Fluorine in PDB 4lgt: Crystal Structure of the Catalytic Domain of Rlub in Complex with A 21-Nucleotide Rna Substrate

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Rlub in Complex with A 21-Nucleotide Rna Substrate:
5.4.99.22;

The structure of Crystal Structure of the Catalytic Domain of Rlub in Complex with A 21-Nucleotide Rna Substrate, PDB code: 4lgt was solved by N.Czudnochowski, J.S.Finer-Moore, R.M.Stroud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.46 / 1.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.940, 42.200, 169.430, 90.00, 102.61, 90.00
R / Rfree (%)	17.3 / 20.3

The binding sites of Fluorine atom in the Crystal Structure of the Catalytic Domain of Rlub in Complex with A 21-Nucleotide Rna Substrate (pdb code 4lgt). 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 Catalytic Domain of Rlub in Complex with A 21-Nucleotide Rna Substrate, PDB code: 4lgt:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Rlub in Complex with A 21-Nucleotide Rna Substrate


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 Catalytic Domain of Rlub in Complex with A 21-Nucleotide Rna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ E:F2605 b:16.3 occ:1.00 F5 E:FHU2605 0.0 16.3 1.0 C5 E:FHU2605 1.3 15.6 1.0 HD23 A:LEU109 2.1 26.2 1.0 C1' E:FHU2605 2.3 15.1 1.0 C4 E:FHU2605 2.3 16.4 1.0 C6 E:FHU2605 2.4 14.9 1.0 H2' E:FHU2605 2.4 16.2 1.0 HA A:LEU109 2.5 13.7 1.0 O4 E:FHU2605 2.6 15.6 1.0 OH A:TYR140 2.6 19.1 1.0 H6 E:FHU2605 2.7 17.9 1.0 H5'' E:FHU2605 2.8 15.5 1.0 C2' E:FHU2605 2.8 13.5 1.0 O4' E:FHU2605 2.8 17.2 1.0 CD2 A:LEU109 3.0 21.9 1.0 O A:ARG108 3.1 24.8 1.0 H1' E:FHU2605 3.2 18.1 1.0 HD22 A:LEU109 3.3 26.2 1.0 CA A:LEU109 3.4 11.4 1.0 C4' E:FHU2605 3.5 12.7 1.0 HD21 A:LEU109 3.5 26.2 1.0 N3 E:FHU2605 3.5 16.9 1.0 H A:ASP110 3.5 12.5 1.0 C3' E:FHU2605 3.5 12.2 1.0 C5' E:FHU2605 3.6 12.9 1.0 H3' E:FHU2605 3.6 14.6 1.0 N1 E:FHU2605 3.6 16.5 1.0 O A:HOH512 3.9 14.5 1.0 CG A:LEU109 4.0 14.9 1.0 CZ A:TYR140 4.0 19.5 1.0 C2 E:FHU2605 4.0 18.6 1.0 C A:ARG108 4.0 13.0 1.0 O2' E:FHU2605 4.1 14.4 1.0 HG A:LEU109 4.1 17.9 1.0 CB A:LEU109 4.1 11.8 1.0 HH11 A:ARG212 4.1 18.5 1.0 HH12 A:ARG212 4.1 18.5 1.0 NH1 A:ARG212 4.2 15.4 1.0 N A:ASP110 4.2 10.4 1.0 HB3 A:LEU109 4.2 14.2 1.0 N A:LEU109 4.2 10.7 1.0 HN3 E:FHU2605 4.3 20.3 1.0 C A:LEU109 4.3 10.6 1.0 O5' E:FHU2605 4.3 11.6 1.0 H5' E:FHU2605 4.4 15.5 1.0 HN1 E:FHU2605 4.4 19.8 1.0 H4' E:FHU2605 4.5 15.3 1.0 HD3 A:ARG212 4.5 20.3 1.0 HG21 A:THR113 4.6 26.6 1.0 HO2' E:FHU2605 4.6 17.3 1.0 HE1 A:TYR140 4.7 21.9 1.0 HE2 A:TYR140 4.7 21.2 1.0 CZ A:ARG212 4.8 15.3 1.0 CE1 A:TYR140 4.8 18.3 1.0 CE2 A:TYR140 4.9 17.7 1.0 O E:HOH2720 4.9 16.6 1.0 O3' E:FHU2605 4.9 11.9 1.0 OP1 E:FHU2605 4.9 12.1 1.0 OD1 A:ASP110 4.9 15.1 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Rlub in Complex with A 21-Nucleotide Rna Substrate


