Bromine in PDB 5stm: Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A03 From the F2X-Universal Library

The structure of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A03 From the F2X-Universal Library, PDB code: 5stm 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)	44.32 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.277, 81.902, 93.366, 90, 108.3, 90
R / Rfree (%)	26.9 / 30.7

The binding sites of Bromine atom in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A03 From the F2X-Universal Library (pdb code 5stm). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A03 From the F2X-Universal Library, PDB code: 5stm:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A03 From the F2X-Universal Library


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A03 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:Br401 b:20.0 occ:0.74 BR B:W9I401 0.0 20.0 0.7 C4 B:W9I401 1.9 20.0 0.7 C3 B:W9I401 2.8 20.0 0.7 C B:W9I401 2.8 20.0 0.7 HB2 B:PRO5 3.0 80.4 1.0 HA B:THR7 3.1 70.5 1.0 HG21 B:ILE92 3.2 106.0 1.0 HG1 B:THR7 3.2 67.0 1.0 HD2 B:TYR68 3.4 65.5 1.0 HE2 B:PHE96 3.4 88.1 1.0 HB2 B:TYR68 3.5 49.2 1.0 OG1 B:THR7 3.5 55.7 1.0 N B:THR7 3.6 47.5 1.0 C B:PHE6 3.7 72.5 1.0 CA B:THR7 3.7 58.5 1.0 C B:PRO5 3.8 56.6 1.0 CB B:PRO5 3.8 66.8 1.0 O B:PHE6 3.9 51.4 1.0 O B:PRO5 3.9 36.9 1.0 N B:PHE6 4.0 32.6 1.0 H B:THR7 4.0 57.2 1.0 CG2 B:ILE92 4.0 88.2 1.0 H B:PHE6 4.0 39.4 1.0 HD2 B:PRO5 4.0 88.0 1.0 CD2 B:TYR68 4.1 54.4 1.0 N B:W9I401 4.1 20.0 0.7 C1 B:W9I401 4.1 20.0 0.7 HG22 B:ILE92 4.1 106.0 1.0 HG23 B:ILE92 4.2 106.0 1.0 CA B:PRO5 4.2 55.9 1.0 CB B:THR7 4.3 77.4 1.0 CB B:TYR68 4.3 40.8 1.0 CE2 B:PHE96 4.3 73.2 1.0 HB3 B:PRO5 4.3 80.4 1.0 CA B:PHE6 4.3 47.6 1.0 HA B:PHE6 4.4 57.4 1.0 HB3 B:TYR68 4.4 49.2 1.0 C2 B:W9I401 4.5 20.0 0.7 CG B:TYR68 4.6 42.7 1.0 HG13 B:ILE92 4.7 95.3 1.0 O B:ILE69 4.8 34.1 1.0 HG2 B:PRO5 4.8 101.7 1.0 CG B:PRO5 4.8 84.5 1.0 HD2 B:PHE96 4.8 101.6 1.0 CD B:PRO5 4.8 73.1 1.0 HA B:PRO5 4.8 67.3 1.0 H B:ILE69 4.8 61.5 1.0 CE2 B:TYR68 4.9 45.3 1.0 HE2 B:TYR68 4.9 54.6 1.0 HG23 B:THR7 4.9 115.9 1.0 HB B:THR7 4.9 93.2 1.0

Bromine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A03 From the F2X-Universal Library


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A03 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:Br402 b:20.0 occ:0.56 BR B:W9I402 0.0 20.0 0.6 C4 B:W9I402 1.8 20.0 0.6 C3 B:W9I402 2.6 20.0 0.6 C B:W9I402 2.8 20.0 0.6 HA B:GLU223 3.0 124.0 1.0 HA B:ILE126 3.0 139.3 1.0 HD12 B:ILE129 3.0 110.8 1.0 HD2 B:PHE226 3.1 51.3 1.0 HD11 B:ILE129 3.3 110.8 1.0 HG12 B:ILE126 3.4 86.1 1.0 HB2 B:PHE226 3.5 38.7 1.0 CD1 B:ILE129 3.5 92.1 1.0 HB3 B:PHE226 3.5 38.7 1.0 CD2 B:PHE226 3.5 42.6 1.0 HD13 B:ILE129 3.7 110.8 1.0 CB B:PHE226 3.9 32.1 1.0 CA B:ILE126 3.9 115.8 1.0 CA B:GLU223 3.9 103.1 1.0 CG B:PHE226 3.9 38.5 1.0 N B:W9I402 4.0 20.0 0.6 C1 B:W9I402 4.0 20.0 0.6 HG3 B:GLU223 4.0 78.9 1.0 N B:ILE126 4.2 78.2 1.0 HB3 B:LYS125 4.2 133.8 1.0 O B:LYS125 4.2 82.7 1.0 O B:GLY222 4.2 34.6 1.0 N B:GLU223 4.3 58.6 1.0 C B:LYS125 4.3 65.5 1.0 CG1 B:ILE126 4.3 71.5 1.0 C B:GLY222 4.3 31.6 1.0 HB2 B:GLU223 4.4 101.8 1.0 CE2 B:PHE226 4.4 41.7 1.0 C2 B:W9I402 4.5 20.0 0.6 O B:HOH508 4.5 53.5 1.0 H B:ILE126 4.5 94.0 1.0 HE2 B:PHE226 4.5 50.3 1.0 HB2 B:LYS125 4.6 133.8 1.0 CB B:GLU223 4.6 84.6 1.0 HG13 B:ILE126 4.6 86.1 1.0 H B:GLU223 4.6 70.6 1.0 CB B:ILE126 4.7 79.6 1.0 CG B:GLU223 4.8 65.5 1.0 HG13 B:VAL121 4.8 46.8 1.0 CB B:LYS125 4.8 111.3 1.0 HG23 B:ILE126 4.8 97.7 1.0 O B:GLU223 4.9 34.3 1.0 HB B:ILE129 4.9 114.4 1.0 C B:ILE126 4.9 42.2 1.0 O B:ILE126 4.9 62.0 1.0 CG1 B:ILE129 4.9 58.1 1.0 C B:GLU223 4.9 41.8 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