Fluorine in PDB 5r0e: Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry D02, Dmso-Free

The structure of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry D02, Dmso-Free, PDB code: 5r0e 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)	26.58 / 1.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.905, 82.050, 94.357, 90.00, 108.99, 90.00
R / Rfree (%)	20.6 / 23.6

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry D02, Dmso-Free (pdb code 5r0e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry D02, Dmso-Free, PDB code: 5r0e:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry D02, 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 D02, Dmso-Free within 5.0Å range: probe atom residue distance (Å) B Occ A:F2501 b:20.0 occ:0.60 F1 A:SY42501 0.0 20.0 0.6 C6 A:SY42501 1.3 20.0 0.6 C7 A:SY42501 2.3 20.0 0.6 C5 A:SY42501 2.4 20.0 0.6 N1 A:SY42501 2.8 20.0 0.6 O A:HOH2681 3.1 30.0 1.0 CZ A:PHE1890 3.3 33.3 1.0 ND1 A:HIS1888 3.4 46.4 1.0 C8 A:SY42501 3.6 20.0 0.6 C4 A:SY42501 3.6 20.0 0.6 CE2 A:PHE1890 3.7 32.9 1.0 CG A:HIS1888 3.8 28.6 1.0 CE1 A:PHE1890 3.9 30.6 1.0 CB A:HIS1888 4.0 25.3 1.0 CE1 A:HIS1888 4.0 47.3 1.0 C3 A:SY42501 4.1 20.0 0.6 CD2 A:HIS1888 4.5 32.3 1.0 O A:HOH2658 4.5 34.6 1.0 CD2 A:PHE1890 4.6 28.4 1.0 NE2 A:HIS1888 4.6 37.8 1.0 F A:SY42501 4.7 20.0 0.6 CD1 A:PHE1890 4.8 27.4 1.0 CD1 A:LEU1988 4.8 36.5 1.0

Fluorine binding site 2 out of 4 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry D02, 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 D02, Dmso-Free within 5.0Å range: probe atom residue distance (Å) B Occ A:F2501 b:20.0 occ:0.60 F A:SY42501 0.0 20.0 0.6 C8 A:SY42501 1.3 20.0 0.6 C3 A:SY42501 2.3 20.0 0.6 C7 A:SY42501 2.3 20.0 0.6 N A:SY42501 2.7 20.0 0.6 O A:HOH2671 3.0 39.2 1.0 C1 A:SY42501 3.0 20.0 0.6 C A:SY42501 3.2 20.0 0.6 C6 A:SY42501 3.6 20.0 0.6 C4 A:SY42501 3.6 20.0 0.6 NE2 A:HIS1888 3.6 37.8 1.0 O A:HOH2683 3.7 41.4 1.0 C2 A:SY42501 3.8 20.0 0.6 CD2 A:HIS1888 3.8 32.3 1.0 S A:SY42501 3.8 20.0 0.6 C5 A:SY42501 4.1 20.0 0.6 CE1 A:HIS1888 4.2 47.3 1.0 O1 A:SY42501 4.3 20.0 0.6 CG A:HIS1888 4.5 28.6 1.0 F1 A:SY42501 4.7 20.0 0.6 ND1 A:HIS1888 4.7 46.4 1.0 O A:SY42501 4.9 20.0 0.6

Fluorine binding site 3 out of 4 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry D02, 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 D02, Dmso-Free within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.66 F1 B:SY4401 0.0 20.0 0.7 C6 B:SY4401 1.3 20.0 0.7 C7 B:SY4401 2.3 20.0 0.7 C5 B:SY4401 2.4 20.0 0.7 N1 B:SY4401 2.9 20.0 0.7 CG B:GLU83 3.2 48.6 1.0 C8 B:SY4401 3.5 20.0 0.7 CB B:GLU83 3.6 44.4 1.0 CD1 B:TYR68 3.6 35.6 1.0 C4 B:SY4401 3.6 20.0 0.7 CE1 B:TYR68 3.6 38.7 1.0 OE1 B:GLU83 3.7 44.4 1.0 CD1 B:PHE89 3.9 44.2 1.0 CD B:GLU83 3.9 50.3 1.0 C3 B:SY4401 4.1 20.0 0.7 CG B:TYR68 4.2 32.8 1.0 CZ B:TYR68 4.3 41.5 1.0 CB B:PHE89 4.3 46.1 1.0 CA B:PHE89 4.4 51.0 1.0 F B:SY4401 4.6 20.0 0.7 CG B:PHE89 4.6 44.3 1.0 N B:PHE89 4.8 51.9 1.0 CE1 B:PHE89 4.8 36.0 1.0 OH B:TYR68 4.8 43.1 1.0 CD2 B:TYR68 4.8 35.1 1.0 CE2 B:TYR68 4.8 36.2 1.0 CG1 B:ILE92 4.9 50.5 1.0 CB B:TYR68 4.9 32.7 1.0 CA B:GLU83 5.0 39.5 1.0 OE2 B:GLU83 5.0 50.3 1.0

Fluorine binding site 4 out of 4 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry D02, Dmso-Free


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment F2X-Entry D02, Dmso-Free within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.66 F B:SY4401 0.0 20.0 0.7 C8 B:SY4401 1.3 20.0 0.7 C7 B:SY4401 2.3 20.0 0.7 C3 B:SY4401 2.3 20.0 0.7 N B:SY4401 2.8 20.0 0.7 CB B:PRO5 3.5 35.7 1.0 C6 B:SY4401 3.5 20.0 0.7 C4 B:SY4401 3.6 20.0 0.7 O1 B:SY4401 3.6 20.0 0.7 CG B:PRO5 3.7 36.1 1.0 CG2 B:ILE92 3.8 58.8 1.0 S B:SY4401 3.9 20.0 0.7 CB B:TYR68 4.0 32.7 1.0 C B:PRO5 4.1 26.9 1.0 C5 B:SY4401 4.1 20.0 0.7 CE2 B:PHE96 4.1 41.4 1.0 CG B:TYR68 4.2 32.8 1.0 CD2 B:TYR68 4.2 35.1 1.0 CA B:PRO5 4.2 34.7 1.0 O B:PHE6 4.2 36.1 1.0 C B:PHE6 4.3 38.2 1.0 N B:PHE6 4.3 31.1 1.0 O B:PRO5 4.4 32.2 1.0 OG1 B:THR7 4.4 37.3 1.0 O B:SY4401 4.5 20.0 0.7 N B:THR7 4.5 36.0 1.0 F1 B:SY4401 4.6 20.0 0.7 CD2 B:PHE96 4.6 51.8 1.0 CA B:THR7 4.7 35.0 1.0 CB B:ILE92 4.9 45.4 1.0 CA B:PHE6 4.9 34.3 1.0 CE2 B:TYR68 4.9 36.2 1.0 CD1 B:TYR68 5.0 35.6 1.0 CD B:PRO5 5.0 31.2 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