Chlorine in PDB 7fm9: Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P06B02 From the F2X-Universal Library

The structure of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P06B02 From the F2X-Universal Library, PDB code: 7fm9 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)	40.83 / 1.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.024, 81.657, 94.429, 90, 109.07, 90
R / Rfree (%)	22 / 25.9

The binding sites of Chlorine atom in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P06B02 From the F2X-Universal Library (pdb code 7fm9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P06B02 From the F2X-Universal Library, PDB code: 7fm9:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P06B02 From the F2X-Universal Library


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P06B02 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:20.0 occ:0.72 CL B:VQQ401 0.0 20.0 0.7 C4 B:VQQ401 1.8 20.0 0.7 C5 B:VQQ401 2.6 20.0 0.7 HB2 B:PRO5 2.6 59.0 1.0 HG2 B:PRO5 2.7 66.0 1.0 C3 B:VQQ401 2.8 20.0 0.7 HB2 B:TYR68 2.8 53.7 1.0 C B:PRO5 3.3 42.6 1.0 CB B:PRO5 3.3 49.2 1.0 O B:PRO5 3.4 45.3 1.0 HG23 B:THR7 3.4 82.2 1.0 CG B:PRO5 3.4 55.0 1.0 HG21 B:ILE92 3.5 87.7 1.0 N B:PHE6 3.5 44.6 1.0 HE2 B:PHE96 3.5 65.8 1.0 C B:PHE6 3.6 45.8 1.0 HG22 B:THR7 3.6 82.2 1.0 H B:PHE6 3.6 53.5 1.0 CB B:TYR68 3.7 44.7 1.0 HD2 B:TYR68 3.7 60.6 1.0 HA B:THR7 3.7 53.9 1.0 CA B:PRO5 3.7 42.1 1.0 HB3 B:TYR68 3.8 53.7 1.0 HG23 B:ILE92 3.8 87.7 1.0 O B:PHE6 3.8 46.1 1.0 C6 B:VQQ401 3.9 20.0 0.7 HA B:PHE6 3.9 56.4 1.0 CD2 B:TYR68 4.0 50.5 1.0 CA B:PHE6 4.0 47.0 1.0 N B:THR7 4.0 50.0 1.0 CG2 B:THR7 4.0 68.5 1.0 CG B:TYR68 4.0 51.7 1.0 HG3 B:PRO5 4.0 66.0 1.0 C2 B:VQQ401 4.0 20.0 0.7 CG2 B:ILE92 4.1 73.1 1.0 HB3 B:PRO5 4.1 59.0 1.0 CA B:THR7 4.3 44.9 1.0 H B:ILE69 4.4 54.4 1.0 HA B:PRO5 4.4 50.5 1.0 H B:THR7 4.4 60.0 1.0 CE2 B:PHE96 4.4 54.8 1.0 HG22 B:ILE92 4.4 87.7 1.0 C1 B:VQQ401 4.5 20.0 0.7 CD B:PRO5 4.5 49.0 1.0 HD2 B:PRO5 4.6 58.8 1.0 HG13 B:ILE92 4.6 82.6 1.0 CB B:THR7 4.7 45.5 1.0 HG21 B:THR7 4.7 82.2 1.0 N B:PRO5 4.8 42.5 1.0 C7 B:VQQ401 4.8 20.0 0.7 HD2 B:PHE96 4.8 72.4 1.0 CE2 B:TYR68 4.8 55.0 1.0 HA B:TYR68 4.8 50.2 1.0 CD1 B:TYR68 4.9 57.5 1.0 CA B:TYR68 4.9 41.8 1.0 O B:ILE69 4.9 42.7 1.0

Chlorine binding site 2 out of 4 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P06B02 From the F2X-Universal Library


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P06B02 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl402 b:20.0 occ:0.62 CL B:VQQ402 0.0 20.0 0.6 C4 B:VQQ402 1.6 20.0 0.6 C3 B:VQQ402 2.5 20.0 0.6 C5 B:VQQ402 2.5 20.0 0.6 HB1 B:ALA231 3.1 52.8 1.0 HA2 B:GLY235 3.1 63.4 1.0 HB2 B:SER240 3.2 55.2 1.0 HD23 B:LEU283 3.2 113.7 1.0 HA B:TYR237 3.4 59.2 1.0 O B:ALA231 3.5 47.5 1.0 HA B:ALA231 3.5 55.6 1.0 HB3 B:SER240 3.6 55.2 1.0 O B:ASN236 3.6 45.2 1.0 C B:GLY235 3.7 54.8 1.0 C2 B:VQQ402 3.7 20.0 0.6 C6 B:VQQ402 3.8 20.0 0.6 CB B:SER240 3.8 46.0 1.0 C B:ASN236 3.9 60.0 1.0 CB B:ALA231 3.9 44.0 1.0 CA B:GLY235 3.9 52.8 1.0 CA B:ALA231 4.0 46.4 1.0 N B:ASN236 4.0 48.1 1.0 CD2 B:LEU283 4.0 94.8 1.0 O B:GLY235 4.0 54.7 1.0 HD21 B:LEU283 4.0 113.7 1.0 C B:ALA231 4.1 52.9 1.0 N B:TYR237 4.1 46.7 1.0 H B:ASN236 4.2 57.7 1.0 CA B:TYR237 4.2 49.4 1.0 HB2 B:ALA231 4.2 52.8 1.0 C1 B:VQQ402 4.2 20.0 0.6 HG B:SER240 4.3 70.6 1.0 HD1 B:TYR237 4.3 80.7 1.0 HG B:LEU283 4.3 107.5 1.0 HA B:LEU283 4.5 82.6 1.0 H B:SER240 4.5 59.7 1.0 H B:GLY235 4.5 55.9 1.0 H B:TYR237 4.6 56.1 1.0 HA3 B:GLY235 4.6 63.4 1.0 OG B:SER240 4.6 58.8 1.0 CA B:ASN236 4.6 44.6 1.0 HB3 B:ALA231 4.6 52.8 1.0 CG B:LEU283 4.7 89.6 1.0 HB2 B:LEU283 4.7 76.2 1.0 N B:GLY235 4.7 46.5 1.0 HD22 B:LEU283 4.7 113.7 1.0 HB2 B:TYR237 4.9 64.7 1.0 CA B:SER240 4.9 51.4 1.0

