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Fluorine in PDB 5sor: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000110510893

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000110510893

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000110510893:
3.4.19.121;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000110510893, PDB code: 5sor was solved by G.J.Correy, J.S.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.74 / 1.05
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 88.863, 88.863, 39.321, 90, 90, 90
R / Rfree (%) 13.8 / 15.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000110510893 (pdb code 5sor). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000110510893, PDB code: 5sor:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5sor

Go back to Fluorine Binding Sites List in 5sor
Fluorine binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000110510893


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 NSP3 Macrodomain in Complex with ZINC000110510893 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:16.1
occ:0.70
F14 A:WWP201 0.0 16.1 0.7
C13 A:WWP201 1.4 14.8 0.7
O A:HOH528 1.4 32.2 0.3
F16 A:WWP201 2.2 15.2 0.7
F15 A:WWP201 2.2 17.4 0.7
HD23 A:LEU160 2.3 21.5 0.3
HD21 A:LEU160 2.3 21.5 0.3
C12 A:WWP201 2.4 12.2 0.7
H111 A:WWP201 2.4 12.7 0.7
HD12 A:LEU126 2.7 16.4 0.7
CD2 A:LEU160 2.7 17.9 0.3
C11 A:WWP201 2.7 10.5 0.7
HG13 A:VAL155 2.8 16.3 0.7
HD12 A:LEU126 2.9 10.7 0.3
HG13 A:VAL155 3.0 15.4 0.3
HB2 A:LEU126 3.1 13.7 0.7
HD22 A:LEU160 3.2 21.5 0.3
HB3 A:PRO136 3.3 23.1 0.7
HB1 A:ALA129 3.4 10.8 0.3
HB1 A:ALA129 3.4 16.2 0.7
O A:HOH385 3.4 16.2 0.7
HB3 A:PRO136 3.5 13.0 0.3
O A:HOH381 3.5 6.2 0.3
O A:HOH447 3.5 27.8 0.3
CD1 A:LEU126 3.6 13.6 0.7
HB2 A:LEU126 3.6 8.9 0.3
C17 A:WWP201 3.6 11.9 0.7
HB3 A:ALA129 3.6 16.2 0.7
HA A:VAL155 3.7 13.0 0.7
H A:PHE156 3.7 13.2 0.7
CG1 A:VAL155 3.7 13.5 0.7
HB3 A:ALA129 3.8 10.8 0.3
HD13 A:LEU126 3.8 16.4 0.7
CG1 A:VAL155 3.8 12.8 0.3
HG22 A:VAL155 3.8 14.7 0.3
HD11 A:LEU164 3.9 26.7 0.3
HG11 A:VAL155 3.9 15.4 0.3
H171 A:WWP201 3.9 14.4 0.7
HG12 A:VAL155 3.9 16.3 0.7
CD1 A:LEU126 3.9 8.9 0.3
CB A:ALA129 3.9 13.5 0.7
HG A:LEU160 3.9 21.4 0.3
CG A:LEU160 3.9 17.8 0.3
CB A:ALA129 4.0 9.0 0.3
CB A:LEU126 4.0 11.4 0.7
HB2 A:PRO136 4.0 13.0 0.3
HB2 A:ALA129 4.0 16.2 0.7
O A:HOH512 4.1 34.2 0.3
O A:HOH418 4.1 15.5 0.3
HD13 A:LEU126 4.1 10.7 0.3
C10 A:WWP201 4.1 10.3 0.7
HD11 A:LEU164 4.1 19.0 0.7
CB A:PRO136 4.1 19.3 0.7
HB2 A:ALA129 4.2 10.8 0.3
CB A:PRO136 4.2 10.8 0.3
HG3 A:PRO136 4.2 24.5 0.7
HD11 A:LEU126 4.2 16.4 0.7
HA A:VAL155 4.2 14.7 0.3
CG A:LEU126 4.2 12.5 0.7
HB2 A:PRO136 4.2 23.1 0.7
H A:ASP157 4.3 15.4 0.7
HB3 A:LEU126 4.3 13.7 0.7
HG A:LEU126 4.3 15.0 0.7
HG22 A:VAL155 4.3 15.3 0.7
HG11 A:VAL155 4.3 16.3 0.7
N A:PHE156 4.4 11.0 0.7
H A:LEU126 4.4 12.3 0.7
CB A:LEU126 4.4 7.4 0.3
HG12 A:VAL155 4.4 15.4 0.3
HD11 A:LEU126 4.4 10.7 0.3
HG3 A:PRO136 4.5 14.1 0.3
CA A:VAL155 4.5 10.8 0.7
O A:HOH475 4.5 27.7 0.3
HD23 A:LEU160 4.5 24.4 0.7
CG2 A:VAL155 4.5 12.2 0.3
CB A:VAL155 4.6 12.1 0.7
H A:GLY130 4.6 9.8 0.3
CB A:VAL155 4.6 12.3 0.3
HD11 A:LEU160 4.6 21.1 0.3
HB3 A:PHE156 4.6 14.8 0.7
CG A:LEU126 4.6 7.8 0.3
HB3 A:LEU160 4.7 19.4 0.7
HB3 A:LEU160 4.7 21.2 0.3
HG21 A:VAL155 4.7 14.7 0.3
CD1 A:LEU164 4.7 22.2 0.3
H A:LEU126 4.7 8.3 0.3
HG A:LEU126 4.7 9.4 0.3
C18 A:WWP201 4.7 11.6 0.7
H092 A:WWP201 4.7 11.9 0.7
CG A:PRO136 4.7 20.4 0.7
HB3 A:LEU126 4.8 8.9 0.3
H A:PHE156 4.8 17.6 0.3
C A:VAL155 4.8 10.5 0.7
HD12 A:LEU164 4.8 26.7 0.3
CA A:VAL155 4.9 12.2 0.3
CD1 A:LEU160 4.9 17.5 0.3
CG A:PRO136 4.9 11.7 0.3
CG2 A:VAL155 4.9 12.8 0.7
H A:GLY130 4.9 15.2 0.7
CD1 A:LEU164 4.9 15.8 0.7
CB A:LEU160 4.9 17.7 0.3
HD12 A:LEU164 4.9 19.0 0.7
C19 A:WWP201 4.9 11.3 0.7

