Fluorine in PDB 7kuo: Fana Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G

The structure of Fana Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G, PDB code: 7kuo 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 / 2.28
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	49.072, 49.072, 81.254, 90, 90, 120
R / Rfree (%)	20.4 / 26.3

The structure of Fana 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)

5 atoms

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

Fluorine binding site 1 out of 2 in the Fana 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 Fana 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:F19 b:23.5 occ:1.00 F A:GFL19 0.0 23.5 1.0 C2' A:GFL19 1.5 19.5 1.0 C3' A:GFL19 2.2 19.3 1.0 C1' A:GFL19 2.5 18.2 1.0 N9 A:GFL19 2.6 19.7 1.0 C8 A:GFL19 3.0 18.6 1.0 O3' A:GFL19 3.1 16.7 1.0 O4' A:GFL19 3.1 19.1 1.0 O5D B:GP3101 3.2 20.5 1.0 C4 A:GFL19 3.3 18.2 1.0 O4D B:GP3101 3.4 18.6 1.0 C4' A:GFL19 3.4 19.2 1.0 C8A B:GP3101 3.5 19.7 1.0 C5D B:GP3101 3.5 18.8 1.0 PA B:GP3101 3.7 18.9 1.0 N7 A:GFL19 3.8 18.2 1.0 O2A B:GP3101 3.9 20.4 1.0 C5 A:GFL19 3.9 18.6 1.0 N3 A:GFL19 4.0 17.9 1.0 O5' A:GFL19 4.0 21.9 1.0 C4D B:GP3101 4.1 18.7 1.0 C5' A:GFL19 4.3 20.4 1.0 N9A B:GP3101 4.3 17.3 1.0 N7A B:GP3101 4.3 16.9 1.0 C1D B:GP3101 4.4 18.5 1.0 O1A B:GP3101 4.4 17.7 1.0 O A:HOH209 4.5 27.9 1.0 O A:HOH221 4.9 33.3 1.0 O A:HOH211 4.9 19.0 1.0

Fluorine binding site 2 out of 2 in the Fana 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 Fana 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:F19 b:22.4 occ:1.00 F B:GFL19 0.0 22.4 1.0 C2' B:GFL19 1.5 19.2 1.0 C3' B:GFL19 2.2 18.9 1.0 C1' B:GFL19 2.6 18.1 1.0 N9 B:GFL19 2.7 19.6 1.0 C8 B:GFL19 3.0 19.0 1.0 O3' B:GFL19 3.1 15.8 1.0 O5D A:GP3101 3.1 20.2 1.0 O4' B:GFL19 3.2 20.1 1.0 C4' B:GFL19 3.4 19.6 1.0 C5D A:GP3101 3.4 19.2 1.0 O4D A:GP3101 3.4 18.2 1.0 C4 B:GFL19 3.4 18.1 1.0 C8A A:GP3101 3.5 18.8 1.0 PA A:GP3101 3.6 19.6 1.0 N7 B:GFL19 3.8 18.2 1.0 O2A A:GP3101 3.9 22.8 1.0 O5' B:GFL19 3.9 23.8 1.0 C5 B:GFL19 4.0 18.6 1.0 C4D A:GP3101 4.0 18.2 1.0 N3 B:GFL19 4.1 17.9 1.0 C5' B:GFL19 4.3 20.5 1.0 N7A A:GP3101 4.3 17.3 1.0 N9A A:GP3101 4.3 17.8 1.0 O1A A:GP3101 4.4 17.9 1.0 O B:HOH208 4.4 28.0 1.0 C1D A:GP3101 4.5 18.1 1.0 O B:HOH213 4.9 19.3 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