Fluorine in PDB 3jxr: X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2

The structure of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2, PDB code: 3jxr was solved by D.A.Adamiak, J.Milecki, R.W.Adamiak, W.Rypniewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.25
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	41.116, 41.116, 143.285, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 27.6

The binding sites of Fluorine atom in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 (pdb code 3jxr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2, PDB code: 3jxr:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F5 b:22.0 occ:1.00 F5 A:5CF5 0.0 22.0 1.0 C5 A:5CF5 1.3 17.2 1.0 C6 A:5CF5 2.3 17.2 1.0 C4 A:5CF5 2.4 16.4 1.0 N4 A:5CF5 2.8 17.4 1.0 O A:HOH18 3.3 29.1 1.0 O A:HOH14 3.3 32.2 1.0 OP2 A:5CF5 3.4 20.0 1.0 N1 A:5CF5 3.6 16.9 1.0 O A:HOH16 3.6 22.6 1.0 N3 A:5CF5 3.6 16.2 1.0 N7 A:G4 3.8 17.2 1.0 C5 A:G4 3.9 16.7 1.0 C8 A:G4 3.9 18.0 1.0 C4 A:G4 4.1 16.1 1.0 N9 A:G4 4.1 16.5 1.0 O5' A:5CF5 4.1 18.4 1.0 C2 A:5CF5 4.1 15.5 1.0 O A:HOH13 4.2 26.0 1.0 C3' A:G4 4.3 16.0 1.0 P A:5CF5 4.4 18.4 1.0 N7 A:G6 4.4 14.2 1.0 C6 A:G4 4.4 17.0 1.0 C2' A:G4 4.5 17.7 1.0 O A:HOH55 4.7 38.2 1.0 N3 A:G4 4.7 16.1 1.0 C1' A:5CF5 4.8 17.4 1.0 O4' A:5CF5 4.8 17.7 1.0 C1' A:G4 4.9 17.9 1.0 O3' A:G4 4.9 17.1 1.0 O6 A:G4 4.9 17.9 1.0 N1 A:G4 5.0 15.9 1.0

Fluorine binding site 2 out of 3 in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 within 5.0Å range: probe atom residue distance (Å) B Occ B:F5 b:28.6 occ:1.00 F5 B:5CF5 0.0 28.6 1.0 C5 B:5CF5 1.3 24.5 1.0 C4 B:5CF5 2.1 25.7 1.0 C6 B:5CF5 2.4 24.1 1.0 N4 B:5CF5 2.5 27.8 1.0 N3 B:5CF5 3.3 24.4 1.0 O B:HOH24 3.4 32.7 1.0 N7 B:G4 3.5 19.1 1.0 N1 B:5CF5 3.6 25.3 1.0 C8 B:G4 3.8 17.9 1.0 OP2 B:5CF5 3.8 27.6 1.0 C5 B:G4 3.8 18.8 1.0 C2 B:5CF5 4.0 25.5 1.0 N9 B:G4 4.2 19.2 1.0 C4 B:G4 4.3 18.3 1.0 C6 B:G4 4.4 17.8 1.0 O5' B:5CF5 4.5 29.4 1.0 N7 B:G6 4.5 29.9 1.0 O B:HOH22 4.6 37.9 1.0 C3' B:G4 4.6 22.7 1.0 P B:5CF5 4.7 26.9 1.0 O6 B:G4 4.8 19.8 1.0 C1' B:5CF5 4.9 24.7 1.0 C2' B:G4 5.0 23.7 1.0

Fluorine binding site 3 out of 3 in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 within 5.0Å range: probe atom residue distance (Å) B Occ K:F5 b:37.2 occ:1.00 F5 K:5CF5 0.0 37.2 1.0 C5 K:5CF5 1.3 34.1 1.0 C6 K:5CF5 2.1 35.3 1.0 C4 K:5CF5 2.4 33.8 1.0 N4 K:5CF5 2.9 34.2 1.0 N1 K:5CF5 3.4 35.2 1.0 OP2 K:5CF5 3.5 47.2 1.0 N3 K:5CF5 3.5 33.0 1.0 N7 K:G4 3.6 32.9 1.0 C8 K:G4 3.7 34.4 1.0 C2 K:5CF5 3.9 34.7 1.0 C5 K:G4 3.9 32.5 1.0 O5' K:5CF5 4.1 44.0 1.0 N9 K:G4 4.1 35.9 1.0 C4 K:G4 4.2 33.7 1.0 C3' K:G4 4.4 41.8 1.0 P K:5CF5 4.4 47.3 1.0 C2' K:G4 4.5 40.7 1.0 O K:HOH53 4.5 37.8 1.0 C6 K:G4 4.6 33.5 1.0 C1' K:5CF5 4.6 37.4 1.0 N7 K:G6 4.6 30.6 1.0 O4' K:5CF5 4.7 40.2 1.0 O3' K:G4 4.9 44.5 1.0 C1' K:G4 4.9 37.4 1.0

D.A.Adamiak, J.Milecki, R.W.Adamiak, W.Rypniewski. The Hydration and Unusual Hydrogen Bonding in the Crystal Structure of An Rna Duplex Containing Alternating Cg Base Pairs New J.Chem. V. 34 903 2010.
ISSN: ISSN 1144-0546
DOI: 10.1039/B9NJ00601J