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Fluorine in PDB 5srb: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562532 - (R) and (S) Isomers

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562532 - (R) and (S) Isomers

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562532 - (R) and (S) Isomers:
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 Z5198562532 - (R) and (S) Isomers, PDB code: 5srb 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) 36.12 / 1.05
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 88.735, 88.735, 39.544, 90, 90, 90
R / Rfree (%) 13.9 / 15.8

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 Z5198562532 - (R) and (S) Isomers (pdb code 5srb). 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 NSP3 Macrodomain in Complex with Z5198562532 - (R) and (S) Isomers, PDB code: 5srb:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5srb

Go back to Fluorine Binding Sites List in 5srb
Fluorine binding site 1 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562532 - (R) and (S) Isomers


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 Z5198562532 - (R) and (S) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:18.8
occ:0.08
 F1 A:R0R201 0.0 18.8 0.1
F1 A:R0W202 0.0 18.7 0.1
O A:HOH548 0.8 39.8 0.8
C9 A:R0W202 1.4 18.6 0.1
C9 A:R0R201 1.4 18.6 0.1
O A:HOH442 2.2 15.5 0.8
C8 A:R0W202 2.4 18.4 0.1
C10 A:R0W202 2.4 18.6 0.1
C8 A:R0R201 2.4 18.5 0.1
C10 A:R0R201 2.4 18.6 0.1
H4 A:R0W202 2.6 22.3 0.1
H3 A:R0W202 2.6 22.1 0.1
H3 A:R0R201 2.6 22.2 0.1
H4 A:R0R201 2.6 22.3 0.1
HB2 A:ALA52 2.6 15.8 1.0
O A:HOH465 2.7 43.9 0.8
O A:HOH547 2.7 53.9 1.0
HB1 A:ALA52 3.1 15.8 1.0
CB A:ALA52 3.3 13.2 1.0
O A:HOH488 3.3 36.4 1.0
C7 A:R0W202 3.6 18.3 0.1
C7 A:R0R201 3.6 18.4 0.1
C11 A:R0W202 3.7 18.6 0.1
C11 A:R0R201 3.7 18.6 0.1
O A:HOH540 3.8 32.2 0.8
HB3 A:ALA52 3.9 15.8 1.0
C6 A:R0W202 4.2 18.4 0.1
C6 A:R0R201 4.2 18.5 0.1
HA A:ALA52 4.2 14.0 1.0
CA A:ALA52 4.4 11.7 1.0
H5 A:R0W202 4.4 22.3 0.1
H5 A:R0R201 4.4 22.3 0.1
O A:GLY48 4.6 12.8 1.0
H A:ALA52 4.8 12.8 1.0
N2 A:R0W202 4.8 18.1 0.1
N2 A:R0R201 4.8 18.2 0.1
O A:HOH510 4.9 42.3 1.0
N A:ALA52 4.9 10.7 1.0

Fluorine binding site 2 out of 4 in 5srb

Go back to Fluorine Binding Sites List in 5srb
Fluorine binding site 2 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562532 - (R) and (S) Isomers


