Fluorine in PDB 7kun: 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G

The structure of 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G, PDB code: 7kun was solved by Z.Fang, C.Giurgiu, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.58
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	48.783, 48.783, 82.434, 90, 90, 120
R / Rfree (%)	19.4 / 23

The structure of 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

The binding sites of Fluorine atom in the 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G (pdb code 7kun). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G, PDB code: 7kun:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ A:F14 b:11.2 occ:1.00 F A:GF214 0.0 11.2 1.0 C2' A:GF214 1.4 9.1 1.0 C1' A:GF214 2.3 7.9 1.0 C3' A:GF214 2.4 9.6 1.0 O3' A:GF214 2.7 11.3 1.0 O A:HOH240 2.8 24.7 1.0 C4' A:GF214 2.8 9.3 1.0 O4' A:GF214 3.1 7.9 1.0 N9 A:GF214 3.6 7.1 1.0 O4D B:GP3101 3.9 7.1 1.0 N3 A:GF214 4.0 5.9 1.0 C4 A:GF214 4.2 6.2 1.0 C5' A:GF214 4.3 10.4 1.0 C4D B:GP3101 4.4 8.3 1.0 C5D B:GP3101 4.5 9.3 1.0 C8 A:GF214 4.7 7.2 1.0 C1D B:GP3101 5.0 7.3 1.0

Fluorine binding site 2 out of 2 in the 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range: probe atom residue distance (Å) B Occ B:F14 b:11.4 occ:1.00 F B:GF214 0.0 11.4 1.0 C2' B:GF214 1.4 9.2 1.0 C1' B:GF214 2.3 7.9 1.0 C3' B:GF214 2.4 9.5 1.0 O3' B:GF214 2.7 11.5 1.0 C4' B:GF214 2.8 9.2 1.0 O4' B:GF214 3.1 8.1 1.0 N9 B:GF214 3.6 7.1 1.0 O4D A:GP3101 3.9 7.0 1.0 N3 B:GF214 4.0 6.1 1.0 C4 B:GF214 4.2 6.2 1.0 C5' B:GF214 4.3 10.4 1.0 C4D A:GP3101 4.4 8.2 1.0 C5D A:GP3101 4.5 9.4 1.0 C8 B:GF214 4.7 7.2 1.0 C1D A:GP3101 5.0 7.0 1.0

C.Giurgiu, Z.Fang, H.R.M.Aitken, S.C.Kim, L.Pazienza, S.Mittal, J.W.Szostak. Structure-Activity Relationships in Nonenzymatic Template-Directed Rna Synthesis. Angew.Chem.Int.Ed.Engl. 2021.
ISSN: ESSN 1521-3773
PubMed: 34428345
DOI: 10.1002/ANIE.202109714