Chlorine in PDB 8rf4: Crystal Structure of N-Terminal Sars-Cov-2 NSP1 in Complex with Fragment Hit 9D4 Refined Against the Anomalous Diffraction Data

The structure of Crystal Structure of N-Terminal Sars-Cov-2 NSP1 in Complex with Fragment Hit 9D4 Refined Against the Anomalous Diffraction Data, PDB code: 8rf4 was solved by S.Ma, S.Damfo, V.Mykhaylyk, F.Kozielski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.76 / 1.11
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	36.958, 36.958, 141.538, 90, 90, 90
R / Rfree (%)	18.7 / 21.2

The binding sites of Chlorine atom in the Crystal Structure of N-Terminal Sars-Cov-2 NSP1 in Complex with Fragment Hit 9D4 Refined Against the Anomalous Diffraction Data (pdb code 8rf4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of N-Terminal Sars-Cov-2 NSP1 in Complex with Fragment Hit 9D4 Refined Against the Anomalous Diffraction Data, PDB code: 8rf4:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of N-Terminal Sars-Cov-2 NSP1 in Complex with Fragment Hit 9D4 Refined Against the Anomalous Diffraction Data


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of N-Terminal Sars-Cov-2 NSP1 in Complex with Fragment Hit 9D4 Refined Against the Anomalous Diffraction Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:39.7 occ:0.19 CL1 A:EQT201 0.0 39.7 0.2 N1 A:EQT201 0.3 37.8 0.4 C2 A:EQT201 1.5 37.1 0.4 C9 A:EQT201 1.7 39.3 0.2 C11 A:EQT201 2.6 37.6 0.4 N3 A:EQT201 2.6 37.3 0.4 C8 A:EQT201 2.7 39.5 0.2 C11 A:EQT201 2.7 39.4 0.2 CL1 A:EQT201 3.2 36.5 0.4 C9 A:EQT201 3.3 37.7 0.4 C2 A:EQT201 3.4 39.4 0.2 N1 A:EQT201 3.4 39.3 0.2 CG1 A:VAL14 3.6 26.4 1.0 N A:LYS47 3.6 21.2 1.0 C A:LEU46 3.6 20.0 1.0 CB A:LEU46 3.6 18.1 1.0 N4 A:EQT201 3.7 38.1 0.4 C5 A:EQT201 3.7 37.4 0.4 CD2 A:LEU123 3.8 30.8 1.0 O A:LEU46 3.8 21.3 1.0 CD1 A:LEU16 3.9 25.3 1.0 CA A:LYS47 3.9 23.8 1.0 C7 A:EQT201 4.0 39.2 0.2 C5 A:EQT201 4.0 39.2 0.2 CA A:LEU46 4.2 17.8 1.0 CB A:LYS47 4.5 26.6 1.0 CD2 A:LEU16 4.5 27.6 1.0 C6 A:EQT201 4.5 39.3 0.2 C8 A:EQT201 4.6 37.8 0.4 N3 A:EQT201 4.7 39.6 0.2 CG A:LEU16 4.7 22.9 1.0 O A:ARG43 4.7 18.8 1.0 CB A:VAL14 4.8 26.0 1.0 CG A:LEU46 4.9 17.2 1.0 CG A:LYS125 4.9 52.1 1.0 CG2 A:VAL14 4.9 28.1 1.0 N4 A:EQT201 4.9 39.2 0.2 C6 A:EQT201 5.0 37.5 0.4

Chlorine binding site 2 out of 2 in the Crystal Structure of N-Terminal Sars-Cov-2 NSP1 in Complex with Fragment Hit 9D4 Refined Against the Anomalous Diffraction Data


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of N-Terminal Sars-Cov-2 NSP1 in Complex with Fragment Hit 9D4 Refined Against the Anomalous Diffraction Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:36.5 occ:0.40 CL1 A:EQT201 0.0 36.5 0.4 N1 A:EQT201 0.4 39.3 0.2 C2 A:EQT201 1.0 39.4 0.2 C9 A:EQT201 1.7 37.7 0.4 N3 A:EQT201 2.1 39.6 0.2 C11 A:EQT201 2.1 39.4 0.2 C8 A:EQT201 2.7 37.8 0.4 C11 A:EQT201 2.7 37.6 0.4 C9 A:EQT201 3.0 39.3 0.2 N4 A:EQT201 3.1 39.2 0.2 CL1 A:EQT201 3.2 39.7 0.2 C5 A:EQT201 3.2 39.2 0.2 C2 A:EQT201 3.3 37.1 0.4 N1 A:EQT201 3.3 37.8 0.4 CD2 A:LEU123 3.4 30.8 1.0 O A:ARG43 3.6 18.8 1.0 CA A:ARG43 3.8 17.1 1.0 CB A:ARG43 3.9 18.3 1.0 CB A:LEU46 3.9 18.1 1.0 C7 A:EQT201 4.0 38.3 0.4 C5 A:EQT201 4.0 37.4 0.4 CG A:ARG43 4.1 21.0 1.0 C A:ARG43 4.1 16.7 1.0 O A:LYS125 4.1 42.3 1.0 CD1 A:LEU46 4.2 18.9 1.0 CA A:LYS125 4.2 41.9 1.0 C8 A:EQT201 4.3 39.5 0.2 CG A:LYS125 4.4 52.1 1.0 CB A:LYS125 4.5 48.4 1.0 C6 A:EQT201 4.5 39.3 0.2 C6 A:EQT201 4.5 37.5 0.4 CG A:LEU123 4.6 26.7 1.0 N3 A:EQT201 4.6 37.3 0.4 C A:LYS125 4.7 45.3 1.0 CG A:LEU46 4.7 17.2 1.0 N A:LYS47 4.8 21.2 1.0 C7 A:EQT201 4.9 39.2 0.2 CD A:ARG43 4.9 24.1 1.0 N4 A:EQT201 4.9 38.1 0.4

S.Ma, S.Damfo, M.W.Bowler, V.Mykhaylyk, F.Kozielski. High-Confidence Placement of Low-Occupancy Fragments Into Electron Density Using the Anomalous Signal of Sulfur and Halogen Atoms. Acta Crystallogr D Struct V. 80 451 2024BIOL.
ISSN: ISSN 2059-7983
PubMed: 38841886
DOI: 10.1107/S2059798324004480