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Fluorine in PDB 5sr7: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z4914649782 - (R,R,S) and (S,S,R) Isomers

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z4914649782 - (R,R,S) and (S,S,R) Isomers

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z4914649782 - (R,R,S) and (S,S,R) 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 Z4914649782 - (R,R,S) and (S,S,R) Isomers, PDB code: 5sr7 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) 44.45 / 1.05
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 88.896, 88.896, 39.453, 90, 90, 90
R / Rfree (%) 15.4 / 17.4

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 Z4914649782 - (R,R,S) and (S,S,R) Isomers (pdb code 5sr7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z4914649782 - (R,R,S) and (S,S,R) Isomers, PDB code: 5sr7:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5sr7

Go back to Fluorine Binding Sites List in 5sr7
Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z4914649782 - (R,R,S) and (S,S,R) 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 Z4914649782 - (R,R,S) and (S,S,R) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:12.7
occ:0.17
 F1 A:QZO201 0.0 12.7 0.2
F1 A:QZX202 0.0 13.9 0.2
O A:HOH538 1.2 33.9 0.7
C11 A:QZX202 1.4 13.9 0.2
C11 A:QZO201 1.4 12.8 0.2
O A:HOH444 1.5 17.3 0.7
C10 A:QZX202 2.3 13.9 0.2
C10 A:QZO201 2.4 12.8 0.2
C12 A:QZO201 2.4 12.7 0.2
C12 A:QZX202 2.4 13.7 0.2
H8 A:QZO201 2.5 15.2 0.2
H7 A:QZX202 2.5 16.7 0.2
H8 A:QZX202 2.6 16.4 0.2
H7 A:QZO201 2.6 15.4 0.2
HB2 A:ALA52 2.6 13.3 0.3
HB2 A:ALA52 2.8 18.9 0.7
O A:HOH535 3.1 18.7 0.3
O A:HOH463 3.4 48.9 0.7
O A:HOH524 3.4 32.5 0.7
CB A:ALA52 3.4 11.1 0.3
HB1 A:ALA52 3.5 13.3 0.3
C9 A:QZX202 3.6 14.1 0.2
C9 A:QZO201 3.6 12.8 0.2
C13 A:QZO201 3.6 12.8 0.2
C13 A:QZX202 3.6 13.9 0.2
CB A:ALA52 3.7 15.8 0.7
O A:HOH526 3.7 40.2 1.0
HB3 A:ALA52 3.8 13.3 0.3
HB1 A:ALA52 3.9 18.9 0.7
C8 A:QZX202 4.1 14.4 0.2
C8 A:QZO201 4.1 13.0 0.2
HB3 A:ALA52 4.1 18.9 0.7
O A:HOH319 4.1 31.5 0.3
O A:GLY48 4.2 13.1 0.7
O A:GLY48 4.3 20.4 0.3
H9 A:QZO201 4.4 15.3 0.2
H9 A:QZX202 4.4 16.7 0.2
CA A:ALA52 4.6 13.3 0.7
CA A:ALA52 4.6 11.0 0.3
HA A:ALA52 4.6 13.2 0.3
HA2 A:GLY48 4.6 24.5 0.3
HA A:ALA52 4.6 15.9 0.7
O A:HOH491 4.7 34.1 0.7
H A:ALA52 4.8 13.7 0.3
C A:GLY48 4.8 19.8 0.3
H A:ALA52 4.8 14.8 0.7
N2 A:QZX202 4.8 14.1 0.2
N2 A:QZO201 4.9 12.5 0.2
C A:GLY48 4.9 12.2 0.7
N A:ALA52 5.0 12.3 0.7

Fluorine binding site 2 out of 2 in 5sr7

Go back to Fluorine Binding Sites List in 5sr7
Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z4914649782 - (R,R,S) and (S,S,R) 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 Z4914649782 - (R,R,S) and (S,S,R) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:13.9
occ:0.17
 F1 A:QZX202 0.0 13.9 0.2
F1 A:QZO201 0.0 12.7 0.2
O A:HOH538 1.2 33.9 0.7
C11 A:QZX202 1.4 13.9 0.2
C11 A:QZO201 1.4 12.8 0.2
O A:HOH444 1.5 17.3 0.7
C10 A:QZX202 2.4 13.9 0.2
C12 A:QZO201 2.4 12.7 0.2
C12 A:QZX202 2.4 13.7 0.2
C10 A:QZO201 2.4 12.8 0.2
H8 A:QZO201 2.5 15.2 0.2
H8 A:QZX202 2.5 16.4 0.2
H7 A:QZX202 2.6 16.7 0.2
H7 A:QZO201 2.6 15.4 0.2
HB2 A:ALA52 2.6 13.3 0.3
HB2 A:ALA52 2.8 18.9 0.7
O A:HOH535 3.1 18.7 0.3
O A:HOH463 3.4 48.9 0.7
O A:HOH524 3.4 32.5 0.7
CB A:ALA52 3.5 11.1 0.3
HB1 A:ALA52 3.6 13.3 0.3
C9 A:QZX202 3.6 14.1 0.2
C9 A:QZO201 3.6 12.8 0.2
C13 A:QZO201 3.6 12.8 0.2
C13 A:QZX202 3.6 13.9 0.2
CB A:ALA52 3.7 15.8 0.7
O A:HOH526 3.7 40.2 1.0
HB3 A:ALA52 3.8 13.3 0.3
HB1 A:ALA52 3.9 18.9 0.7
C8 A:QZX202 4.1 14.4 0.2
C8 A:QZO201 4.1 13.0 0.2
HB3 A:ALA52 4.1 18.9 0.7
O A:HOH319 4.2 31.5 0.3
O A:GLY48 4.2 13.1 0.7
O A:GLY48 4.2 20.4 0.3
H9 A:QZO201 4.4 15.3 0.2
H9 A:QZX202 4.4 16.7 0.2
HA2 A:GLY48 4.6 24.5 0.3
CA A:ALA52 4.6 13.3 0.7
CA A:ALA52 4.6 11.0 0.3
HA A:ALA52 4.6 13.2 0.3
HA A:ALA52 4.7 15.9 0.7
O A:HOH491 4.7 34.1 0.7
C A:GLY48 4.8 19.8 0.3
H A:ALA52 4.8 13.7 0.3
H A:ALA52 4.8 14.8 0.7
N2 A:QZX202 4.9 14.1 0.2
N2 A:QZO201 4.9 12.5 0.2
C A:GLY48 4.9 12.2 0.7
N A:ALA52 5.0 12.3 0.7

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 14:47:53 2024

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