0 C5 A:NF24 2.4 28.7 1.0 CM A:NF24 2.8 32.7 1.0 N4 A:C3 3.1 28.2 1.0 C2 A:NF24 3.4 29.3 1.0 C4 A:C3 3.5 29.4 1.0 C6 A:NF24 3.5 28.5 1.0 N6 A:A5 3.6 33.2 1.0 N7 A:A5 3.8 28.6 1.0 N6 B:A21 3.9 31.8 1.0 C1 A:NF24 4.0 27.0 1.0 C5 A:C3 4.0 28.2 1.0 O B:HOH123 4.0 44.7 1.0 N3 A:C3 4.1 27.7 1.0 N1 B:A21 4.1 28.7 1.0 C5 A:A5 4.2 30.2 1.0 C6 A:A5 4.2 29.8 1.0 C6 B:A21 4.5 30.0 1.0 F2 A:NF24 4.5 31.4 1.0 O6 B:G22 4.6 27.8 1.0 C8 A:A5 4.8 30.6 1.0 C6 A:C3 4.9 27.0 1.0 N1 B:G22 4.9 27.9 1.0 C2 A:C3 5.0 25.8 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure Analysis of the Rna Dodecamer Cgc-(NF2)-Aauuagcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure Analysis of the Rna Dodecamer Cgc-(NF2)-Aauuagcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2) within 5.0Å range: probe atom residue distance (Å) B Occ B:F16 b:40.9 occ:1.00 F2 B:NF216 0.0 40.9 1.0 C2 B:NF216 1.3 37.5 1.0 C3 B:NF216 2.2 36.8 1.0 C1 B:NF216 2.3 38.7 1.0 C1' B:NF216 2.8 39.4 1.0 C2 A:G10 2.9 33.4 1.0 N1 A:G10 2.9 32.5 1.0 N2 A:G10 3.1 34.0 1.0 C4 B:NF216 3.3 40.8 1.0 C2' B:NF216 3.4 39.4 1.0 C6 B:NF216 3.5 38.9 1.0 N3 A:G10 3.5 33.9 1.0 N1 A:A9 3.6 44.3 1.0 C6 A:G10 3.6 33.8 1.0 C2 A:A9 3.7 44.1 1.0 C5 B:NF216 3.9 40.6 1.0 O2' B:NF216 3.9 37.2 1.0 C4 A:G10 4.0 33.8 1.0 C8 B:A17 4.0 34.7 1.0 C5 A:G10 4.1 34.8 1.0 O4' B:NF216 4.1 39.7 1.0 N3 B:C15 4.1 33.6 1.0 N7 B:A17 4.2 31.1 1.0 N9 B:A17 4.2 38.0 1.0 O6 A:G10 4.2 33.1 1.0 F4 B:NF216 4.3 42.2 1.0 C5 B:A17 4.4 34.5 1.0 O4' B:A17 4.4 41.3 1.0 C4 B:A17 4.4 36.0 1.0 O2 B:C15 4.5 33.3 1.0 C2 B:C15 4.6 31.3 1.0 C3' B:NF216 4.7 40.9 1.0 C1' B:A17 4.7 38.6 1.0 C6 A:A9 4.8 45.4 1.0 C4 B:C15 4.9 28.3 1.0 N3 A:A9 5.0 44.4 1.0 N4 B:C15 5.0 29.4 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure Analysis of the Rna Dodecamer Cgc-(NF2)-Aauuagcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure Analysis of the Rna Dodecamer Cgc-(NF2)-Aauuagcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2) within 5.0Å range: probe atom residue distance (Å) B Occ B:F16 b:42.2 occ:1.00 F4 B:NF216 0.0 42.2 1.0 C4 B:NF216 1.3 40.8 1.0 C3 B:NF216 2.2 36.8 1.0 C5 B:NF216 2.5 40.6 1.0 N4 B:C15 2.8 29.4 1.0 CM B:NF216 3.0 42.6 1.0 C4 B:C15 3.3 28.3 1.0 C2 B:NF216 3.3 37.5 1.0 C6 B:NF216 3.5 38.9 1.0 C5 B:C15 3.8 30.4 1.0 N6 A:A9 3.8 45.3 1.0 N7 B:A17 3.8 31.1 1.0 C1 B:NF216 3.9 38.7 1.0 N6 B:A17 3.9 35.4 1.0 N3 B:C15 4.0 33.6 1.0 N1 A:A9 4.2 44.3 1.0 O6 A:G10 4.3 33.1 1.0 C5 B:A17 4.3 34.5 1.0 F2 B:NF216 4.3 40.9 1.0 C6 B:A17 4.4 36.3 1.0 C6 A:A9 4.5 45.4 1.0 O B:HOH111 4.7 47.4 1.0 C6 B:C15 4.7 29.9 1.0 C8 B:A17 4.8 34.7 1.0 C6 A:G10 4.9 33.8 1.0 C2 B:C15 4.9 31.3 1.0 N1 A:G10 4.9 32.5 1.0

J.Xia, A.Noronha, I.Toudjarska, F.Li, A.Akinc, R.Braich, M.Frank-Kamenetsky, K.G.Rajeev, M.Egli, M.Manoharan. Gene Silencing Activity of Sirnas with A Ribo-Difluorotoluyl Nucleotide. Acs Chem.Biol. V. 1 176 2006.
ISSN: ISSN 1554-8929
PubMed: 17163665
DOI: 10.1021/CB600063P