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 Catalytic Domain of Rlub in Complex with A 21-Nucleotide Rna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ F:F2605 b:37.7 occ:1.00 F5 F:FHU2605 0.0 37.7 1.0 C5 F:FHU2605 1.3 35.3 1.0 C1' F:FHU2605 2.3 28.5 1.0 H5' F:FHU2605 2.3 31.9 1.0 C4 F:FHU2605 2.3 31.7 1.0 C6 F:FHU2605 2.4 36.9 1.0 H2' F:FHU2605 2.4 33.4 1.0 HD23 D:LEU109 2.5 50.6 1.0 O4 F:FHU2605 2.6 32.0 1.0 H6 F:FHU2605 2.6 44.3 1.0 HA D:LEU109 2.7 40.9 1.0 HH D:TYR140 2.8 49.2 1.0 O4' F:FHU2605 2.8 25.6 1.0 C2' F:FHU2605 2.8 27.8 1.0 O6 F:FHU2605 2.8 39.9 1.0 O D:ARG108 3.1 35.0 1.0 C5' F:FHU2605 3.2 26.6 1.0 C4' F:FHU2605 3.2 26.8 1.0 H1' F:FHU2605 3.3 34.2 1.0 OH D:TYR140 3.3 41.0 1.0 C3' F:FHU2605 3.4 27.1 1.0 CD2 D:LEU109 3.4 42.1 1.0 H3' F:FHU2605 3.4 32.5 1.0 N3 F:FHU2605 3.5 30.9 1.0 N1 F:FHU2605 3.6 36.3 1.0 H D:ASP110 3.6 44.6 1.0 HD22 D:LEU109 3.6 50.6 1.0 CA D:LEU109 3.7 34.1 1.0 HO6 F:FHU2605 3.7 47.8 1.0 HD21 D:LEU109 3.9 50.6 1.0 O D:HOH312 3.9 32.6 1.0 H5'' F:FHU2605 3.9 31.9 1.0 C2 F:FHU2605 4.0 33.4 1.0 O5' F:FHU2605 4.0 25.4 1.0 O2' F:FHU2605 4.1 29.1 1.0 C D:ARG108 4.1 35.4 1.0 HH12 D:ARG212 4.1 40.9 1.0 N D:ASP110 4.2 37.2 1.0 H4' F:FHU2605 4.3 32.1 1.0 HN1 F:FHU2605 4.3 43.5 1.0 N D:LEU109 4.3 34.4 1.0 HN3 F:FHU2605 4.3 37.1 1.0 NH1 D:ARG212 4.3 34.0 1.0 HH11 D:ARG212 4.4 40.9 1.0 CZ D:TYR140 4.4 37.2 1.0 CG D:LEU109 4.4 40.2 1.0 C D:LEU109 4.4 35.0 1.0 CB D:LEU109 4.4 35.6 1.0 HG21 D:THR113 4.5 59.7 1.0 HG D:LEU109 4.5 48.2 1.0 HB3 D:LEU109 4.6 42.7 1.0 HO2' F:FHU2605 4.6 34.9 1.0 OD1 D:ASP110 4.7 43.9 1.0 HE1 D:TYR140 4.7 45.6 1.0 O F:HOH2719 4.7 36.0 1.0 O3' F:FHU2605 4.8 25.3 1.0 H5'' F:C2606 4.9 42.0 1.0 CE1 D:TYR140 4.9 38.0 1.0 OP1 F:FHU2605 4.9 26.6 1.0

N.Czudnochowski, G.W.Ashley, D.V.Santi, A.Alian, J.Finer-Moore, R.M.Stroud. The Mechanism of Pseudouridine Synthases From A Covalent Complex with Rna, and Alternate Specificity For U2605 Versus U2604 Between Close Homologs. Nucleic Acids Res. V. 42 2037 2014.
ISSN: ISSN 0305-1048
PubMed: 24214967
DOI: 10.1093/NAR/GKT1050