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Fluorine in PDB 5srz: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5281440906 - (R,S) and (S,R) Isomers

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5281440906 - (R,S) and (S,R) Isomers

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5281440906 - (R,S) and (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 Z5281440906 - (R,S) and (S,R) Isomers, PDB code: 5srz 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) 44.39 / 1.05
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 88.775, 88.775, 39.477, 90, 90, 90
R / Rfree (%) 14.5 / 16.1

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 Z5281440906 - (R,S) and (S,R) Isomers (pdb code 5srz). 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 Z5281440906 - (R,S) and (S,R) Isomers, PDB code: 5srz:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5srz

Go back to Fluorine Binding Sites List in 5srz
Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5281440906 - (R,S) and (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 Z5281440906 - (R,S) and (S,R) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:15.7
occ:0.12
 F18 A:RIZ201 0.0 15.7 0.1
F18 A:RJ9202 0.1 15.9 0.1
C15 A:RJ9202 1.3 15.7 0.1
O A:HOH538 1.3 36.5 0.8
C15 A:RIZ201 1.4 15.5 0.1
O A:HOH446 1.4 15.3 0.8
C16 A:RJ9202 2.3 15.7 0.1
C14 A:RJ9202 2.4 15.7 0.1
C14 A:RIZ201 2.4 15.5 0.1
C16 A:RIZ201 2.4 15.5 0.1
H161 A:RJ9202 2.5 18.9 0.1
HB2 A:ALA52 2.6 15.6 0.2
H161 A:RIZ201 2.6 18.6 0.1
H141 A:RIZ201 2.6 18.6 0.1
H141 A:RJ9202 2.6 18.8 0.1
HB2 A:ALA52 2.7 15.8 0.8
O A:HOH536 3.1 56.5 1.0
CB A:ALA52 3.5 13.0 0.2
CB A:ALA52 3.6 13.2 0.8
C17 A:RJ9202 3.6 15.8 0.1
O A:HOH531 3.6 29.5 0.8
HB1 A:ALA52 3.6 15.6 0.2
C13 A:RJ9202 3.6 15.7 0.1
C13 A:RIZ201 3.7 15.6 0.1
C17 A:RIZ201 3.7 15.6 0.1
HB1 A:ALA52 3.8 15.8 0.8
HB3 A:ALA52 3.9 15.6 0.2
O A:HOH479 3.9 38.7 1.0
HB3 A:ALA52 4.0 15.8 0.8
O A:GLY48 4.1 12.2 0.8
C12 A:RJ9202 4.1 15.9 0.1
C12 A:RIZ201 4.2 15.8 0.1
O A:GLY48 4.2 17.7 0.2
H171 A:RJ9202 4.5 18.9 0.1
H171 A:RIZ201 4.5 18.7 0.1
HA A:ALA52 4.5 15.3 0.2
CA A:ALA52 4.5 11.3 0.8
HA A:ALA52 4.5 13.6 0.8
CA A:ALA52 4.6 12.7 0.2
H A:ALA52 4.7 12.1 0.8
H A:ALA52 4.7 16.1 0.2
HA2 A:GLY48 4.7 21.8 0.2
C A:GLY48 4.8 17.7 0.2
C A:GLY48 4.8 11.5 0.8
N19 A:RIZ201 4.8 15.6 0.1
N A:ALA52 4.9 10.1 0.8
N19 A:RJ9202 4.9 15.8 0.1
N A:ALA52 4.9 13.4 0.2
HA2 A:GLY48 5.0 15.9 0.8

Fluorine binding site 2 out of 2 in 5srz

Go back to Fluorine Binding Sites List in 5srz
Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5281440906 - (R,S) and (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 Z5281440906 - (R,S) and (S,R) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:15.9
occ:0.12
 F18 A:RJ9202 0.0 15.9 0.1
F18 A:RIZ201 0.1 15.7 0.1
O A:HOH538 1.3 36.5 0.8
C15 A:RJ9202 1.4 15.7 0.1
C15 A:RIZ201 1.4 15.5 0.1
O A:HOH446 1.5 15.3 0.8
C14 A:RJ9202 2.4 15.7 0.1
C16 A:RJ9202 2.4 15.7 0.1
C14 A:RIZ201 2.4 15.5 0.1
C16 A:RIZ201 2.5 15.5 0.1
H141 A:RIZ201 2.6 18.6 0.1
HB2 A:ALA52 2.6 15.6 0.2
H141 A:RJ9202 2.6 18.8 0.1
H161 A:RJ9202 2.6 18.9 0.1
HB2 A:ALA52 2.7 15.8 0.8
H161 A:RIZ201 2.7 18.6 0.1
O A:HOH536 3.0 56.5 1.0
CB A:ALA52 3.5 13.0 0.2
CB A:ALA52 3.6 13.2 0.8
HB1 A:ALA52 3.6 15.6 0.2
C17 A:RJ9202 3.6 15.8 0.1
O A:HOH531 3.7 29.5 0.8
C13 A:RJ9202 3.7 15.7 0.1
C13 A:RIZ201 3.7 15.6 0.1
C17 A:RIZ201 3.7 15.6 0.1
HB1 A:ALA52 3.8 15.8 0.8
O A:HOH479 3.8 38.7 1.0
HB3 A:ALA52 3.9 15.6 0.2
HB3 A:ALA52 4.0 15.8 0.8
C12 A:RJ9202 4.1 15.9 0.1
O A:GLY48 4.1 12.2 0.8
C12 A:RIZ201 4.2 15.8 0.1
O A:GLY48 4.3 17.7 0.2
HA A:ALA52 4.5 15.3 0.2
HA A:ALA52 4.5 13.6 0.8
H171 A:RJ9202 4.5 18.9 0.1
CA A:ALA52 4.5 11.3 0.8
CA A:ALA52 4.6 12.7 0.2
H171 A:RIZ201 4.6 18.7 0.1
H A:ALA52 4.7 12.1 0.8
H A:ALA52 4.7 16.1 0.2
HA2 A:GLY48 4.8 21.8 0.2
C A:GLY48 4.9 17.7 0.2
N A:ALA52 4.9 10.1 0.8
N19 A:RIZ201 4.9 15.6 0.1
N19 A:RJ9202 4.9 15.8 0.1
C A:GLY48 4.9 11.5 0.8
N A:ALA52 5.0 13.4 0.2

Reference:

G.J.Correy, J.S.Fraser. Ligand Screen Against Sars-Cov-2 NSP3 Macrodomain To Be Published.
Page generated: Thu Aug 1 14:55:49 2024

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