The binding sites of Fluorine atom in the structure of 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 with 5.0 Angstroms radius around Fluorine atom.
The 2g92 structure was solved by M.EGLI, F.LI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 24.8-1.6 | | Space group | P31 | | a (A) | 28.614 | | b (A) | 28.614 | | c (A) | 63.171 | | alpha (°) | 90.00 | | beta (°) | 90.00 | | gamma (°) | 120.00 | | Rfactor (%) | 19.6 | | Rfree (%) | 23.1 |
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Fluorine binding site 1 out of 4 in 2g92
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Fluorine in the PDB 2g92. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: C3, A: Nf24, A: A5, B: A21, B: G22, | conact list:
| Atom | Atom | Distance (A) | | F | N3 A:C3 | 4.50 | | F | C2 A:C3 | 4.83 | | F | O2 A:C3 | 4.62 | | F | F4 A:Nf24 | 4.51 | | F | C1 A:Nf24 | 2.28 | | F | C3' A:Nf24 | 4.52 | | F | F2 A:Nf24 | 0.00 | | F | C2 A:Nf24 | 1.31 | | F | C6 A:Nf24 | 3.44 | | F | C5 A:Nf24 | 3.90 | | F | C1' A:Nf24 | 2.74 | | F | O4' A:Nf24 | 4.10 | | F | C4 A:Nf24 | 3.38 | | F | C2' A:Nf24 | 3.27 | | F | C3 A:Nf24 | 2.22 | | F | O2' A:Nf24 | 4.04 | | F | N9 A:A5 | 4.02 | | F | C8 A:A5 | 3.83 | | F | C5 A:A5 | 4.41 | | F | C1' A:A5 | 4.49 | | F | N7 A:A5 | 4.09 | | F | O4' A:A5 | 4.17 | | F | C4 A:A5 | 4.38 | | F | C2 B:A21 | 3.84 | | F | N1 B:A21 | 3.93 | | F | N3 B:G22 | 3.98 | | F | N2 B:G22 | 3.32 | | F | C2 B:G22 | 3.42 | | F | C6 B:G22 | 4.47 | | F | N1 B:G22 | 3.65 | | F | C5 B:G22 | 4.91 | | F | C4 B:G22 | 4.63 |
| interactive model:
| Fluorine binding site 2 out of 4 in 2g92
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Fluorine in the PDB 2g92. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: C3, A: Nf24, A: A5, B: A21, B: G22, B: Hoh123, | conact list:
| Atom | Atom | Distance (A) | | F | N3 A:C3 | 4.09 | | F | C2 A:C3 | 4.99 | | F | C6 A:C3 | 4.91 | | F | C5 A:C3 | 4.00 | | F | C4 A:C3 | 3.46 | | F | N4 A:C3 | 3.07 | | F | F4 A:Nf24 | 0.00 | | F | C1 A:Nf24 | 3.96 | | F | F2 A:Nf24 | 4.51 | | F | C2 A:Nf24 | 3.44 | | F | C6 A:Nf24 | 3.54 | | F | C5 A:Nf24 | 2.39 | | F | CM A:Nf24 | 2.80 | | F | C4 A:Nf24 | 1.33 | | F | C3 A:Nf24 | 2.29 | | F | C8 A:A5 | 4.77 | | F | C6 A:A5 | 4.21 | | F | C5 A:A5 | 4.19 | | F | N6 A:A5 | 3.64 | | F | N7 A:A5 | 3.76 | | F | C6 B:A21 | 4.47 | | F | N1 B:A21 | 4.10 | | F | N6 B:A21 | 3.92 | | F | N1 B:G22 | 4.93 | | F | O6 B:G22 | 4.57 | | F | O B:Hoh123 | 4.04 |
| interactive model:
| Fluorine binding site 3 out of 4 in 2g92
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Fluorine in the PDB 2g92. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: A9, A: G10, B: C15, B: Nf216, B: A17, | conact list:
| Atom | Atom | Distance (A) | | F | N3 A:A9 | 4.97 | | F | C2 A:A9 | 3.71 | | F | C6 A:A9 | 4.81 | | F | N1 A:A9 | 3.56 | | F | N3 A:G10 | 3.48 | | F | N2 A:G10 | 3.09 | | F | C2 A:G10 | 2.86 | | F | C6 A:G10 | 3.60 | | F | N1 A:G10 | 2.92 | | F | C5 A:G10 | 4.06 | | F | C4 A:G10 | 3.96 | | F | O6 A:G10 | 4.24 | | F | N3 B:C15 | 4.14 | | F | C2 B:C15 | 4.57 | | F | O2 B:C15 | 4.46 | | F | C4 B:C15 | 4.87 | | F | N4 B:C15 | 4.97 | | F | F4 B:Nf216 | 4.35 | | F | C1 B:Nf216 | 2.31 | | F | C3' B:Nf216 | 4.68 | | F | F2 B:Nf216 | 0.00 | | F | C2 B:Nf216 | 1.31 | | F | C6 B:Nf216 | 3.46 | | F | C5 B:Nf216 | 3.89 | | F | C1' B:Nf216 | 2.76 | | F | O4' B:Nf216 | 4.07 | | F | C4 B:Nf216 | 3.32 | | F | C2' B:Nf216 | 3.38 | | F | C3 B:Nf216 | 2.17 | | F | O2' B:Nf216 | 3.89 | | F | N9 B:A17 | 4.18 | | F | C8 B:A17 | 4.00 | | F | C5 B:A17 | 4.36 | | F | C1' B:A17 | 4.68 | | F | N7 B:A17 | 4.17 | | F | O4' B:A17 | 4.39 | | F | C4 B:A17 | 4.41 |
| interactive model:
| Fluorine binding site 4 out of 4 in 2g92
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Fluorine in the PDB 2g92. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: A9, A: G10, B: C15, B: Nf216, B: A17, B: Hoh111, | conact list:
| Atom | Atom | Distance (A) | | F | C6 A:A9 | 4.49 | | F | N1 A:A9 | 4.23 | | F | N6 A:A9 | 3.78 | | F | C6 A:G10 | 4.88 | | F | N1 A:G10 | 4.94 | | F | O6 A:G10 | 4.25 | | F | N3 B:C15 | 3.97 | | F | C2 B:C15 | 4.89 | | F | C6 B:C15 | 4.74 | | F | C5 B:C15 | 3.78 | | F | C4 B:C15 | 3.30 | | F | N4 B:C15 | 2.84 | | F | F4 B:Nf216 | 0.00 | | F | C1 B:Nf216 | 3.89 | | F | F2 B:Nf216 | 4.35 | | F | C2 B:Nf216 | 3.33 | | F | C6 B:Nf216 | 3.55 | | F | C5 B:Nf216 | 2.45 | | F | CM B:Nf216 | 2.99 | | F | C4 B:Nf216 | 1.32 | | F | C3 B:Nf216 | 2.18 | | F | C8 B:A17 | 4.75 | | F | C6 B:A17 | 4.41 | | F | C5 B:A17 | 4.30 | | F | N6 B:A17 | 3.91 | | F | N7 B:A17 | 3.79 | | F | O B:Hoh111 | 4.72 |
| interactive model:
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