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 Z5198562532 - (R) and (S) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:19.1
occ:0.08
 F2 A:R0R201 0.0 19.1 0.1
F2 A:R0W202 0.6 18.6 0.1
C2 A:R0R201 1.4 18.9 0.1
C2 A:R0W202 1.7 18.5 0.1
O A:HOH522 2.1 30.8 0.8
C15 A:R0W202 2.3 18.4 0.1
H1 A:R0R201 2.3 22.5 0.1
C3 A:R0R201 2.3 18.7 0.1
C15 A:R0R201 2.4 18.8 0.1
C1 A:R0R201 2.4 19.0 0.1
O A:HOH543 2.5 33.2 0.8
H8 A:R0W202 2.6 22.1 0.1
H12 A:R0W202 2.6 22.1 0.1
O3 A:R0R201 2.6 19.2 0.1
C3 A:R0W202 2.7 18.5 0.1
O A:HOH445 2.7 22.8 0.9
C17 A:R0W202 2.7 18.4 0.1
C1 A:R0W202 2.8 18.7 0.1
C14 A:R0W202 2.8 18.4 0.1
H2 A:R0W202 2.8 22.2 0.1
H9 A:R0R201 2.9 22.5 0.1
C14 A:R0R201 2.9 18.7 0.1
H13 A:R0W202 3.0 22.1 0.1
O2 A:R0W202 3.0 18.7 0.1
H13 A:R0R201 3.1 22.6 0.1
N1 A:R0R201 3.1 18.7 0.1
N1 A:R0W202 3.1 18.4 0.1
C17 A:R0R201 3.1 18.8 0.1
H2 A:R0R201 3.1 22.5 0.1
HB3 A:PHE156 3.3 26.4 1.0
H12 A:R0R201 3.4 22.6 0.1
O A:HOH500 3.4 30.8 0.8
H1 A:R0W202 3.5 22.2 0.1
O2 A:R0R201 3.5 18.9 0.1
HD2 A:PHE156 3.6 30.2 1.0
C16 A:R0R201 3.7 18.8 0.1
C16 A:R0W202 3.7 18.4 0.1
O A:HOH464 3.7 17.9 0.8
H9 A:R0W202 3.7 22.1 0.1
H8 A:R0R201 3.9 22.5 0.1
H11 A:R0R201 3.9 22.5 0.1
O A:HOH534 3.9 39.4 0.9
O3 A:R0W202 3.9 18.7 0.1
H11 A:R0W202 4.0 22.1 0.1
C4 A:R0R201 4.0 18.5 0.1
C4 A:R0W202 4.0 18.4 0.1
O1 A:R0W202 4.0 18.4 0.1
HA2 A:GLY130 4.1 16.5 0.8
HB2 A:ASP157 4.1 20.9 0.2
HA3 A:GLY130 4.1 16.5 0.8
H5 A:R0R201 4.2 22.3 0.1
H5 A:R0W202 4.2 22.3 0.1
CB A:PHE156 4.2 22.0 1.0
O1 A:R0R201 4.3 18.8 0.1
H10 A:R0R201 4.3 22.5 0.1
HB2 A:ASP157 4.3 27.5 0.8
HB2 A:PHE156 4.3 26.4 1.0
H A:ASP157 4.3 23.0 0.2
H10 A:R0W202 4.3 22.1 0.1
HA3 A:GLY130 4.4 16.1 0.2
CD2 A:PHE156 4.4 25.2 1.0
H A:ASP157 4.5 23.6 0.8
O A:HOH426 4.6 16.1 0.8
CA A:GLY130 4.6 13.7 0.8
C5 A:R0R201 4.6 18.4 0.1
C5 A:R0W202 4.6 18.3 0.1
O A:HOH540 4.7 32.2 0.8
H A:PHE156 4.7 22.3 1.0
N4 A:R0W202 4.7 18.3 0.1
C11 A:R0R201 4.7 18.6 0.1
N4 A:R0R201 4.7 18.4 0.1
C11 A:R0W202 4.8 18.6 0.1
HA2 A:GLY130 4.8 16.1 0.2
CG A:PHE156 4.8 24.4 1.0
C6 A:R0R201 4.9 18.5 0.1
C6 A:R0W202 4.9 18.4 0.1
N A:ASP157 5.0 19.1 0.2

Fluorine binding site 3 out of 4 in 5srb

Go back to Fluorine Binding Sites List in 5srb
Fluorine binding site 3 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562532 - (R) and (S) Isomers


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 Z5198562532 - (R) and (S) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:18.7
occ:0.08
 F1 A:R0W202 0.0 18.7 0.1
F1 A:R0R201 0.0 18.8 0.1
O A:HOH548 0.8 39.8 0.8
C9 A:R0W202 1.4 18.6 0.1
C9 A:R0R201 1.4 18.6 0.1
O A:HOH442 2.2 15.5 0.8
C8 A:R0W202 2.4 18.4 0.1
C10 A:R0W202 2.4 18.6 0.1
C8 A:R0R201 2.4 18.5 0.1
C10 A:R0R201 2.4 18.6 0.1
H3 A:R0W202 2.6 22.1 0.1
H4 A:R0W202 2.6 22.3 0.1
H3 A:R0R201 2.6 22.2 0.1
H4 A:R0R201 2.6 22.3 0.1
HB2 A:ALA52 2.6 15.8 1.0
O A:HOH465 2.7 43.9 0.8
O A:HOH547 2.7 53.9 1.0
HB1 A:ALA52 3.2 15.8 1.0
O A:HOH488 3.3 36.4 1.0
CB A:ALA52 3.3 13.2 1.0
C7 A:R0W202 3.6 18.3 0.1
C7 A:R0R201 3.7 18.4 0.1
C11 A:R0W202 3.7 18.6 0.1
C11 A:R0R201 3.7 18.6 0.1
O A:HOH540 3.8 32.2 0.8
HB3 A:ALA52 3.9 15.8 1.0
C6 A:R0W202 4.2 18.4 0.1
HA A:ALA52 4.2 14.0 1.0
C6 A:R0R201 4.2 18.5 0.1
CA A:ALA52 4.4 11.7 1.0
H5 A:R0W202 4.4 22.3 0.1
H5 A:R0R201 4.4 22.3 0.1
O A:GLY48 4.6 12.8 1.0
H A:ALA52 4.8 12.8 1.0
N2 A:R0W202 4.8 18.1 0.1
N2 A:R0R201 4.8 18.2 0.1
O A:HOH510 4.9 42.3 1.0
N A:ALA52 4.9 10.7 1.0

