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Fluorine in PDB 5sro: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (R) and (S) Isomers

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (R) and (S) Isomers

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (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 Z5198562509 - (R) and (S) Isomers, PDB code: 5sro 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) 39.69 / 1.05
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 88.753, 88.753, 39.576, 90, 90, 90
R / Rfree (%) 13.6 / 15.3

Other elements in 5sro:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (R) and (S) Isomers also contains other interesting chemical elements:

Bromine (Br) 2 atoms

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 Z5198562509 - (R) and (S) Isomers (pdb code 5sro). 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 Z5198562509 - (R) and (S) Isomers, PDB code: 5sro:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5sro

Go back to Fluorine Binding Sites List in 5sro
Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (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 Z5198562509 - (R) and (S) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:15.3
occ:0.06
 F25 A:RCR201 0.0 15.3 0.1
H201 A:RD6202 1.1 17.5 0.1
C03 A:RCR201 1.3 15.2 0.1
C21 A:RD6202 1.4 14.7 0.1
C20 A:RD6202 1.5 14.6 0.1
O A:HOH545 1.6 27.4 0.8
H202 A:RD6202 2.1 17.5 0.1
C24 A:RD6202 2.1 14.8 0.1
HA3 A:GLY130 2.2 15.5 0.8
H241 A:RD6202 2.2 17.8 0.1
C04 A:RCR201 2.4 15.1 0.1
C02 A:RCR201 2.4 15.1 0.1
C03 A:RD6202 2.4 14.5 0.1
C21 A:RCR201 2.4 15.2 0.1
HA3 A:GLY130 2.4 17.3 0.2
O A:HOH530 2.4 31.8 0.8
H042 A:RCR201 2.5 18.1 0.1
O26 A:RCR201 2.6 15.1 0.1
F25 A:RD6202 2.6 14.4 0.1
N05 A:RD6202 2.7 14.5 0.1
HA2 A:GLY130 2.7 15.5 0.8
C22 A:RD6202 2.8 14.9 0.1
CA A:GLY130 2.8 13.0 0.8
H242 A:RD6202 2.8 17.8 0.1
H242 A:RCR201 2.9 18.2 0.1
C24 A:RCR201 3.0 15.2 0.1
H221 A:RD6202 3.0 17.8 0.1
H201 A:RCR201 3.0 18.1 0.1
C20 A:RCR201 3.0 15.2 0.1
C04 A:RD6202 3.1 14.5 0.1
H041 A:RCR201 3.1 18.1 0.1
O A:HOH452 3.2 15.3 0.8
C23 A:RD6202 3.2 14.9 0.1
CA A:GLY130 3.3 14.4 0.2
N A:GLY130 3.3 12.2 0.8
H241 A:RCR201 3.4 18.2 0.1
N05 A:RCR201 3.4 15.1 0.1
HA2 A:GLY130 3.4 17.3 0.2
N19 A:RD6202 3.4 14.1 0.1
C06 A:RD6202 3.4 14.3 0.1
H A:GLY130 3.5 14.6 0.8
O01 A:RCR201 3.5 15.2 0.1
O A:HOH553 3.5 34.5 0.8
H222 A:RD6202 3.6 17.8 0.1
H231 A:RD6202 3.7 17.9 0.1
H041 A:RD6202 3.7 17.4 0.1
O A:HOH522 3.7 34.7 0.9
C22 A:RCR201 3.8 15.2 0.1
N A:GLY130 3.8 14.1 0.2
C02 A:RD6202 3.8 14.3 0.1
H042 A:RD6202 3.9 17.4 0.1
H A:GLY130 4.0 16.8 0.2
H221 A:RCR201 4.0 18.2 0.1
H A:ILE131 4.1 14.8 0.8
C A:ALA129 4.1 10.9 0.8
H232 A:RD6202 4.1 17.9 0.1
H202 A:RCR201 4.1 18.1 0.1
O A:HOH451 4.1 26.3 0.9
O A:HOH472 4.1 20.2 0.8
C A:GLY130 4.1 12.1 0.8
H A:ILE131 4.1 18.1 0.2
C23 A:RCR201 4.3 15.2 0.1
O A:HOH323 4.3 26.5 1.0
O A:HOH354 4.3 16.7 0.8
HB1 A:ALA129 4.4 14.7 0.8
O A:ALA129 4.4 10.9 0.8
HG23 A:VAL49 4.4 16.2 0.8
HB3 A:ALA129 4.4 14.7 0.8
C A:ALA129 4.5 13.7 0.2
N A:ILE131 4.5 12.4 0.8
H222 A:RCR201 4.5 18.2 0.1
O01 A:RD6202 4.5 14.3 0.1
O26 A:RD6202 4.5 14.0 0.1
C A:GLY130 4.5 14.9 0.2
C06 A:RCR201 4.5 14.9 0.1
HB3 A:ALA129 4.6 15.5 0.2
C18 A:RD6202 4.7 14.2 0.1
N A:ILE131 4.7 15.2 0.2
O A:ALA129 4.7 14.0 0.2
H131 A:RCR201 4.7 18.1 0.1
O A:HOH560 4.7 14.8 0.1
C07 A:RD6202 4.7 14.3 0.1
CB A:ALA129 4.8 12.3 0.8
O A:HOH456 4.9 12.4 0.8
H231 A:RCR201 4.9 18.2 0.1

