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Fluorine in PDB 5sqp: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5028367859 - (S) Isomer

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5028367859 - (S) Isomer

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5028367859 - (S) Isomer:
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 Z5028367859 - (S) Isomer, PDB code: 5sqp 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) 39.72 / 1.05
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 88.807, 88.807, 39.549, 90, 90, 90
R / Rfree (%) 14.3 / 15.9

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 Z5028367859 - (S) Isomer (pdb code 5sqp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5028367859 - (S) Isomer, PDB code: 5sqp:

Fluorine binding site 1 out of 1 in 5sqp

Go back to Fluorine Binding Sites List in 5sqp
Fluorine binding site 1 out of 1 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5028367859 - (S) Isomer


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 Z5028367859 - (S) Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:19.1
occ:0.28
 F24 A:QTO201 0.0 19.1 0.3
O A:HOH430 1.0 15.5 0.7
C03 A:QTO201 1.4 18.4 0.3
O A:HOH458 2.1 13.8 0.7
H041 A:QTO201 2.3 20.5 0.3
C04 A:QTO201 2.4 17.1 0.3
H211 A:QTO201 2.4 20.3 0.3
C02 A:QTO201 2.4 19.5 0.3
C20 A:QTO201 2.5 17.6 0.3
O01 A:QTO201 2.6 19.6 0.3
HA3 A:GLY48 2.7 17.0 0.3
H A:VAL49 2.7 13.2 0.7
H042 A:QTO201 2.8 20.5 0.3
O A:HOH534 2.8 29.2 0.7
HA3 A:GLY48 2.8 14.7 0.7
H A:ILE131 2.9 15.6 0.7
C21 A:QTO201 2.9 16.9 0.3
HA2 A:GLY48 2.9 14.7 0.7
HG12 A:ILE131 2.9 22.1 0.3
HA3 A:GLY130 3.0 16.2 0.7
HG12 A:ILE131 3.1 19.5 0.7
HA2 A:GLY48 3.1 17.0 0.3
CA A:GLY48 3.2 12.2 0.7
HG23 A:VAL49 3.2 17.5 0.7
O A:HOH480 3.3 25.5 0.3
H A:VAL49 3.3 15.4 0.3
HD13 A:ILE131 3.3 22.7 0.3
H231 A:QTO201 3.3 21.6 0.3
CA A:GLY48 3.4 14.2 0.3
N A:VAL49 3.4 11.0 0.7
C23 A:QTO201 3.4 18.0 0.3
HG23 A:ILE131 3.6 18.9 0.7
H212 A:QTO201 3.6 20.3 0.3
O25 A:QTO201 3.6 20.0 0.3
N05 A:QTO201 3.6 16.1 0.3
C19 A:QTO201 3.7 17.2 0.3
N A:ILE131 3.7 13.0 0.7
H A:ILE131 3.7 18.8 0.3
C A:GLY48 3.8 11.3 0.7
CG1 A:ILE131 3.8 18.4 0.3
C22 A:QTO201 3.8 17.7 0.3
O A:HOH508 3.9 30.8 0.7
N A:VAL49 3.9 12.8 0.3
CD1 A:ILE131 3.9 18.9 0.3
CA A:GLY130 4.0 13.5 0.7
O A:HOH422 4.0 12.7 0.7
CG1 A:ILE131 4.0 16.2 0.7
HG23 A:VAL49 4.0 15.7 0.3
H222 A:QTO201 4.1 21.3 0.3
C A:GLY48 4.2 13.8 0.3
CG2 A:VAL49 4.2 14.5 0.7
HD11 A:ILE131 4.2 22.7 0.3
HG23 A:ILE131 4.3 20.8 0.3
O A:HOH418 4.3 14.0 0.3
HG13 A:ILE131 4.3 22.1 0.3
HA3 A:GLY130 4.3 18.2 0.3
C A:GLY130 4.4 13.0 0.7
O A:HOH545 4.4 35.4 0.7
HA2 A:GLY130 4.4 16.2 0.7
H191 A:QTO201 4.4 20.7 0.3
H232 A:QTO201 4.4 21.6 0.3
HD1 A:PHE132 4.4 20.0 0.3
HB A:VAL49 4.5 15.2 0.7
O A:ALA129 4.5 11.5 0.7
CG2 A:ILE131 4.5 15.7 0.7
HE1 A:PHE132 4.5 20.5 0.3
N A:GLY48 4.5 15.0 0.3
H192 A:QTO201 4.5 20.7 0.3
N A:GLY48 4.5 12.3 0.7
N A:ILE131 4.5 15.6 0.3
HD13 A:ILE131 4.5 21.6 0.7
HG13 A:ILE131 4.5 19.5 0.7
O A:HOH425 4.5 12.7 0.7
O A:HOH356 4.5 18.0 0.7
CA A:VAL49 4.6 11.2 0.7
CB A:ILE131 4.6 14.9 0.7
HG21 A:VAL49 4.6 17.5 0.7
CB A:VAL49 4.7 12.7 0.7
HD1 A:PHE132 4.7 14.7 0.7
H181 A:QTO201 4.7 16.5 0.3
HG22 A:VAL49 4.7 17.5 0.7
CA A:ILE131 4.7 12.9 0.7
CD1 A:ILE131 4.7 18.0 0.7
C06 A:QTO201 4.8 14.6 0.3
H A:GLY48 4.8 18.0 0.3
HD12 A:ILE131 4.8 22.7 0.3
H A:PHE132 4.8 13.9 0.7
HD11 A:ILE131 4.8 21.6 0.7
H A:GLY48 4.8 14.8 0.7
CB A:ILE131 4.8 17.3 0.3
H221 A:QTO201 4.8 21.3 0.3
N A:GLY130 4.9 12.9 0.7
CG2 A:ILE131 4.9 17.3 0.3
HB A:VAL49 4.9 15.3 0.3
HA A:VAL49 4.9 13.4 0.7
HG21 A:ILE131 4.9 18.9 0.7
HG21 A:ILE131 4.9 20.8 0.3
CG2 A:VAL49 5.0 13.1 0.3
O A:GLY48 5.0 11.6 0.7
C A:ALA129 5.0 11.3 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: Tue Jul 15 07:34:58 2025

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