Fluorine in PDB 4oi1: Structure of A Rna-Processing Protein

The structure of Structure of A Rna-Processing Protein, PDB code: 4oi1 was solved by A.Dikfidan, B.Loll, C.Zeymer, T.Clausen, A.Meinhart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.66 / 2.30
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	100.740, 100.740, 40.410, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 24.2

The structure of Structure of A Rna-Processing Protein also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Aluminium	(Al)	1 atom

The binding sites of Fluorine atom in the Structure of A Rna-Processing Protein (pdb code 4oi1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of A Rna-Processing Protein, PDB code: 4oi1:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Structure of A Rna-Processing Protein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of A Rna-Processing Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:21.0 occ:1.00 F1 A:ALF503 0.0 21.0 1.0 AL A:ALF503 1.8 20.4 1.0 MG A:MG502 1.9 17.3 1.0 F3 A:ALF503 2.5 20.4 1.0 F4 A:ALF503 2.6 20.2 1.0 O3B A:ADP501 2.6 18.8 1.0 O5' B:G1 2.6 22.4 1.0 O A:HOH601 2.7 14.9 1.0 O A:HOH602 2.7 17.4 1.0 O A:HOH603 2.9 14.2 1.0 OD2 A:ASP151 3.0 19.5 1.0 O2B A:ADP501 3.0 19.1 1.0 PB A:ADP501 3.2 18.8 1.0 F2 A:ALF503 3.6 20.5 1.0 CE A:LYS127 3.9 17.6 1.0 NZ A:LYS127 3.9 17.9 1.0 C5' B:G1 3.9 22.8 1.0 O1B A:ADP501 4.0 17.6 1.0 OG1 A:THR128 4.1 16.4 1.0 CG A:ASP151 4.2 19.5 1.0 O A:THR230 4.2 19.3 1.0 N A:GLY232 4.3 21.4 1.0 CA A:CYS231 4.5 21.1 1.0 O3A A:ADP501 4.6 18.2 1.0 CB A:GLN154 4.6 22.2 1.0 C A:CYS231 4.8 20.8 1.0 NH2 A:ARG288 4.9 32.4 1.0 CB A:ASP151 4.9 19.1 1.0 C4' B:G1 5.0 24.2 1.0

Fluorine binding site 2 out of 4 in the Structure of A Rna-Processing Protein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of A Rna-Processing Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:20.5 occ:1.00 F2 A:ALF503 0.0 20.5 1.0 AL A:ALF503 1.8 20.4 1.0 F4 A:ALF503 2.5 20.2 1.0 F3 A:ALF503 2.6 20.4 1.0 NH2 A:ARG293 2.6 28.3 1.0 O3B A:ADP501 2.7 18.8 1.0 NH1 A:ARG293 3.0 27.9 1.0 O5' B:G1 3.1 22.4 1.0 CB A:THR123 3.1 21.8 1.0 CG2 A:THR123 3.2 22.1 1.0 C5' B:G1 3.2 22.8 1.0 CA A:THR123 3.2 21.3 1.0 CZ A:ARG293 3.2 28.9 1.0 N A:ASP124 3.3 21.1 1.0 NH2 A:ARG288 3.6 32.4 1.0 F1 A:ALF503 3.6 21.0 1.0 C A:THR123 3.8 21.3 1.0 PB A:ADP501 4.2 18.8 1.0 OD1 A:ASP124 4.2 23.3 1.0 N A:THR123 4.4 20.6 1.0 CG A:ASP124 4.4 22.9 1.0 CA A:ASP124 4.4 20.8 1.0 OG1 A:THR123 4.5 22.5 1.0 NE A:ARG293 4.5 29.9 1.0 C4' B:G1 4.7 24.2 1.0 OD2 A:ASP124 4.7 23.7 1.0 NZ A:LYS127 4.8 17.9 1.0 O1B A:ADP501 4.8 17.6 1.0 CZ A:ARG288 4.8 33.7 1.0 O A:HOH603 4.8 14.2 1.0 N A:GLY232 4.9 21.4 1.0 CA A:GLY232 4.9 22.3 1.0 O3A A:ADP501 5.0 18.2 1.0 CB A:ASP124 5.0 21.9 1.0 O A:THR123 5.0 21.5 1.0