Fluorine binding site 2 out of 3 in 5sor

Go back to Fluorine Binding Sites List in 5sor
Fluorine binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000110510893


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 NSP3 Macrodomain in Complex with ZINC000110510893 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:17.4
occ:0.70
F15 A:WWP201 0.0 17.4 0.7
C13 A:WWP201 1.4 14.8 0.7
HD21 A:LEU160 1.5 21.5 0.3
HD22 A:LEU160 1.6 21.5 0.3
CD2 A:LEU160 1.8 17.9 0.3
HD23 A:LEU160 2.1 21.5 0.3
F16 A:WWP201 2.2 15.2 0.7
F14 A:WWP201 2.2 16.1 0.7
O A:HOH418 2.3 15.5 0.3
C12 A:WWP201 2.4 12.2 0.7
HG3 A:PRO136 2.4 24.5 0.7
HG3 A:PRO136 2.7 14.1 0.3
HB3 A:PRO136 2.7 23.1 0.7
HD23 A:LEU160 2.7 24.4 0.7
H171 A:WWP201 2.7 14.4 0.7
HB3 A:PRO136 2.8 13.0 0.3
C17 A:WWP201 2.9 11.9 0.7
HB1 A:ALA129 2.9 16.2 0.7
O A:HOH528 3.0 32.2 0.3
HB1 A:ALA129 3.2 10.8 0.3
CG A:LEU160 3.2 17.8 0.3
CG A:PRO136 3.2 20.4 0.7
O A:HOH411 3.2 20.2 0.7
CB A:PRO136 3.3 19.3 0.7
CB A:PRO136 3.4 10.8 0.3
CG A:PRO136 3.4 11.7 0.3
C11 A:WWP201 3.5 10.5 0.7
HG A:LEU160 3.5 23.8 0.7
HB2 A:PRO136 3.5 13.0 0.3
HD11 A:LEU160 3.5 21.1 0.3
CD2 A:LEU160 3.6 20.3 0.7
H111 A:WWP201 3.6 12.7 0.7
HG A:LEU160 3.7 21.4 0.3
HB2 A:PRO136 3.7 23.1 0.7
H A:GLY130 3.7 9.8 0.3
CD1 A:LEU160 3.7 17.5 0.3
HD13 A:LEU160 3.7 21.1 0.3
HD21 A:LEU160 3.8 24.4 0.7
HB3 A:LEU160 3.8 19.4 0.7
HG2 A:PRO136 3.8 24.5 0.7
H A:GLY130 3.8 15.2 0.7
CB A:ALA129 3.8 13.5 0.7
CG A:LEU160 3.9 19.8 0.7
HD3 A:PRO136 4.0 23.3 0.7
O A:HOH521 4.0 27.8 0.3
HG2 A:PRO136 4.0 14.1 0.3
HB2 A:ALA129 4.0 16.2 0.7
HB2 A:LEU160 4.1 21.2 0.3
HB3 A:ALA129 4.1 16.2 0.7
HD12 A:LEU126 4.1 16.4 0.7
CB A:ALA129 4.1 9.0 0.3
CB A:LEU160 4.1 17.7 0.3
O A:HOH447 4.2 27.8 0.3
CD A:PRO136 4.2 19.4 0.7
HG13 A:VAL155 4.2 16.3 0.7
C18 A:WWP201 4.2 11.6 0.7
HB3 A:LEU160 4.2 21.2 0.3
O A:HOH552 4.2 31.0 0.3
HD3 A:PRO136 4.2 12.9 0.3
CB A:LEU160 4.3 16.2 0.7
HD22 A:LEU160 4.3 24.4 0.7
HB2 A:LEU160 4.3 19.4 0.7
HB3 A:ASP157 4.4 18.5 0.7
HB2 A:ALA129 4.4 10.8 0.3
HB3 A:ALA129 4.4 10.8 0.3
HG13 A:VAL155 4.4 15.4 0.3
CD A:PRO136 4.4 10.7 0.3
HD12 A:LEU126 4.5 10.7 0.3
HD11 A:LEU164 4.5 26.7 0.3
N A:GLY130 4.5 8.1 0.3
HD11 A:LEU164 4.5 19.0 0.7
N A:GLY130 4.5 12.7 0.7
C10 A:WWP201 4.6 10.3 0.7
HD12 A:LEU160 4.7 21.1 0.3
CA A:PRO136 4.7 17.4 0.7
HD13 A:LEU126 4.7 16.4 0.7
H A:ASP157 4.7 15.4 0.7
HA A:PRO136 4.7 20.9 0.7
HB2 A:LEU126 4.7 13.7 0.7
H181 A:WWP201 4.8 14.0 0.7
CA A:PRO136 4.8 10.7 0.3
HB2 A:ASP157 4.8 18.5 0.7
HA2 A:GLY130 4.8 10.8 0.3
CD1 A:LEU126 4.8 13.6 0.7
HD2 A:PRO136 4.9 23.3 0.7
C19 A:WWP201 4.9 11.3 0.7
HG12 A:VAL155 4.9 16.3 0.7
HA A:PRO136 5.0 12.9 0.3
CG1 A:VAL155 5.0 13.5 0.7
HG11 A:VAL155 5.0 15.4 0.3
CA A:ALA129 5.0 12.7 0.7

