Fluorine in PDB 5der: Rna Oligonucleotide Containing (R)-C5'-Me-2'F U

The structure of Rna Oligonucleotide Containing (R)-C5'-Me-2'F U, PDB code: 5der was solved by J.M.Harp, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.34 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	44.116, 44.116, 86.927, 90.00, 90.00, 90.00
R / Rfree (%)	25.7 / 27.4

The binding sites of Fluorine atom in the Rna Oligonucleotide Containing (R)-C5'-Me-2'F U (pdb code 5der). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Rna Oligonucleotide Containing (R)-C5'-Me-2'F U, PDB code: 5der:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Rna Oligonucleotide Containing (R)-C5'-Me-2'F U


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Rna Oligonucleotide Containing (R)-C5'-Me-2'F U within 5.0Å range: probe atom residue distance (Å) B Occ A:F105 b:22.9 occ:1.00 F2' A:U5R105 0.0 22.9 1.0 C2' A:U5R105 1.3 16.9 1.0 C3' A:U5R105 2.2 18.1 1.0 C1' A:U5R105 2.3 18.8 1.0 C4' A:U5R105 2.5 16.8 1.0 O3' A:U5R105 2.6 18.7 1.0 O4' A:U5R105 2.9 16.1 1.0 N1 A:U5R105 3.6 14.2 1.0 C5' A:U106 3.7 17.3 1.0 O4' A:U106 3.7 21.5 1.0 O5' A:U106 3.8 18.6 1.0 P A:U106 3.9 21.6 1.0 C5' A:U5R105 4.0 22.1 1.0 O2 A:U5R105 4.1 15.4 1.0 C4' A:U106 4.3 18.3 1.0 C2 A:U5R105 4.3 15.4 1.0 C5M A:U5R105 4.5 27.3 1.0 C6 A:U5R105 4.6 15.4 1.0 O A:HOH218 4.7 30.4 1.0 OP1 A:U106 4.7 23.0 1.0 C6 A:U106 4.7 13.7 1.0 O5' A:U5R105 4.8 24.6 1.0 OP2 A:U106 4.8 20.0 1.0 C1' A:U106 5.0 13.7 1.0

Fluorine binding site 2 out of 4 in the Rna Oligonucleotide Containing (R)-C5'-Me-2'F U


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Rna Oligonucleotide Containing (R)-C5'-Me-2'F U within 5.0Å range: probe atom residue distance (Å) B Occ B:F213 b:19.8 occ:1.00 F2' B:U5R213 0.0 19.8 1.0 C2' B:U5R213 1.3 17.1 1.0 C3' B:U5R213 2.2 17.6 1.0 C1' B:U5R213 2.3 12.6 1.0 C4' B:U5R213 2.5 18.5 1.0 O3' B:U5R213 2.6 22.3 1.0 O4' B:U5R213 2.9 21.7 1.0 C5' B:U214 3.6 19.1 1.0 N1 B:U5R213 3.6 17.1 1.0 O5' B:U214 3.8 17.9 1.0 O4' B:U214 3.8 21.1 1.0 O B:HOH326 3.8 30.4 1.0 P B:U214 3.8 23.7 1.0 C5' B:U5R213 4.0 24.7 1.0 O2 B:U5R213 4.1 15.1 1.0 C4' B:U214 4.2 16.6 1.0 C2 B:U5R213 4.3 13.2 1.0 C5M B:U5R213 4.5 22.4 1.0 C6 B:U5R213 4.6 13.2 1.0 OP1 B:U214 4.6 25.3 1.0 O5' B:U5R213 4.8 23.3 1.0 OP2 B:U214 4.8 22.4 1.0 C6 B:U214 4.8 15.2 1.0

Fluorine binding site 3 out of 4 in the Rna Oligonucleotide Containing (R)-C5'-Me-2'F U


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Rna Oligonucleotide Containing (R)-C5'-Me-2'F U within 5.0Å range: probe atom residue distance (Å) B Occ C:F105 b:21.1 occ:1.00 F2' C:U5R105 0.0 21.1 1.0 C2' C:U5R105 1.3 15.7 1.0 C3' C:U5R105 2.2 19.6 1.0 C1' C:U5R105 2.3 16.3 1.0 C4' C:U5R105 2.5 19.1 1.0 O3' C:U5R105 2.6 21.4 1.0 O4' C:U5R105 2.9 19.1 1.0 C5' C:U106 3.6 17.1 1.0 N1 C:U5R105 3.6 12.9 1.0 O4' C:U106 3.7 20.4 1.0 O A:HOH203 3.8 23.0 1.0 O5' C:U106 3.8 18.9 1.0 P C:U106 3.9 20.2 1.0 C5' C:U5R105 4.0 22.4 1.0 O2 C:U5R105 4.0 14.4 1.0 O C:HOH217 4.1 27.5 1.0 C4' C:U106 4.2 15.4 1.0 C2 C:U5R105 4.3 13.9 1.0 C5M C:U5R105 4.5 27.5 1.0 C6 C:U5R105 4.6 14.2 1.0 OP1 C:U106 4.7 26.9 1.0 OP2 C:U106 4.8 21.6 1.0 O5' C:U5R105 4.8 23.4 1.0 C6 C:U106 4.8 12.3 1.0 O2' A:G108 5.0 19.7 1.0

Fluorine binding site 4 out of 4 in the Rna Oligonucleotide Containing (R)-C5'-Me-2'F U


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Rna Oligonucleotide Containing (R)-C5'-Me-2'F U within 5.0Å range: probe atom residue distance (Å) B Occ D:F213 b:19.8 occ:1.00 F2' D:U5R213 0.0 19.8 1.0 C2' D:U5R213 1.3 17.9 1.0 C3' D:U5R213 2.2 19.5 1.0 C1' D:U5R213 2.3 15.9 1.0 C4' D:U5R213 2.5 15.6 1.0 O3' D:U5R213 2.6 17.2 1.0 O4' D:U5R213 2.8 18.1 1.0 O B:HOH301 3.0 22.9 1.0 O D:HOH337 3.1 31.5 1.0 O2' B:A211 3.2 17.6 1.0 O B:HOH329 3.4 26.5 1.0 N1 D:U5R213 3.6 14.8 1.0 C5' D:U214 3.7 17.8 1.0 O4' D:U214 3.7 17.6 1.0 O5' D:U214 3.8 16.8 1.0 P D:U214 3.9 20.7 1.0 C5' D:U5R213 4.0 19.9 1.0 O2 D:U5R213 4.1 12.7 1.0 O B:HOH340 4.2 33.7 1.0 C4' D:U214 4.3 17.4 1.0 C2 D:U5R213 4.3 12.0 1.0 O D:HOH314 4.4 31.4 1.0 C5M D:U5R213 4.5 28.2 1.0 C2' B:A211 4.6 14.0 1.0 C6 D:U5R213 4.6 15.5 1.0 C6 D:U214 4.7 11.4 1.0 OP1 D:U214 4.7 24.0 1.0 O5' D:U5R213 4.8 23.9 1.0 OP2 D:U214 4.8 26.0 1.0 O D:HOH330 4.9 22.1 1.0 C1' D:U214 4.9 16.4 1.0

A.V.Kel In, I.Zlatev, J.Harp, M.Jayaraman, A.Bisbe, J.O Shea, N.Taneja, R.M.Manoharan, S.Khan, K.Charisse, M.A.Maier, M.Egli, K.G.Rajeev, M.Manoharan. Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides. J.Org.Chem. V. 81 2261 2016.
ISSN: ISSN 0022-3263
PubMed: 26940174
DOI: 10.1021/ACS.JOC.5B02375