Fluorine in PDB 5ste: Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P02F11 From the F2X-Universal Library

The structure of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P02F11 From the F2X-Universal Library, PDB code: 5ste was solved by T.Barthel, J.Wollenhaupt, G.M.A.Lima, M.C.Wahl, M.S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.48 / 1.51
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.768, 81.971, 93.76, 90, 108.41, 90
R / Rfree (%)	20.4 / 23.7

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P02F11 From the F2X-Universal Library (pdb code 5ste). 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 P02F11 From the F2X-Universal Library, PDB code: 5ste:
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 P02F11 From the F2X-Universal Library


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 P02F11 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.28 F2 B:VAV401 0.0 20.0 0.3 C4 B:VAV401 1.4 20.0 0.3 F1 B:VAV401 2.1 20.0 0.3 F B:VAV401 2.2 20.0 0.3 C2 B:VAV401 2.4 20.0 0.3 HB2 B:SER240 2.8 46.1 1.0 C1 B:VAV401 3.0 20.0 0.3 HG B:SER240 3.1 47.8 1.0 HB3 B:SER240 3.2 46.1 1.0 HA B:TYR237 3.3 42.6 1.0 CB B:SER240 3.3 38.4 1.0 HA B:LEU283 3.4 54.5 1.0 HD1 B:TYR237 3.5 61.0 1.0 O B:ILE282 3.5 57.4 1.0 OG B:SER240 3.6 39.9 1.0 HD23 B:LEU283 3.6 75.1 1.0 N B:VAV401 3.7 20.0 0.3 HB1 B:ALA231 4.0 40.7 1.0 HG13 B:ILE282 4.0 77.5 1.0 O B:HOH534 4.1 56.0 1.0 CA B:TYR237 4.2 35.6 1.0 C B:ILE282 4.3 55.1 1.0 C B:VAV401 4.3 20.0 0.3 CA B:LEU283 4.3 45.5 1.0 HD21 B:LEU283 4.3 75.1 1.0 CD2 B:LEU283 4.4 62.6 1.0 CD1 B:TYR237 4.4 50.9 1.0 HA2 B:GLY235 4.4 46.6 1.0 N1 B:VAV401 4.5 20.0 0.3 O B:ASN236 4.6 33.1 1.0 HG B:LEU283 4.6 73.0 1.0 N B:LEU283 4.7 48.1 1.0 HB B:ILE282 4.7 72.8 1.0 H B:SER240 4.7 40.6 1.0 N B:TYR237 4.8 35.0 1.0 CA B:SER240 4.8 31.0 1.0 C B:ASN236 4.8 37.0 1.0 CB B:ALA231 4.9 34.0 1.0 O B:TYR237 4.9 35.9 1.0 HB2 B:TYR237 4.9 43.6 1.0 CG1 B:ILE282 4.9 64.7 1.0 HA B:ALA231 4.9 40.4 1.0 CG B:LEU283 5.0 60.9 1.0

Fluorine binding site 2 out of 3 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P02F11 From the F2X-Universal Library


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 P02F11 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.28 F B:VAV401 0.0 20.0 0.3 C4 B:VAV401 1.3 20.0 0.3 F1 B:VAV401 2.1 20.0 0.3 F2 B:VAV401 2.2 20.0 0.3 C2 B:VAV401 2.4 20.0 0.3 HG13 B:ILE282 2.7 77.5 1.0 HD21 B:LEU283 2.8 75.1 1.0 HD23 B:LEU283 2.8 75.1 1.0 N B:VAV401 2.9 20.0 0.3 HG B:LEU283 3.0 73.0 1.0 HA2 B:GLY235 3.2 46.6 1.0 CD2 B:LEU283 3.2 62.6 1.0 HA B:LEU283 3.3 54.5 1.0 CG B:LEU283 3.6 60.9 1.0 CG1 B:ILE282 3.7 64.7 1.0 C1 B:VAV401 3.7 20.0 0.3 HB1 B:ALA231 3.9 40.7 1.0 O B:ALA231 4.0 35.6 1.0 CA B:LEU283 4.0 45.5 1.0 HG12 B:ILE282 4.0 77.5 1.0 O B:ILE282 4.0 57.4 1.0 HD22 B:LEU283 4.1 75.1 1.0 CA B:GLY235 4.1 38.9 1.0 N1 B:VAV401 4.1 20.0 0.3 C B:ILE282 4.1 55.1 1.0 HB2 B:SER240 4.2 46.1 1.0 O B:HOH543 4.2 46.9 1.0 N B:LEU283 4.2 48.1 1.0 HD11 B:ILE282 4.2 94.9 1.0 HD12 B:ILE282 4.3 94.9 1.0 HB B:ILE282 4.3 72.8 1.0 CD1 B:ILE282 4.3 79.2 1.0 CB B:LEU283 4.3 49.2 1.0 HA3 B:GLY235 4.4 46.6 1.0 CB B:ILE282 4.5 60.7 1.0 C B:VAV401 4.6 20.0 0.3 C B:ALA231 4.6 38.7 1.0 C B:GLY235 4.6 43.4 1.0 HA B:ALA231 4.6 40.4 1.0 HG B:SER240 4.7 47.8 1.0 HD11 B:LEU283 4.8 68.8 1.0 H B:LEU283 4.8 57.7 1.0 CD1 B:LEU283 4.8 57.4 1.0 CB B:ALA231 4.8 34.0 1.0 HB3 B:LEU283 4.9 59.0 1.0 HA B:TYR237 4.9 42.6 1.0 CA B:ALA231 4.9 33.7 1.0 H B:GLY235 4.9 40.9 1.0 CB B:SER240 5.0 38.4 1.0 CA B:ILE282 5.0 60.2 1.0