Fluorine binding site 3 out of 3 in 5sor

Go back to Fluorine Binding Sites List in 5sor
Fluorine binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000110510893


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 NSP3 Macrodomain in Complex with ZINC000110510893 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:15.2
occ:0.70
F16 A:WWP201 0.0 15.2 0.7
HD23 A:LEU160 0.6 21.5 0.3
C13 A:WWP201 1.4 14.8 0.7
CD2 A:LEU160 1.5 17.9 0.3
HD22 A:LEU160 1.9 21.5 0.3
HD21 A:LEU160 2.1 21.5 0.3
F14 A:WWP201 2.2 16.1 0.7
F15 A:WWP201 2.2 17.4 0.7
C12 A:WWP201 2.4 12.2 0.7
O A:HOH528 2.6 32.2 0.3
HG13 A:VAL155 2.6 15.4 0.3
H A:ASP157 2.6 15.4 0.7
CG A:LEU160 2.6 17.8 0.3
O A:HOH447 2.6 27.8 0.3
HB3 A:LEU160 2.6 21.2 0.3
H171 A:WWP201 2.7 14.4 0.7
HG A:LEU160 2.9 21.4 0.3
HG13 A:VAL155 2.9 16.3 0.7
C17 A:WWP201 2.9 11.9 0.7
HB3 A:ASP157 2.9 18.5 0.7
HD23 A:LEU160 3.0 24.4 0.7
HG12 A:VAL155 3.0 16.3 0.7
CB A:LEU160 3.0 17.7 0.3
HB3 A:LEU160 3.2 19.4 0.7
HB3 A:ASP157 3.2 19.6 0.3
CG1 A:VAL155 3.2 12.8 0.3
HB2 A:LEU160 3.2 21.2 0.3
HG11 A:VAL155 3.3 15.4 0.3
CG1 A:VAL155 3.3 13.5 0.7
HB2 A:ASP157 3.4 18.5 0.7
HB2 A:LEU160 3.4 19.4 0.7
N A:ASP157 3.4 12.8 0.7
C11 A:WWP201 3.4 10.5 0.7
HG12 A:VAL155 3.4 15.4 0.3
CB A:ASP157 3.5 15.4 0.7
H A:ASP157 3.6 18.9 0.3
H111 A:WWP201 3.6 12.7 0.7
H A:PHE156 3.7 13.2 0.7
CB A:LEU160 3.7 16.2 0.7
CD2 A:LEU160 3.8 20.3 0.7
HG11 A:VAL155 3.8 16.3 0.7
CD1 A:LEU160 3.9 17.5 0.3
N A:PHE156 4.0 11.0 0.7
HB3 A:PHE156 4.0 14.8 0.7
CA A:ASP157 4.0 13.6 0.7
CB A:ASP157 4.0 16.3 0.3
HB2 A:ASP157 4.0 19.6 0.3
HG A:LEU160 4.1 23.8 0.7
HD11 A:LEU160 4.1 21.1 0.3
HD13 A:LEU160 4.1 21.1 0.3
CG A:LEU160 4.1 19.8 0.7
C18 A:WWP201 4.2 11.6 0.7
O A:ASP157 4.2 12.5 0.7
HG3 A:PRO136 4.2 24.5 0.7
