Fluorine in PDB 5r0a: Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry C02, Dmso-Free

The structure of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry C02, Dmso-Free, PDB code: 5r0a was solved by J.Wollenhaupt, A.Metz, T.Barthel, G.M.A.Lima, A.Heine, U.Mueller, G.Klebe, M.S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.40 / 1.54
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.201, 81.928, 93.721, 90.00, 108.51, 90.00
R / Rfree (%)	22.1 / 25.5

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry C02, Dmso-Free (pdb code 5r0a). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry C02, Dmso-Free, PDB code: 5r0a:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry C02, Dmso-Free


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry C02, Dmso-Free within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.74 F2 B:SYA401 0.0 20.0 0.7 C2 B:SYA401 1.3 20.0 0.7 C1 B:SYA401 2.3 20.0 0.7 C3 B:SYA401 2.3 20.0 0.7 O B:SYA401 2.6 20.0 0.7 O2 B:SYA401 2.9 20.0 0.7 C7 B:SYA401 2.9 20.0 0.7 OG1 B:THR7 3.0 43.7 1.0 NE2 B:GLN70 3.1 44.6 1.0 C6 B:SYA401 3.6 20.0 0.7 C4 B:SYA401 3.6 20.0 0.7 C B:SYA401 3.9 20.0 0.7 CG2 B:THR7 3.9 47.3 1.0 O1 B:SYA401 4.0 20.0 0.7 CB B:THR7 4.0 38.9 1.0 C5 B:SYA401 4.0 20.0 0.7 CD B:GLN70 4.4 75.5 1.0 F B:SYA401 4.7 20.0 0.7 CA B:THR7 4.7 40.8 1.0 CE2 B:TYR68 4.7 35.2 1.0

Fluorine binding site 2 out of 3 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry C02, Dmso-Free


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry C02, Dmso-Free within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.74 F1 B:SYA401 0.0 20.0 0.7 C5 B:SYA401 1.3 20.0 0.7 C6 B:SYA401 2.3 20.0 0.7 C4 B:SYA401 2.3 20.0 0.7 F B:SYA401 2.6 20.0 0.7 CG B:GLU83 3.2 39.2 1.0 OE1 B:GLU83 3.4 44.4 1.0 CB B:GLU83 3.4 37.1 1.0 CD1 B:TYR68 3.4 40.5 1.0 C1 B:SYA401 3.6 20.0 0.7 CE1 B:TYR68 3.6 39.9 1.0 C3 B:SYA401 3.6 20.0 0.7 CD B:GLU83 3.8 41.4 1.0 CG B:TYR68 3.8 32.9 1.0 CD1 B:PHE89 3.9 43.1 1.0 C2 B:SYA401 4.0 20.0 0.7 CZ B:TYR68 4.1 39.4 1.0 CD2 B:TYR68 4.4 35.9 1.0 CB B:TYR68 4.5 38.6 1.0 CE2 B:TYR68 4.5 35.2 1.0 CE B:LYS88 4.6 51.1 1.0 CE1 B:PHE89 4.6 38.3 1.0 CD B:LYS88 4.6 46.9 1.0 NZ B:LYS88 4.6 53.3 1.0 O B:SYA401 4.7 20.0 0.7 CA B:PHE89 4.7 49.5 1.0 C7 B:SYA401 4.7 20.0 0.7 CA B:GLU83 4.8 44.1 1.0 CB B:PHE89 4.8 43.2 1.0 OH B:TYR68 4.8 40.1 1.0 O1 B:SYA401 4.8 20.0 0.7 CG B:PHE89 4.8 38.7 1.0 OE2 B:GLU83 4.9 48.8 1.0

Fluorine binding site 3 out of 3 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry C02, Dmso-Free


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry C02, Dmso-Free within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.74 F B:SYA401 0.0 20.0 0.7 C6 B:SYA401 1.3 20.0 0.7 C5 B:SYA401 2.3 20.0 0.7 C1 B:SYA401 2.3 20.0 0.7 F1 B:SYA401 2.6 20.0 0.7 C B:SYA401 2.7 20.0 0.7 O B:SYA401 2.8 20.0 0.7 CG2 B:ILE92 3.4 55.0 1.0 C4 B:SYA401 3.6 20.0 0.7 C2 B:SYA401 3.6 20.0 0.7 CG B:PRO5 3.6 40.2 1.0 CB B:TYR68 3.6 38.6 1.0 CG B:TYR68 3.7 32.9 1.0 CD2 B:TYR68 4.0 35.9 1.0 C3 B:SYA401 4.1 20.0 0.7 CB B:PRO5 4.1 37.8 1.0 CD1 B:TYR68 4.2 40.5 1.0 CB B:ILE92 4.3 51.0 1.0 CD1 B:PHE89 4.4 43.1 1.0 CE1 B:PHE89 4.5 38.3 1.0 CG1 B:ILE92 4.6 47.7 1.0 F2 B:SYA401 4.7 20.0 0.7 CE2 B:TYR68 4.7 35.2 1.0 CD B:PRO5 4.9 37.5 1.0 CE1 B:TYR68 4.9 39.9 1.0 O B:PRO5 5.0 35.6 1.0

J.Wollenhaupt, A.Metz, T.Barthel, G.M.A.Lima, A.Heine, U.Mueller, G.Klebe, M.S.Weiss. F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries For Crystallographic Fragment Screening. Structure 2020.
ISSN: ISSN 0969-2126
PubMed: 32413289
DOI: 10.1016/J.STR.2020.04.019