Fluorine binding site 3 out of 3 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P02F11 From the F2X-Universal Library


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 P02F11 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.28 F1 B:VAV401 0.0 20.0 0.3 C4 B:VAV401 1.4 20.0 0.3 F B:VAV401 2.1 20.0 0.3 F2 B:VAV401 2.1 20.0 0.3 C2 B:VAV401 2.4 20.0 0.3 HA2 B:GLY235 2.5 46.6 1.0 N B:VAV401 3.1 20.0 0.3 C B:GLY235 3.2 43.4 1.0 HA B:ALA231 3.2 40.4 1.0 CA B:GLY235 3.3 38.9 1.0 HB1 B:ALA231 3.3 40.7 1.0 HA B:TYR237 3.3 42.6 1.0 N B:ASN236 3.3 34.4 1.0 HB2 B:SER240 3.3 46.1 1.0 C1 B:VAV401 3.4 20.0 0.3 O B:ASN236 3.4 33.1 1.0 H B:ASN236 3.4 41.2 1.0 C B:ASN236 3.5 37.0 1.0 O B:ALA231 3.6 35.6 1.0 O B:GLY235 3.7 40.4 1.0 HD23 B:LEU283 3.8 75.1 1.0 N B:TYR237 3.8 35.0 1.0 HD21 B:LEU283 3.8 75.1 1.0 HA3 B:GLY235 3.9 46.6 1.0 CA B:ALA231 3.9 33.7 1.0 CB B:ALA231 4.0 34.0 1.0 CA B:TYR237 4.0 35.6 1.0 HB3 B:SER240 4.0 46.1 1.0 CA B:ASN236 4.1 34.7 1.0 C B:ALA231 4.1 38.7 1.0 CB B:SER240 4.1 38.4 1.0 N1 B:VAV401 4.2 20.0 0.3 HB2 B:ALA231 4.2 40.7 1.0 H B:TYR237 4.2 42.0 1.0 CD2 B:LEU283 4.3 62.6 1.0 N B:GLY235 4.3 34.2 1.0 C B:VAV401 4.4 20.0 0.3 H B:GLY235 4.4 40.9 1.0 H B:SER240 4.5 40.6 1.0 HD1 B:TYR237 4.6 61.0 1.0 HG B:SER240 4.6 47.8 1.0 HA B:ASN236 4.7 41.5 1.0 HG13 B:ILE282 4.7 77.5 1.0 HA B:LEU283 4.7 54.5 1.0 HB3 B:ALA231 4.8 40.7 1.0 HB2 B:TYR237 4.9 43.6 1.0 HG B:LEU283 4.9 73.0 1.0 OG B:SER240 4.9 39.9 1.0 HD22 B:LEU283 5.0 75.1 1.0 C B:TYR237 5.0 31.9 1.0

T.Barthel, J.Wollenhaupt, G.M.A.Lima, M.C.Wahl, M.S.Weiss. Large-Scale Crystallographic Fragment Screening Expedites Compound Optimization and Identifies Putative Protein-Protein Interaction Sites. J.Med.Chem. V. 65 14630 2022.
ISSN: ISSN 0022-2623
PubMed: 36260741
DOI: 10.1021/ACS.JMEDCHEM.2C01165