Fluorine binding site 2 out of 2 in 5sro

Go back to Fluorine Binding Sites List in 5sro
Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (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 Z5198562509 - (R) and (S) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:14.4
occ:0.10
 F25 A:RD6202 0.0 14.4 0.1
C03 A:RD6202 1.3 14.5 0.1
H042 A:RCR201 1.9 18.1 0.1
O A:HOH451 2.3 26.3 0.9
H041 A:RD6202 2.3 17.4 0.1
C04 A:RD6202 2.3 14.5 0.1
C02 A:RD6202 2.4 14.3 0.1
C21 A:RD6202 2.4 14.7 0.1
O A:HOH553 2.5 34.5 0.8
O A:HOH545 2.5 27.4 0.8
O01 A:RD6202 2.6 14.3 0.1
F25 A:RCR201 2.6 15.3 0.1
HB3 A:PHE156 2.8 25.3 0.8
C04 A:RCR201 2.9 15.1 0.1
H242 A:RD6202 2.9 17.8 0.1
H201 A:RD6202 3.0 17.5 0.1
C24 A:RD6202 3.1 14.8 0.1
H042 A:RD6202 3.1 17.4 0.1
C20 A:RD6202 3.2 14.6 0.1
N05 A:RD6202 3.2 14.5 0.1
HD2 A:PHE156 3.3 28.4 0.8
C03 A:RCR201 3.3 15.2 0.1
HB3 A:PHE156 3.3 20.6 0.2
O A:HOH472 3.4 20.2 0.8
HB2 A:ASP157 3.4 22.1 0.2
O26 A:RD6202 3.5 14.0 0.1
O A:HOH530 3.6 31.8 0.8
H041 A:RCR201 3.6 18.1 0.1
O A:HOH522 3.6 34.7 0.9
H201 A:RCR201 3.6 18.1 0.1
HD2 A:PHE156 3.7 21.1 0.2
H241 A:RD6202 3.7 17.8 0.1
CB A:PHE156 3.7 21.1 0.8
C06 A:RD6202 3.7 14.3 0.1
N05 A:RCR201 3.8 15.1 0.1
H A:ASP157 3.8 21.2 0.2
C22 A:RD6202 3.9 14.9 0.1
HB2 A:PHE156 3.9 25.3 0.8
H A:ASP157 3.9 24.2 0.8
HB2 A:ASP157 4.0 27.4 0.8
C20 A:RCR201 4.0 15.2 0.1
H A:PHE156 4.0 21.7 0.8
CD2 A:PHE156 4.1 23.7 0.8
H222 A:RD6202 4.1 17.8 0.1
N19 A:RD6202 4.2 14.1 0.1
C06 A:RCR201 4.2 14.9 0.1
H202 A:RD6202 4.2 17.5 0.1
C23 A:RD6202 4.3 14.9 0.1
CB A:PHE156 4.3 17.2 0.2
CB A:ASP157 4.3 18.4 0.2
C21 A:RCR201 4.3 15.2 0.1
CG A:PHE156 4.4 22.9 0.8
C02 A:RCR201 4.4 15.1 0.1
CD2 A:PHE156 4.4 17.6 0.2
N A:ASP157 4.4 17.7 0.2
HB3 A:ASP157 4.4 22.1 0.2
C07 A:RD6202 4.5 14.3 0.1
N A:ASP157 4.5 20.2 0.8
O A:HOH548 4.5 29.6 0.8
HD23 A:LEU160 4.5 19.6 0.2
HD22 A:LEU160 4.5 19.6 0.2
O26 A:RCR201 4.6 15.1 0.1
H131 A:RCR201 4.6 18.1 0.1
H221 A:RD6202 4.6 17.8 0.1
H131 A:RD6202 4.6 17.9 0.1
N A:PHE156 4.7 18.1 0.8
H232 A:RD6202 4.7 17.9 0.1
HA2 A:GLY130 4.7 15.5 0.8
HA3 A:GLY130 4.7 15.5 0.8
H A:PHE156 4.7 20.1 0.2
CA A:PHE156 4.7 19.7 0.8
C07 A:RCR201 4.7 14.9 0.1
HB2 A:PHE156 4.7 20.6 0.2
HA3 A:GLY130 4.7 17.3 0.2
CB A:ASP157 4.8 22.9 0.8
HB3 A:ASP157 4.8 27.4 0.8
CG A:PHE156 4.8 17.4 0.2
N19 A:RCR201 4.8 14.7 0.1
HD23 A:LEU160 4.9 23.2 0.8
C A:PHE156 5.0 20.1 0.8
CA A:ASP157 5.0 18.3 0.2
CD2 A:LEU160 5.0 16.4 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 14:52:54 2024

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