Fluorine in PDB 8ftq: Crystal Structure of HRPN13 Pru Domain in Complex with Ubiquitin and XL44

The structure of Crystal Structure of HRPN13 Pru Domain in Complex with Ubiquitin and XL44, PDB code: 8ftq was solved by K.J.Walters, X.Lu, M.Chandravanshi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.14 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.35, 90.283, 65.027, 90, 113.24, 90
R / Rfree (%)	22 / 24.7

The binding sites of Fluorine atom in the Crystal Structure of HRPN13 Pru Domain in Complex with Ubiquitin and XL44 (pdb code 8ftq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of HRPN13 Pru Domain in Complex with Ubiquitin and XL44, PDB code: 8ftq:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of HRPN13 Pru Domain in Complex with Ubiquitin and XL44


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of HRPN13 Pru Domain in Complex with Ubiquitin and XL44 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:70.0 occ:0.93 F1 A:ZTO201 0.0 70.0 0.9 C1 A:ZTO201 1.4 67.7 0.9 C6 A:ZTO201 2.4 62.1 0.9 C2 A:ZTO201 2.5 70.9 0.9 CE A:MET31 2.6 64.5 1.0 CG A:MET31 3.0 51.0 1.0 SD A:MET31 3.3 64.3 1.0 C5 A:ZTO201 3.6 63.7 0.9 C3 A:ZTO201 3.6 69.7 0.9 CB A:MET31 3.6 54.2 1.0 O A:SER32 3.7 81.2 1.0 C A:SER32 3.9 78.3 1.0 CG1 A:VAL38 4.0 80.7 1.0 N A:LEU33 4.0 79.9 1.0 C4 A:ZTO201 4.1 66.5 0.9 N A:SER32 4.1 71.1 1.0 C A:MET31 4.1 62.7 1.0 CB A:PHE106 4.4 42.6 1.0 O A:MET31 4.4 62.8 1.0 CA A:SER32 4.5 73.0 1.0 CG A:PHE106 4.5 40.5 1.0 CA A:MET31 4.6 58.0 1.0 CA A:LEU33 4.6 86.1 1.0 CB A:VAL38 4.8 85.0 1.0 CA A:VAL38 4.8 86.0 1.0 N A:THR39 4.8 82.4 1.0 CD2 A:PHE106 4.9 38.2 1.0 C7 A:ZTO201 4.9 68.6 0.9 CB A:LEU33 4.9 86.0 1.0 CG2 A:VAL38 5.0 83.1 1.0 CD1 A:PHE106 5.0 42.3 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of HRPN13 Pru Domain in Complex with Ubiquitin and XL44


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of HRPN13 Pru Domain in Complex with Ubiquitin and XL44 within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:71.4 occ:0.92 F1 B:ZTO201 0.0 71.4 0.9 C1 B:ZTO201 1.3 66.8 0.9 C6 B:ZTO201 2.3 64.1 0.9 C2 B:ZTO201 2.4 73.7 0.9 CE B:MET31 3.2 66.1 1.0 CG B:MET31 3.3 52.8 1.0 C5 B:ZTO201 3.5 66.4 0.9 C3 B:ZTO201 3.6 70.6 0.9 O B:SER32 3.8 81.7 1.0 SD B:MET31 3.8 60.6 1.0 N B:LEU33 3.8 81.8 1.0 C B:SER32 3.8 80.6 1.0 CB B:MET31 4.0 55.1 1.0 C4 B:ZTO201 4.0 68.2 0.9 N B:SER32 4.2 71.8 1.0 CB B:PHE106 4.3 43.3 1.0 CG B:PHE106 4.3 44.4 1.0 C B:MET31 4.3 63.7 1.0 CG1 B:VAL38 4.4 82.5 1.0 CA B:LEU33 4.5 90.9 1.0 CB B:LEU33 4.5 87.8 1.0 O B:MET31 4.5 63.6 1.0 CA B:SER32 4.5 73.1 1.0 CD1 B:PHE106 4.7 42.8 1.0 CD2 B:PHE106 4.8 42.4 1.0 CA B:MET31 4.9 58.9 1.0 C7 B:ZTO201 4.9 71.5 0.9 CD1 B:LEU33 4.9 91.0 1.0 CG B:LEU33 5.0 87.8 1.0 CD2 B:LEU33 5.0 82.1 1.0

X.Lu, M.Chandravanshi, V.R.Sabbasani, S.Gaikwad, V.K.Hughitt, N.Gyabaah-Kessie, B.T.Scroggins, S.Das, W.Myint, M.E.Clapp, C.D.Schwieters, M.A.Dyba, D.L.Bolhuis, J.W.Koscielniak, T.Andresson, M.J.Emanuele, N.G.Brown, H.Matsuo, R.Chari, D.E.Citrin, B.A.Mock, R.E.Swenson, K.J.Walters. A Structure-Based Designed Small Molecule Depletes HRPN13 Pru and A Select Group of Ken Box Proteins. Nat Commun V. 15 2485 2024.
ISSN: ESSN 2041-1723
PubMed: 38509117
DOI: 10.1038/S41467-024-46644-7