HD11 A:LEU164 4.2 26.7 0.3
HD12 A:LEU126 4.2 16.4 0.7
HD22 A:LEU160 4.2 24.4 0.7
HA A:VAL155 4.3 13.0 0.7
O A:HOH418 4.3 15.5 0.3
HB3 A:PRO136 4.3 23.1 0.7
N A:ASP157 4.4 15.7 0.3
C A:VAL155 4.4 10.5 0.7
HD11 A:LEU164 4.5 19.0 0.7
CA A:LEU160 4.5 17.8 0.3
C A:PHE156 4.5 12.5 0.7
HG3 A:PRO136 4.5 14.1 0.3
HD21 A:LEU160 4.5 24.4 0.7
HB3 A:PRO136 4.6 13.0 0.3
CB A:VAL155 4.6 12.3 0.3
H A:PHE156 4.6 17.6 0.3
CB A:VAL155 4.6 12.1 0.7
C10 A:WWP201 4.6 10.3 0.7
CA A:PHE156 4.6 12.0 0.7
O A:ASP157 4.6 15.8 0.3
C A:ASP157 4.6 13.0 0.7
HD12 A:LEU160 4.6 21.1 0.3
HA A:VAL155 4.6 14.7 0.3
HD12 A:LEU126 4.6 10.7 0.3
H A:TYR161 4.7 15.6 0.7
CA A:VAL155 4.7 10.8 0.7
HD12 A:LEU164 4.7 26.7 0.3
HD12 A:LEU164 4.7 19.0 0.7
H181 A:WWP201 4.7 14.0 0.7
HG22 A:VAL155 4.7 14.7 0.3
CB A:PHE156 4.7 12.3 0.7
HB1 A:ALA129 4.8 16.2 0.7
CA A:ASP157 4.8 16.1 0.3
HB2 A:PRO136 4.8 13.0 0.3
CG A:ASP157 4.8 18.1 0.7
C19 A:WWP201 4.9 11.3 0.7
HA A:ASP157 4.9 16.4 0.7
C A:LEU160 4.9 18.5 0.3
HB2 A:PRO136 4.9 23.1 0.7
N A:PHE156 4.9 14.7 0.3
H A:LEU160 4.9 20.8 0.3
H A:TYR161 4.9 23.1 0.3
CB A:PRO136 4.9 19.3 0.7
HB1 A:ALA129 4.9 10.8 0.3
CD1 A:LEU164 4.9 22.2 0.3
CG A:PRO136 4.9 20.4 0.7
O A:HOH552 4.9 31.0 0.3
CA A:VAL155 5.0 12.2 0.3

Reference:

S.Gahbauer, G.J.Correy, M.Schuller, M.P.Ferla, Y.U.Doruk, M.Rachman, T.Wu, M.Diolaiti, S.Wang, R.J.Neitz, D.Fearon, D.Radchenko, Y.Moroz, J.J.Irwin, A.R.Renslo, J.C.Taylor, J.E.Gestwicki, F.Von Delft, A.Ashworth, I.Ahel, B.K.Shoichet, J.S.Fraser. Structure-Based Inhibitor Optimization For the NSP3 Macrodomain of Sars-Cov-2. Biorxiv 2022.
ISSN: ISSN 2692-8205
PubMed: 35794891
DOI: 10.1101/2022.06.27.497816
Page generated: Thu Aug 1 14:46:00 2024

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