Fluorine in PDB 3dh3: Crystal Structure of Rluf in Complex with A 22 Nucleotide Rna Substrate

The structure of Crystal Structure of Rluf in Complex with A 22 Nucleotide Rna Substrate, PDB code: 3dh3 was solved by A.Alian, A.Degiovanni, R.M.Stroud, J.S.Finer-Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.51 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.552, 84.128, 91.354, 90.00, 94.87, 90.00
R / Rfree (%)	23.1 / 27.9

The binding sites of Fluorine atom in the Crystal Structure of Rluf in Complex with A 22 Nucleotide Rna Substrate (pdb code 3dh3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Rluf in Complex with A 22 Nucleotide Rna Substrate, PDB code: 3dh3:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Rluf in Complex with A 22 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 Rluf in Complex with A 22 Nucleotide Rna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ E:F2604 b:38.0 occ:1.00 F5 E:FHU2604 0.0 38.0 1.0 C5 E:FHU2604 1.3 36.5 1.0 C6 E:FHU2604 2.2 37.6 1.0 O6 E:FHU2604 2.3 38.2 1.0 C4 E:FHU2604 2.3 36.5 1.0 C1' E:FHU2604 2.4 33.4 1.0 O4 E:FHU2604 2.7 33.5 1.0 O4' E:FHU2604 2.7 31.4 1.0 C2' E:FHU2604 3.1 32.4 1.0 C5' E:FHU2604 3.1 30.3 1.0 O5' E:FHU2604 3.2 30.3 1.0 C4' E:FHU2604 3.4 31.1 1.0 N1 E:FHU2604 3.4 40.2 1.0 N3 E:FHU2604 3.5 38.1 1.0 OH A:TYR137 3.5 49.4 1.0 C3' E:FHU2604 3.8 32.1 1.0 C2 E:FHU2604 3.9 40.0 1.0 CE2 A:TYR137 3.9 48.9 1.0 CZ A:TYR137 4.0 49.1 1.0 CD2 A:LEU106 4.0 35.3 1.0 O A:ARG105 4.1 36.6 1.0 O2' E:FHU2604 4.2 32.8 1.0 NH1 A:ARG205 4.6 40.8 1.0 P E:FHU2604 4.7 29.7 1.0 CA A:LEU106 4.8 37.4 1.0 CD2 A:TYR137 5.0 48.6 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Rluf in Complex with A 22 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 Rluf in Complex with A 22 Nucleotide Rna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ F:F2604 b:37.6 occ:1.00 F5 F:FHU2604 0.0 37.6 1.0 C5 F:FHU2604 1.3 37.1 1.0 C6 F:FHU2604 2.3 39.0 1.0 C4 F:FHU2604 2.4 36.8 1.0 C1' F:FHU2604 2.4 34.8 1.0 O6 F:FHU2604 2.5 40.5 1.0 O4 F:FHU2604 2.7 34.8 1.0 O4' F:FHU2604 2.8 34.0 1.0 C2' F:FHU2604 3.1 34.0 1.0 C5' F:FHU2604 3.1 31.7 1.0 C4' F:FHU2604 3.4 32.8 1.0 OH B:TYR137 3.5 49.7 1.0 N3 F:FHU2604 3.5 38.4 1.0 N1 F:FHU2604 3.5 39.8 1.0 C3' F:FHU2604 3.8 32.9 1.0 O5' F:FHU2604 3.9 31.3 1.0 CD2 B:LEU106 3.9 35.4 1.0 O B:ARG105 4.0 36.7 1.0 C2 F:FHU2604 4.0 39.7 1.0 CZ B:TYR137 4.0 49.3 1.0 CE2 B:TYR137 4.0 48.8 1.0 O2' F:FHU2604 4.3 