Fluorine in PDB 6r5e: Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp

The structure of Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp, PDB code: 6r5e was solved by M.L.Kilkenny, L.Pellegrini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.41 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	110.500, 117.180, 152.090, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.6

The structure of Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp also contains other interesting chemical elements:

Manganese	(Mn)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp (pdb code 6r5e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp, PDB code: 6r5e:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:86.0 occ:1.00 F2 A:JSQ504 0.0 86.0 1.0 C2 A:JSQ504 1.3 84.6 1.0 N1 A:JSQ504 2.2 85.2 1.0 N3 A:JSQ504 2.2 83.9 1.0 HD12 A:LEU316 2.6 52.1 1.0 O A:HOH750 3.0 43.5 1.0 C4 A:JSQ504 3.4 83.8 1.0 C6 A:JSQ504 3.5 87.6 1.0 CD1 A:LEU316 3.5 43.5 1.0 HD11 A:LEU316 3.8 52.1 1.0 HB2 A:LEU316 3.9 45.3 1.0 C5 A:JSQ504 3.9 84.6 1.0 HH11 A:ARG56 4.0 64.4 1.0 HD13 A:LEU316 4.0 52.1 1.0 HD3 A:ARG56 4.2 56.3 1.0 HG A:LEU316 4.3 47.4 1.0 NH1 A:ARG56 4.3 53.6 1.0 CG A:LEU316 4.4 39.5 1.0 HH12 A:ARG56 4.5 64.4 1.0 N6 A:JSQ504 4.5 91.3 1.0 HN61 A:JSQ504 4.6 0.6 1.0 N9 A:JSQ504 4.6 80.8 1.0 CB A:LEU316 4.7 37.8 1.0 H A:LEU316 4.7 43.2 1.0 H1' A:JSQ504 4.7 84.0 1.0 HE2 A:TYR54 4.8 47.3 1.0 O A:HOH764 4.8 57.3 1.0 HH A:TYR54 4.9 49.6 1.0 O A:HOH769 4.9 48.2 1.0 CZ A:ARG56 5.0 52.3 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp within 5.0Å range: probe atom residue distance (Å) B Occ E:F504 b:84.0 occ:1.00 F2 E:JSQ504 0.0 84.0 1.0 C2 E:JSQ504 1.3 82.2 1.0 N1 E:JSQ504 2.2 81.4 1.0 N3 E:JSQ504 2.2 81.7 1.0 HD12 E:LEU316 2.4 49.2 1.0 HH11 E:ARG56 2.9 64.0 1.0 O E:HOH647 2.9 48.2 1.0 HH12 E:ARG56 3.1 64.0 1.0 NH1 E:ARG56 3.2 53.3 1.0 CD1 E:LEU316 3.2 41.0 1.0 HD11 E:LEU316 3.3 49.2 1.0 C4 E:JSQ504 3.4 80.6 1.0 O E:HOH759 3.4 40.3 1.0 HG E:LEU316 3.4 44.1 1.0 C6 E:JSQ504 3.5 81.8 1.0 HB2 E:LEU316 3.7 41.1 1.0 CG E:LEU316 3.8 36.8 1.0 HD2 E:ARG56 3.9 63.0 1.0 HD13 E:LEU316 3.9 49.2 1.0 C5 E:JSQ504 3.9 80.3 1.0 O E:HOH707 4.0 58.9 1.0 CZ E:ARG56 4.0 51.4 1.0 H E:LEU316 4.2 40.3 1.0 CB E:LEU316 4.3 34.2 1.0 HE2 E:TYR54 4.5 42.6 1.0 N6 E:JSQ504 4.5 81.4 1.0 CD E:ARG56 4.6 52.5 1.0 HN61 E:JSQ504 4.6 97.7 1.0 NE E:ARG56 4.6 52.5 1.0 N9 E:JSQ504 4.6 77.1 1.0 HH E:TYR54 4.7 47.2 1.0 H1' E:JSQ504 4.7 77.9 1.0 HD3 E:ARG56 4.7 63.0 1.0 HH22 E:ARG56 4.8 56.6 1.0 NH2 E:ARG56 4.8 47.1 1.0 HB3 E:LEU316 4.9 41.1 1.0

S.Holzer, N.J.Rzechorzek, I.R.Short, M.Jenkyn-Bedford, L.Pellegrini, M.L.Kilkenny. Structural Basis For Inhibition of Human Primase By Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine. Acs Chem.Biol. V. 14 1904 2019.
ISSN: ESSN 1554-8937
PubMed: 31479243
DOI: 10.1021/ACSCHEMBIO.9B00367