Chlorine binding site 3 out of 4 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P06B02 From the F2X-Universal Library


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P06B02 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl403 b:20.0 occ:0.50 CL B:VQQ403 0.0 20.0 0.5 C4 B:VQQ403 1.6 20.0 0.5 C5 B:VQQ403 2.6 20.0 0.5 C3 B:VQQ403 2.6 20.0 0.5 HD12 B:LEU316 2.9 102.7 1.0 HB2 B:TRP289 3.0 70.3 1.0 HD11 B:LEU316 3.3 102.7 1.0 HB3 B:TRP289 3.4 70.3 1.0 CD1 B:LEU316 3.4 85.6 1.0 HD13 B:LEU316 3.5 102.7 1.0 HE2 B:MET309 3.5 80.7 1.0 HB3 B:LEU284 3.6 66.3 1.0 CB B:TRP289 3.6 58.6 1.0 HD13 B:LEU284 3.7 71.4 1.0 HA B:GLU286 3.8 82.5 1.0 C6 B:VQQ403 3.8 20.0 0.5 C2 B:VQQ403 3.9 20.0 0.5 HE3 B:MET309 3.9 80.7 1.0 CE B:MET309 4.1 67.2 1.0 CG B:TRP289 4.2 52.0 1.0 C1 B:VQQ403 4.3 20.0 0.5 HE1 B:MET309 4.3 80.7 1.0 HD1 B:TRP289 4.4 57.4 1.0 CB B:LEU284 4.5 55.2 1.0 CD1 B:LEU284 4.5 59.5 1.0 CD1 B:TRP289 4.5 47.8 1.0 HD12 B:LEU284 4.6 71.4 1.0 HB2 B:LEU284 4.6 66.3 1.0 HG3 B:GLU286 4.7 119.2 1.0 CA B:GLU286 4.8 68.8 1.0 O B:ASN285 4.9 60.6 1.0 CG B:LEU316 4.9 114.3 1.0 CA B:TRP289 4.9 66.5 1.0 HD21 B:ASN290 4.9 124.2 1.0 HB2 B:LEU316 5.0 155.1 1.0 HG2 B:GLU286 5.0 119.2 1.0

Chlorine binding site 4 out of 4 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P06B02 From the F2X-Universal Library


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P06B02 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl404 b:20.0 occ:0.62 CL B:VQQ404 0.0 20.0 0.6 C4 B:VQQ404 1.5 20.0 0.6 C3 B:VQQ404 2.2 20.0 0.6 C5 B:VQQ404 2.6 20.0 0.6 NH1 B:ARG55 3.3 86.4 1.0 CZ B:ARG55 3.3 96.9 1.0 HH11 B:ARG55 3.4 103.7 1.0 C2 B:VQQ404 3.4 20.0 0.6 NE B:ARG55 3.5 92.1 1.0 HE B:ARG55 3.5 110.6 1.0 HA B:PHE233 3.5 48.3 1.0 O B:PHE233 3.7 46.8 1.0 OH B:TYR279 3.7 99.7 1.0 O B:MET232 3.7 47.1 1.0 C6 B:VQQ404 3.7 20.0 0.6 HH12 B:ARG55 3.8 103.7 1.0 NH2 B:ARG55 4.0 91.5 1.0 CZ B:TYR279 4.0 101.5 1.0 HD3 B:ARG55 4.0 88.7 1.0 HD1 B:PHE233 4.1 59.7 1.0 C1 B:VQQ404 4.1 20.0 0.6 HE2 B:TYR279 4.2 127.2 1.0 CD B:ARG55 4.2 73.9 1.0 C B:PHE233 4.2 44.4 1.0 CE2 B:TYR279 4.3 106.0 1.0 CA B:PHE233 4.3 40.3 1.0 HH22 B:ARG55 4.3 109.8 1.0 HH21 B:ARG55 4.4 109.8 1.0 HH B:TYR279 4.4 119.7 1.0 HD2 B:ARG55 4.5 88.7 1.0 HE1 B:HIS45 4.7 78.8 1.0 CE1 B:TYR279 4.7 89.4 1.0 C B:MET232 4.7 48.4 1.0 C7 B:VQQ404 4.8 20.0 0.6 HE1 B:TYR279 4.9 107.3 1.0 CD1 B:PHE233 4.9 49.8 1.0 N B:PHE233 5.0 44.2 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