Fluorine in PDB 5sm2: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474, PDB code: 5sm2 was solved by N.Imprachim, Y.Yosaatmadja, F.Von-Delft, C.Bountra, O.Gileadi, J.A.Newman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.26 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.646, 67.43, 138.52, 90, 90, 90
R / Rfree (%)	25 / 27

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474 also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474 (pdb code 5sm2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474, PDB code: 5sm2:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474


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 -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474 within 5.0Å range: probe atom residue distance (Å) B Occ D:F606 b:48.2 occ:0.60 F1 D:LQ3606 0.0 48.2 0.6 C1 D:LQ3606 1.3 47.9 0.6 F2 D:LQ3606 2.1 48.0 0.6 O1 D:LQ3606 2.2 46.9 0.6 CG D:PHE401 3.0 35.3 1.0 CB D:PHE401 3.1 35.0 1.0 C2 D:LQ3606 3.4 46.7 0.6 CD2 D:PHE401 3.4 36.1 1.0 CD2 D:TYR420 3.4 36.2 1.0 CD1 D:PHE401 3.4 35.9 1.0 CG D:TYR420 3.7 35.1 1.0 CE2 D:PHE506 3.8 37.1 1.0 CE2 D:TYR420 4.0 37.0 1.0 CB D:TYR420 4.0 33.9 1.0 OG1 D:THR428 4.0 34.4 1.0 CZ D:PHE506 4.0 37.0 1.0 CE2 D:PHE401 4.1 36.5 1.0 C3 D:LQ3606 4.1 46.6 0.6 CE1 D:PHE401 4.1 36.2 1.0 C6 D:LQ3606 4.3 46.7 0.6 CZ D:PHE401 4.4 35.5 1.0 CD1 D:TYR420 4.5 35.8 1.0 CA D:PHE401 4.6 34.6 1.0 CZ D:TYR420 4.7 38.1 1.0 O D:HOH788 4.7 37.9 1.0 CG2 D:THR428 4.8 33.4 1.0 CD2 D:PHE506 4.9 36.6 1.0 CB D:THR428 4.9 34.4 1.0 O D:HOH838 4.9 50.6 1.0 CE1 D:TYR420 5.0 37.0 1.0 OD1 D:ASN386 5.0 46.5 1.0

Fluorine binding site 2 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474


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 -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474 within 5.0Å range: probe atom residue distance (Å) B Occ D:F606 b:48.0 occ:0.60 F2 D:LQ3606 0.0 48.0 0.6 C1 D:LQ3606 1.3 47.9 0.6 F1 D:LQ3606 2.1 48.2 0.6 O1 D:LQ3606 2.2 46.9 0.6 OG1 D:THR428 3.0 34.4 1.0 C2 D:LQ3606 3.0 46.7 0.6 O D:HOH838 3.1 50.6 1.0 C6 D:LQ3606 3.2 46.7 0.6 CB D:PHE401 3.5 35.0 1.0 CG2 D:THR428 3.5 33.4 1.0 O D:HOH788 3.6 37.9 1.0 CB D:THR428 3.8 34.4 1.0 CG D:PHE401 4.0 35.3 1.0 CD1 D:PHE401 4.2 35.9 1.0 C3 D:LQ3606 4.2 46.6 0.6 ND2 D:ASN388 4.3 49.5 1.0 N1 D:LQ3606 4.5 47.1 0.6 OD1 D:ASN386 4.8 46.5 1.0 CA D:PHE401 4.9 34.6 1.0 CD2 D:PHE401 4.9 36.1 1.0 CB D:ASN386 4.9 40.1 1.0 CB D:PHE426 5.0 41.2 1.0 CA D:THR428 5.0 34.6 1.0

Fluorine binding site 3 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474


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 -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474 within 5.0Å range: probe atom residue distance (Å) B Occ D:F607 b:52.5 occ:0.60 F1 D:LQ3607 0.0 52.5 0.6 C1 D:LQ3607 1.3 52.1 0.6 F2 D:LQ3607 2.1 52.6 0.6 O1 D:LQ3607 2.2 50.9 0.6 C2 D:LQ3607 2.7 50.1 0.6 O D:TYR69 2.9 45.8 1.0 C3 D:LQ3607 2.9 49.5 0.6 CD2 D:TYR69 3.1 43.2 1.0 CE2 D:TYR69 3.5 43.5 1.0 C6 D:LQ3607 3.9 50.0 0.6 CG D:TYR69 4.0 43.3 1.0 C D:TYR69 4.1 45.8 1.0 C4 D:LQ3607 4.1 49.3 0.6 CD1 D:ILE201 4.2 39.1 1.0 SD D:MET62 4.2 74.1 1.0 C D:PRO70 4.4 41.4 1.0 CB D:TYR69 4.4 45.4 1.0 N D:ASN71 4.5 39.5 1.0 O D:PRO70 4.6 41.5 1.0 CZ D:TYR69 4.6 42.9 1.0 CB D:VAL66 4.6 69.4 1.0 CG2 D:VAL66 4.8 69.5 1.0 N1 D:LQ3607 4.8 49.7 0.6 CA D:ASN71 4.8 38.2 1.0 CA D:PRO70 4.9 43.4 1.0 CA D:TYR69 4.9 47.4 1.0 N D:PRO70 4.9 44.5 1.0 CD1 D:TYR69 5.0 42.4 1.0 N D:MET72 5.0 36.8 1.0 C D:ASN71 5.0 37.9 1.0 C5 D:LQ3607 5.0 49.3 0.6

Fluorine binding site 4 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474 within 5.0Å range: probe atom residue distance (Å) B Occ D:F607 b:52.6 occ:0.60 F2 D:LQ3607 0.0 52.6 0.6 C1 D:LQ3607 1.3 52.1 0.6 F1 D:LQ3607 2.1 52.5 0.6 O1 D:LQ3607 2.2 50.9 0.6 C2 D:LQ3607 2.9 50.1 0.6 CG D:MET72 2.9 39.3 1.0 C3 D:LQ3607 2.9 49.5 0.6 CE2 D:TYR69 3.0 43.5 1.0 CD2 D:TYR69 3.5 43.2 1.0 N D:MET72 3.5 36.8 1.0 CZ D:TYR69 3.7 42.9 1.0 CD1 D:ILE201 3.7 39.1 1.0 CB D:MET72 4.0 37.5 1.0 OH D:TYR69 4.0 42.4 1.0 CA D:MET72 4.0 36.5 1.0 SD D:MET72 4.0 46.2 1.0 C D:ASN71 4.1 37.9 1.0 C6 D:LQ3607 4.2 50.0 0.6 C4 D:LQ3607 4.2 49.3 0.6 O D:TYR69 4.4 45.8 1.0 CG D:TYR69 4.4 43.3 1.0 CA D:ASN71 4.4 38.2 1.0 CE1 D:TYR69 4.6 42.2 1.0 N D:ASN71 4.7 39.5 1.0 CB D:ILE201 4.8 37.5 1.0 CG1 D:ILE201 4.8 38.2 1.0 CG2 D:ILE201 4.8 36.3 1.0 O D:ASN71 4.8 38.4 1.0 CD1 D:TYR69 4.9 42.4 1.0 CD1 D:ILE55 4.9 37.1 1.0

N.Imprachim, Y.Yosaatmadja, F.Von-Delft, C.Bountra, O.Gileadi, J.A.Newman. Pandda Analysis Group Deposition To Be Published.