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Fluorine in PDB 5srs: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z2614735107 - (R) and (S) Isomers

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z2614735107 - (R) and (S) Isomers

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z2614735107 - (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 Z2614735107 - (R) and (S) Isomers, PDB code: 5srs 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) 39.68 / 1.05
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 88.723, 88.723, 39.604, 90, 90, 90
R / Rfree (%) 12.9 / 14.4

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 Z2614735107 - (R) and (S) Isomers (pdb code 5srs). 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 Z2614735107 - (R) and (S) Isomers, PDB code: 5srs:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5srs

Go back to Fluorine Binding Sites List in 5srs
Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z2614735107 - (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 Z2614735107 - (R) and (S) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:12.9
occ:0.06
 F01 A:RFI201 0.0 12.9 0.1
F01 A:RFU202 0.1 12.1 0.1
O A:HOH453 1.4 13.6 0.9
C02 A:RFI201 1.4 13.2 0.1
C02 A:RFU202 1.4 12.4 0.1
O A:HOH569 1.4 44.6 0.9
C03 A:RFU202 2.4 12.5 0.1
C03 A:RFI201 2.4 13.4 0.1
C25 A:RFU202 2.4 12.5 0.1
C25 A:RFI201 2.4 13.3 0.1
HB2 A:ALA52 2.5 12.7 1.0
H031 A:RFU202 2.6 15.0 0.1
H031 A:RFI201 2.7 16.1 0.1
H251 A:RFI201 2.7 16.0 0.1
H251 A:RFU202 2.7 15.0 0.1
O A:HOH571 2.9 9.2 0.1
O A:HOH481 3.3 47.0 0.9
O A:HOH555 3.4 34.5 0.9
CB A:ALA52 3.4 10.6 1.0
HB1 A:ALA52 3.6 12.7 1.0
O A:HOH557 3.6 40.0 1.0
C24 A:RFI201 3.7 13.4 0.1
C04 A:RFI201 3.7 13.6 0.1
C04 A:RFU202 3.7 12.7 0.1
C24 A:RFU202 3.7 12.5 0.1
HB3 A:ALA52 3.9 12.7 1.0
O A:HOH313 4.0 24.1 0.1
O A:GLY48 4.0 10.6 0.9
C23 A:RFI201 4.2 13.7 0.1
C23 A:RFU202 4.2 12.7 0.1
O A:GLY48 4.3 8.3 0.1
HA A:ALA52 4.4 11.2 1.0
CA A:ALA52 4.5 9.3 1.0
H241 A:RFI201 4.5 16.1 0.1
H A:ALA52 4.5 10.5 1.0
H241 A:RFU202 4.6 15.1 0.1
C A:GLY48 4.8 10.0 0.9
O A:HOH520 4.8 38.3 1.0
N A:ALA52 4.8 8.8 1.0
N05 A:RFU202 4.9 12.6 0.1
N05 A:RFI201 4.9 13.6 0.1
HA2 A:GLY48 5.0 13.4 0.9
C A:GLY48 5.0 8.2 0.1
HA2 A:GLY48 5.0 10.2 0.1

Fluorine binding site 2 out of 2 in 5srs

Go back to Fluorine Binding Sites List in 5srs
Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z2614735107 - (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 Z2614735107 - (R) and (S) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:12.1
occ:0.06
 F01 A:RFU202 0.0 12.1 0.1
F01 A:RFI201 0.1 12.9 0.1
O A:HOH453 1.3 13.6 0.9
C02 A:RFI201 1.4 13.2 0.1
C02 A:RFU202 1.4 12.4 0.1
O A:HOH569 1.4 44.6 0.9
C03 A:RFU202 2.4 12.5 0.1
C25 A:RFU202 2.4 12.5 0.1
C25 A:RFI201 2.4 13.3 0.1
C03 A:RFI201 2.4 13.4 0.1
HB2 A:ALA52 2.6 12.7 1.0
H251 A:RFI201 2.6 16.0 0.1
H031 A:RFU202 2.7 15.0 0.1
H251 A:RFU202 2.7 15.0 0.1
H031 A:RFI201 2.7 16.1 0.1
O A:HOH571 2.9 9.2 0.1
O A:HOH481 3.4 47.0 0.9
O A:HOH555 3.4 34.5 0.9
CB A:ALA52 3.5 10.6 1.0
HB1 A:ALA52 3.6 12.7 1.0
C24 A:RFI201 3.7 13.4 0.1
O A:HOH557 3.7 40.0 1.0
C24 A:RFU202 3.7 12.5 0.1
C04 A:RFI201 3.7 13.6 0.1
C04 A:RFU202 3.7 12.7 0.1
HB3 A:ALA52 3.9 12.7 1.0
O A:GLY48 4.0 10.6 0.9
O A:HOH313 4.1 24.1 0.1
C23 A:RFI201 4.2 13.7 0.1
C23 A:RFU202 4.2 12.7 0.1
O A:GLY48 4.3 8.3 0.1
HA A:ALA52 4.4 11.2 1.0
H241 A:RFI201 4.5 16.1 0.1
CA A:ALA52 4.5 9.3 1.0
H A:ALA52 4.5 10.5 1.0
H241 A:RFU202 4.6 15.1 0.1
C A:GLY48 4.7 10.0 0.9
N A:ALA52 4.8 8.8 1.0
O A:HOH520 4.8 38.3 1.0
HA2 A:GLY48 4.9 13.4 0.9
N05 A:RFU202 4.9 12.6 0.1
N05 A:RFI201 4.9 13.6 0.1
HA2 A:GLY48 5.0 10.2 0.1
C A:GLY48 5.0 8.2 0.1

Reference:

G.J.Correy, J.S.Fraser. Ligand Screen Against Sars-Cov-2 NSP3 Macrodomain To Be Published.
Page generated: Thu Aug 1 14:52:55 2024

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