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Fluorine in PDB 5src: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562500 - (R,R) and (R,S) Isomers

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562500 - (R,R) and (R,S) Isomers

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562500 - (R,R) and (R,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 Z5198562500 - (R,R) and (R,S) Isomers, PDB code: 5src 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) 39.66 / 1.05
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 88.677, 88.677, 39.227, 90, 90, 90
R / Rfree (%) 15.6 / 17.5

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 Z5198562500 - (R,R) and (R,S) Isomers (pdb code 5src). 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 Z5198562500 - (R,R) and (R,S) Isomers, PDB code: 5src:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5src

Go back to Fluorine Binding Sites List in 5src
Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562500 - (R,R) and (R,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 Z5198562500 - (R,R) and (R,S) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:16.5
occ:0.24
 F19 A:QIO201 0.0 16.5 0.2
F19 A:QIR202 0.0 16.9 0.2
C16 A:QIO201 1.4 15.8 0.2
C16 A:QIR202 1.4 16.3 0.2
O A:HOH495 1.4 32.3 0.5
O A:HOH429 1.4 14.5 0.5
C15 A:QIO201 2.4 15.8 0.2
C15 A:QIR202 2.4 16.3 0.2
C17 A:QIO201 2.4 15.5 0.2
C17 A:QIR202 2.4 16.0 0.2
H151 A:QIO201 2.6 18.9 0.2
HB2 A:ALA52 2.6 17.9 0.5
H171 A:QIO201 2.6 18.5 0.2
H151 A:QIR202 2.6 19.5 0.2
H171 A:QIR202 2.6 19.1 0.2
HB2 A:ALA52 2.7 15.1 0.5
CB A:ALA52 3.4 15.0 0.5
HB1 A:ALA52 3.6 17.9 0.5
CB A:ALA52 3.6 12.7 0.5
O A:HOH491 3.6 26.7 0.5
C14 A:QIO201 3.6 15.5 0.2
C14 A:QIR202 3.6 16.1 0.2
C18 A:QIO201 3.7 15.9 0.2
C18 A:QIR202 3.7 16.5 0.2
HB3 A:ALA52 3.7 17.9 0.5
HB1 A:ALA52 3.8 15.1 0.5
O A:HOH456 3.9 36.5 1.0
HB3 A:ALA52 4.0 15.1 0.5
O A:GLY48 4.1 13.0 0.5
C13 A:QIO201 4.1 16.0 0.2
C13 A:QIR202 4.1 16.7 0.2
O A:GLY48 4.2 22.2 0.5
H181 A:QIO201 4.5 19.1 0.2
H181 A:QIR202 4.5 19.8 0.2
CA A:ALA52 4.6 10.6 0.5
CA A:ALA52 4.6 14.9 0.5
HA A:ALA52 4.6 12.7 0.5
HA A:ALA52 4.7 17.8 0.5
C A:GLY48 4.7 21.7 0.5
HA2 A:GLY48 4.7 26.1 0.5
H A:ALA52 4.7 10.8 0.5
HE2 A:PHE156 4.7 25.9 0.5
H A:ALA52 4.7 20.1 0.5
HZ A:PHE156 4.7 26.0 0.5
C A:GLY48 4.8 12.4 0.5
N20 A:QIO201 4.8 15.1 0.2
N20 A:QIR202 4.8 15.8 0.2
HA A:VAL49 4.9 26.2 0.5
CZ A:PHE156 4.9 21.7 0.5
CE2 A:PHE156 4.9 21.6 0.5
N A:ALA52 4.9 9.1 0.5
HA2 A:GLY48 4.9 16.0 0.5
N A:ALA52 5.0 16.8 0.5

Fluorine binding site 2 out of 2 in 5src

Go back to Fluorine Binding Sites List in 5src
Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562500 - (R,R) and (R,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 Z5198562500 - (R,R) and (R,S) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:16.9
occ:0.24
 F19 A:QIR202 0.0 16.9 0.2
F19 A:QIO201 0.0 16.5 0.2
C16 A:QIO201 1.4 15.8 0.2
C16 A:QIR202 1.4 16.3 0.2
O A:HOH495 1.4 32.3 0.5
O A:HOH429 1.4 14.5 0.5
C15 A:QIO201 2.4 15.8 0.2
C15 A:QIR202 2.4 16.3 0.2
C17 A:QIO201 2.4 15.5 0.2
C17 A:QIR202 2.4 16.0 0.2
H151 A:QIO201 2.6 18.9 0.2
HB2 A:ALA52 2.6 17.9 0.5
H151 A:QIR202 2.6 19.5 0.2
H171 A:QIO201 2.6 18.5 0.2
H171 A:QIR202 2.6 19.1 0.2
HB2 A:ALA52 2.7 15.1 0.5
CB A:ALA52 3.4 15.0 0.5
HB1 A:ALA52 3.6 17.9 0.5
CB A:ALA52 3.6 12.7 0.5
O A:HOH491 3.6 26.7 0.5
C14 A:QIO201 3.6 15.5 0.2
C14 A:QIR202 3.6 16.1 0.2
C18 A:QIO201 3.6 15.9 0.2
C18 A:QIR202 3.6 16.5 0.2
HB3 A:ALA52 3.7 17.9 0.5
HB1 A:ALA52 3.8 15.1 0.5
O A:HOH456 3.9 36.5 1.0
HB3 A:ALA52 4.0 15.1 0.5
O A:GLY48 4.1 13.0 0.5
C13 A:QIO201 4.1 16.0 0.2
C13 A:QIR202 4.1 16.7 0.2
O A:GLY48 4.2 22.2 0.5
H181 A:QIO201 4.5 19.1 0.2
H181 A:QIR202 4.5 19.8 0.2
CA A:ALA52 4.6 10.6 0.5
CA A:ALA52 4.6 14.9 0.5
HA A:ALA52 4.6 12.7 0.5
HA A:ALA52 4.7 17.8 0.5
C A:GLY48 4.7 21.7 0.5
HE2 A:PHE156 4.7 25.9 0.5
HA2 A:GLY48 4.7 26.1 0.5
H A:ALA52 4.7 10.8 0.5
HZ A:PHE156 4.7 26.0 0.5
H A:ALA52 4.7 20.1 0.5
C A:GLY48 4.8 12.4 0.5
N20 A:QIO201 4.8 15.1 0.2
N20 A:QIR202 4.8 15.8 0.2
HA A:VAL49 4.9 26.2 0.5
CZ A:PHE156 4.9 21.7 0.5
CE2 A:PHE156 4.9 21.6 0.5
N A:ALA52 4.9 9.1 0.5
HA2 A:GLY48 4.9 16.0 0.5
N A:ALA52 5.0 16.8 0.5

Reference:

G.J.Correy, J.S.Fraser. Ligand Screen Against Sars-Cov-2 NSP3 Macrodomain To Be Published.
Page generated: Tue Jul 15 07:36:28 2025

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