Fluorine binding site 3 out of 4 in the Structure of A Rna-Processing Protein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of A Rna-Processing Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:20.4 occ:1.00 F3 A:ALF503 0.0 20.4 1.0 AL A:ALF503 1.8 20.4 1.0 F1 A:ALF503 2.5 21.0 1.0 F2 A:ALF503 2.6 20.5 1.0 O A:HOH603 2.6 14.2 1.0 O3B A:ADP501 2.7 18.8 1.0 NH2 A:ARG288 2.8 32.4 1.0 O5' B:G1 2.9 22.4 1.0 CG A:GLN154 3.2 22.2 1.0 C5' B:G1 3.3 22.8 1.0 CB A:GLN154 3.4 22.2 1.0 NH1 A:ARG293 3.5 27.9 1.0 MG A:MG502 3.5 17.3 1.0 F4 A:ALF503 3.6 20.2 1.0 CZ A:ARG288 3.9 33.7 1.0 PB A:ADP501 3.9 18.8 1.0 OD2 A:ASP151 4.0 19.5 1.0 O A:HOH601 4.0 14.9 1.0 NH2 A:ARG293 4.1 28.3 1.0 O2B A:ADP501 4.2 19.1 1.0 CZ A:ARG293 4.2 28.9 1.0 NH1 A:ARG288 4.2 35.5 1.0 CD A:GLN154 4.5 22.7 1.0 O1A A:ADP501 4.6 20.8 1.0 O3A A:ADP501 4.6 18.2 1.0 C4' B:G1 4.7 24.2 1.0 OE1 A:GLN154 4.9 22.8 1.0 CA A:GLN154 4.9 22.4 1.0 OD1 A:ASP124 4.9 23.3 1.0

Fluorine binding site 4 out of 4 in the Structure of A Rna-Processing Protein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of A Rna-Processing Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:20.2 occ:1.00 F4 A:ALF503 0.0 20.2 1.0 AL A:ALF503 1.8 20.4 1.0 NZ A:LYS127 2.5 17.9 1.0 F2 A:ALF503 2.5 20.5 1.0 F1 A:ALF503 2.6 21.0 1.0 O3B A:ADP501 2.6 18.8 1.0 O5' B:G1 2.8 22.4 1.0 N A:GLY232 3.1 21.4 1.0 CA A:GLY232 3.2 22.3 1.0 CE A:LYS127 3.2 17.6 1.0 CA A:THR123 3.3 21.3 1.0 O1B A:ADP501 3.6 17.6 1.0 PB A:ADP501 3.6 18.8 1.0 F3 A:ALF503 3.6 20.4 1.0 C5' B:G1 3.8 22.8 1.0 O A:PRO122 3.8 19.3 1.0 N A:ASP124 3.9 21.1 1.0 N A:THR123 3.9 20.6 1.0 C A:CYS231 4.0 20.8 1.0 CG2 A:THR123 4.0 22.1 1.0 C A:PRO122 4.1 20.1 1.0 C A:THR123 4.1 21.3 1.0 CB A:THR123 4.1 21.8 1.0 MG A:MG502 4.2 17.3 1.0 O2B A:ADP501 4.4 19.1 1.0 O A:HOH602 4.4 17.4 1.0 OD2 A:ASP151 4.6 19.5 1.0 C A:GLY232 4.6 23.5 1.0 CD A:LYS127 4.6 17.0 1.0 CA A:CYS231 4.6 21.1 1.0 O A:GLY121 4.7 19.1 1.0 O A:CYS231 4.8 19.8 1.0 O4' B:G1 4.9 26.2 1.0 C4' B:G1 4.9 24.2 1.0 O A:THR230 5.0 19.3 1.0 O3A A:ADP501 5.0 18.2 1.0

A.Dikfidan, B.Loll, C.Zeymer, I.Magler, T.Clausen, A.Meinhart. Rna Specificity and Regulation of Catalysis in the Eukaryotic Polynucleotide Kinase CLP1. Mol.Cell V. 54 975 2014.
ISSN: ISSN 1097-2765
PubMed: 24813946
DOI: 10.1016/J.MOLCEL.2014.04.005