Fluorine binding site 4 out of 4 in 5srb

Go back to Fluorine Binding Sites List in 5srb
Fluorine binding site 4 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562532 - (R) and (S) Isomers


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 NSP3 Macrodomain in Complex with Z5198562532 - (R) and (S) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:18.6
occ:0.08
 F2 A:R0W202 0.0 18.6 0.1
F2 A:R0R201 0.6 19.1 0.1
C2 A:R0W202 1.4 18.5 0.1
C2 A:R0R201 1.5 18.9 0.1
C15 A:R0R201 2.0 18.8 0.1
O A:HOH522 2.3 30.8 0.8
C3 A:R0W202 2.3 18.5 0.1
O A:HOH445 2.3 22.8 0.9
C1 A:R0W202 2.4 18.7 0.1
C15 A:R0W202 2.4 18.4 0.1
H2 A:R0W202 2.4 22.2 0.1
H9 A:R0R201 2.4 22.5 0.1
C3 A:R0R201 2.5 18.7 0.1
C14 A:R0R201 2.6 18.7 0.1
H1 A:R0R201 2.6 22.5 0.1
C17 A:R0R201 2.6 18.8 0.1
C1 A:R0R201 2.6 19.0 0.1
H13 A:R0R201 2.7 22.6 0.1
O2 A:R0W202 2.7 18.7 0.1
O A:HOH543 2.7 33.2 0.8
H12 A:R0R201 2.8 22.6 0.1
H8 A:R0W202 2.9 22.1 0.1
H12 A:R0W202 2.9 22.1 0.1
C14 A:R0W202 2.9 18.4 0.1
N1 A:R0R201 3.0 18.7 0.1
O3 A:R0R201 3.0 19.2 0.1
N1 A:R0W202 3.0 18.4 0.1
C17 A:R0W202 3.1 18.4 0.1
O A:HOH500 3.1 30.8 0.8
H1 A:R0W202 3.1 22.2 0.1
HB3 A:PHE156 3.3 26.4 1.0
H2 A:R0R201 3.3 22.5 0.1
O A:HOH534 3.4 39.4 0.9
O A:HOH464 3.4 17.9 0.8
H13 A:R0W202 3.4 22.1 0.1
C16 A:R0R201 3.4 18.8 0.1
H8 A:R0R201 3.5 22.5 0.1
O3 A:R0W202 3.5 18.7 0.1
C16 A:R0W202 3.7 18.4 0.1
H11 A:R0R201 3.7 22.5 0.1
O2 A:R0R201 3.8 18.9 0.1
H11 A:R0W202 3.9 22.1 0.1
O1 A:R0R201 3.9 18.8 0.1
H9 A:R0W202 3.9 22.1 0.1
C4 A:R0R201 3.9 18.5 0.1
C4 A:R0W202 3.9 18.4 0.1
HD2 A:PHE156 4.0 30.2 1.0
HB2 A:ASP157 4.0 20.9 0.2
H10 A:R0R201 4.0 22.5 0.1
HA2 A:GLY130 4.1 16.5 0.8
HA3 A:GLY130 4.1 16.5 0.8
H A:ASP157 4.1 23.0 0.2
O1 A:R0W202 4.2 18.4 0.1
CB A:PHE156 4.2 22.0 1.0
HB2 A:ASP157 4.2 27.5 0.8
H A:ASP157 4.3 23.6 0.8
HB2 A:PHE156 4.3 26.4 1.0
HA3 A:GLY130 4.3 16.1 0.2
H10 A:R0W202 4.3 22.1 0.1
H A:PHE156 4.4 22.3 1.0
CA A:GLY130 4.5 13.7 0.8
N4 A:R0W202 4.5 18.3 0.1
H5 A:R0R201 4.5 22.3 0.1
N4 A:R0R201 4.5 18.4 0.1
H5 A:R0W202 4.6 22.3 0.1
HD23 A:LEU160 4.6 24.7 1.0
C5 A:R0R201 4.7 18.4 0.1
C5 A:R0W202 4.7 18.3 0.1
HA2 A:GLY130 4.7 16.1 0.2
CD2 A:PHE156 4.7 25.2 1.0
O A:HOH426 4.8 16.1 0.8
H A:GLY130 4.8 15.6 0.8
N A:ASP157 4.8 19.1 0.2
N A:ASP157 4.9 19.7 0.8
CB A:ASP157 4.9 17.4 0.2
O A:HOH424 4.9 27.9 0.9
N A:GLY130 4.9 13.0 0.8
HB3 A:ASP157 4.9 27.5 0.8
HB3 A:ASP157 4.9 20.9 0.2
CG A:PHE156 5.0 24.4 1.0
N A:PHE156 5.0 18.6 1.0
O A:HOH540 5.0 32.2 0.8

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 14:49:02 2024

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