33.7 1.0 NH1 B:ARG205 4.6 40.6 1.0 P F:FHU2604 4.7 33.6 1.0 CA B:LEU106 4.7 37.4 1.0 C B:ARG105 4.9 36.9 1.0 OP1 F:FHU2604 5.0 31.2 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Rluf in Complex with A 22 Nucleotide Rna Substrate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Rluf in Complex with A 22 Nucleotide Rna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ G:F2604 b:37.0 occ:1.00 F5 G:FHU2604 0.0 37.0 1.0 C5 G:FHU2604 1.3 36.0 1.0 C6 G:FHU2604 2.2 37.3 1.0 C4 G:FHU2604 2.3 35.6 1.0 C1' G:FHU2604 2.4 33.9 1.0 O6 G:FHU2604 2.4 37.9 1.0 O4' G:FHU2604 2.6 32.4 1.0 O4 G:FHU2604 2.7 33.7 1.0 C5' G:FHU2604 3.1 31.5 1.0 C2' G:FHU2604 3.1 32.5 1.0 C4' G:FHU2604 3.3 31.5 1.0 OH C:TYR137 3.4 49.4 1.0 N1 G:FHU2604 3.5 39.4 1.0 N3 G:FHU2604 3.5 37.0 1.0 C3' G:FHU2604 3.6 32.2 1.0 CE2 C:TYR137 3.8 48.8 1.0 O5' G:FHU2604 3.9 31.5 1.0 CZ C:TYR137 3.9 49.1 1.0 CD2 C:LEU106 3.9 35.2 1.0 C2 G:FHU2604 4.0 38.5 1.0 O C:ARG105 4.2 36.6 1.0 O2' G:FHU2604 4.3 31.5 1.0 NH1 C:ARG205 4.6 40.7 1.0 OP1 G:FHU2604 4.8 29.7 1.0 CA C:LEU106 4.8 37.3 1.0 CD2 C:TYR137 4.9 48.7 1.0 CE1 C:TYR137 4.9 49.1 1.0 O3' G:FHU2604 5.0 33.9 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Rluf in Complex with A 22 Nucleotide Rna Substrate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Rluf in Complex with A 22 Nucleotide Rna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ H:F2604 b:38.0 occ:1.00 F5 H:FHU2604 0.0 38.0 1.0 C5 H:FHU2604 1.3 37.3 1.0 C6 H:FHU2604 2.3 38.0 1.0 C4 H:FHU2604 2.3 37.2 1.0 C1' H:FHU2604 2.4 34.6 1.0 O6 H:FHU2604 2.4 38.9 1.0 O4' H:FHU2604 2.7 33.9 1.0 O4 H:FHU2604 2.7 35.0 1.0 C2' H:FHU2604 3.1 32.7 1.0 C5' H:FHU2604 3.2 32.0 1.0 C4' H:FHU2604 3.4 33.0 1.0 OH D:TYR137 3.4 49.8 1.0 N3 H:FHU2604 3.5 37.3 1.0 N1 H:FHU2604 3.5 39.2 1.0 O5' H:FHU2604 3.6 31.3 1.0 C3' H:FHU2604 3.8 32.8 1.0 CZ D:TYR137 3.9 49.3 1.0 CE2 D:TYR137 3.9 48.9 1.0 C2 H:FHU2604 3.9 38.9 1.0 CD2 D:LEU106 3.9 35.4 1.0 O D:ARG105 4.2 36.5 1.0 O2' H:FHU2604 4.2 31.1 1.0 NH1 D:ARG205 4.7 40.9 1.0 CA D:LEU106 4.9 37.3 1.0 CE1 D:TYR137 4.9 49.3 1.0 CD2 D:TYR137 4.9 48.7 1.0 P H:FHU2604 5.0 34.0 1.0 O3' H:FHU2604 5.0 33.2 1.0

A.Alian, A.Degiovanni, S.L.Griner, J.S.Finer-Moore, R.M.Stroud. Crystal Structure of An Rluf-Rna Complex: A Base-Pair Rearrangement Is the Key to Selectivity of Rluf For U2604 of the Ribosome. J.Mol.Biol. V. 388 785 2009.
ISSN: ISSN 0022-2836
PubMed: 19298824
DOI: 10.1016/J.JMB.2009.03.029