Fluorine in PDB 4oi0: Structure of A Rna-Processing Protein

The structure of Structure of A Rna-Processing Protein, PDB code: 4oi0 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 / 2.20
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	100.710, 100.710, 40.400, 90.00, 90.00, 120.00
R / Rfree (%)	22.7 / 28

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 4oi0). 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: 4oi0:
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:19.9 occ:1.00 F1 A:ALF503 0.0 19.9 1.0 AL A:ALF503 1.8 21.1 1.0 F4 A:ALF503 2.5 22.8 1.0 F3 A:ALF503 2.5 22.4 1.0 O A:HOH603 2.6 12.6 1.0 NH2 A:ARG288 2.6 28.8 1.0 O3B A:ADP501 2.7 18.6 1.0 O5' B:G1 2.9 24.1 1.0 C5' B:G1 3.3 24.6 1.0 CG A:GLN154 3.3 20.8 1.0 MG A:MG502 3.5 17.9 1.0 CB A:GLN154 3.5 19.9 1.0 NH1 A:ARG293 3.5 24.4 1.0 F2 A:ALF503 3.6 20.9 1.0 CZ A:ARG288 3.8 31.0 1.0 PB A:ADP501 3.9 18.1 1.0 O A:HOH601 4.0 12.5 1.0 OD2 A:ASP151 4.0 14.8 1.0 NH1 A:ARG288 4.1 33.6 1.0 O2B A:ADP501 4.1 18.2 1.0 NH2 A:ARG293 4.1 25.5 1.0 CZ A:ARG293 4.3 25.5 1.0 O1A A:ADP501 4.5 20.2 1.0 CD A:GLN154 4.5 21.6 1.0 O3A A:ADP501 4.6 17.5 1.0 C4' B:G1 4.7 25.2 1.0 OE1 A:GLN154 4.9 21.6 1.0 O A:HOH649 4.9 31.2 1.0 OD1 A:ASP124 4.9 19.4 1.0 NE A:ARG288 4.9 29.5 1.0 CA A:GLN154 5.0 20.3 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:20.9 occ:1.00 F2 A:ALF503 0.0 20.9 1.0 AL A:ALF503 1.8 21.1 1.0 F3 A:ALF503 2.5 22.4 1.0 F4 A:ALF503 2.5 22.8 1.0 NZ A:LYS127 2.6 16.9 1.0 O3B A:ADP501 2.7 18.6 1.0 O5' B:G1 2.7 24.1 1.0 N A:GLY232 3.2 17.9 1.0 CE A:LYS127 3.2 16.1 1.0 CA A:THR123 3.3 18.4 1.0 CA A:GLY232 3.3 18.4 1.0 F1 A:ALF503 3.6 19.9 1.0 PB A:ADP501 3.6 18.1 1.0 O1B A:ADP501 3.6 17.5 1.0 C5' B:G1 3.7 24.6 1.0 N A:THR123 3.8 18.6 1.0 O A:PRO122 3.9 17.0 1.0 N A:ASP124 3.9 18.2 1.0 CG2 A:THR123 4.0 19.2 1.0 C A:PRO122 4.1 17.9 1.0 C A:CYS231 4.1 17.5 1.0 C A:THR123 4.1 18.8 1.0 CB A:THR123 4.2 19.6 1.0 MG A:MG502 4.2 17.9 1.0 O2B A:ADP501 4.2 18.2 1.0 O A:HOH602 4.4 19.1 1.0 OD2 A:ASP151 4.6 14.8 1.0 CA A:CYS231 4.7 18.0 1.0 CD A:LYS127 4.7 15.3 1.0 C A:GLY232 4.7 19.6 1.0 O4' B:G1 4.8 26.8 1.0 O A:CYS231 4.9 16.4 1.0 O A:GLY121 4.9 17.1 1.0 C4' B:G1 4.9 25.2 1.0 O3A A:ADP501 5.0 17.5 1.0 O A:THR230 5.0 15.8 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:22.4 occ:1.00 F3 A:ALF503 0.0 22.4 1.0 AL A:ALF503 1.8 21.1 1.0 F2 A:ALF503 2.5 20.9 1.0 F1 A:ALF503 2.5 19.9 1.0 NH2 A:ARG293 2.6 25.5 1.0 O3B A:ADP501 2.8 18.6 1.0 O5' B:G1 2.9 24.1 1.0 NH1 A:ARG293 2.9 24.4 1.0 C5' B:G1 3.1 24.6 1.0 CG2 A:THR123 3.2 19.2 1.0 CZ A:ARG293 3.2 25.5 1.0 CB A:THR123 3.2 19.6 1.0 CA A:THR123 3.2 18.4 1.0 N A:ASP124 3.5 18.2 1.0 NH2 A:ARG288 3.5 28.8 1.0 F4 A:ALF503 3.6 22.8 1.0 C A:THR123 3.9 18.8 1.0 OD1 A:ASP124 4.2 19.4 1.0 PB A:ADP501 4.2 18.1 1.0 N A:THR123 4.5 18.6 1.0 CG A:ASP124 4.5 20.4 1.0 NE A:ARG293 4.5 27.1 1.0 C4' B:G1 4.6 25.2 1.0 CA A:ASP124 4.6 18.2 1.0 OG1 A:THR123 4.7 19.9 1.0 CZ A:ARG288 4.7 31.0 1.0 OD2 A:ASP124 4.8 20.9 1.0 O1B A:ADP501 4.8 17.5 1.0 O A:HOH603 4.8 12.6 1.0 NZ A:LYS127 4.9 16.9 1.0 N A:GLY232 5.0 17.9 1.0 O4' B:G1 5.0 26.8 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:22.8 occ:1.00 F4 A:ALF503 0.0 22.8 1.0 AL A:ALF503 1.8 21.1 1.0 MG A:MG502 1.8 17.9 1.0 F1 A:ALF503 2.5 19.9 1.0 F2 A:ALF503 2.5 20.9 1.0 O3B A:ADP501 2.6 18.6 1.0 O A:HOH602 2.6 19.1 1.0 O5' B:G1 2.7 24.1 1.0 O A:HOH601 2.8 12.5 1.0 O2B A:ADP501 2.8 18.2 1.0 O A:HOH603 2.9 12.6 1.0 OD2 A:ASP151 3.1 14.8 1.0 PB A:ADP501 3.1 18.1 1.0 F3 A:ALF503 3.6 22.4 1.0 CE A:LYS127 3.9 16.1 1.0 O1B A:ADP501 3.9 17.5 1.0 NZ A:LYS127 3.9 16.9 1.0 C5' B:G1 4.0 24.6 1.0 OG1 A:THR128 4.0 13.9 1.0 O A:THR230 4.3 15.8 1.0 CG A:ASP151 4.3 16.4 1.0 O3A A:ADP501 4.5 17.5 1.0 N A:GLY232 4.5 17.9 1.0 CB A:GLN154 4.7 19.9 1.0 NH2 A:ARG288 4.7 28.8 1.0 CA A:CYS231 4.7 18.0 1.0 C A:CYS231 4.9 17.5 1.0 O1A A:ADP501 5.0 20.2 1.0 ND2 A:ASN229 5.0 14.0 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