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Fluorine in PDB 5srp: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) 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 Z5340019182 - (R) Isomer, PDB code: 5srp 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 (°) 88.757, 88.757, 39.644, 90, 90, 90
R / Rfree (%) 13.2 / 15

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 Z5340019182 - (R) Isomer (pdb code 5srp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer, PDB code: 5srp:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5srp

Go back to Fluorine Binding Sites List in 5srp
Fluorine binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) 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 Z5340019182 - (R) Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:9.3
occ:0.14
F1 A:TFA202 0.0 9.3 0.1
C2 A:TFA202 1.4 8.3 0.1
F2 A:TFA202 2.2 8.8 0.1
F3 A:TFA202 2.2 8.9 0.1
O A:HOH543 2.3 39.8 0.7
O A:HOH419 2.3 23.6 0.7
C1 A:TFA202 2.4 6.4 0.1
O2 A:RDN201 2.4 13.6 0.1
O A:TFA202 2.7 7.1 0.1
HD22 A:LEU160 2.7 23.3 0.7
HD23 A:LEU160 2.8 21.6 0.3
H1 A:RDN201 2.8 15.6 0.1
HD23 A:LEU160 2.8 23.3 0.7
O A:HOH310 3.0 16.6 0.3
H A:GLY130 3.0 12.7 0.7
CD2 A:LEU160 3.0 19.4 0.7
H A:GLY130 3.0 14.2 0.3
HD21 A:LEU160 3.1 23.3 0.7
C1 A:RDN201 3.1 13.3 0.1
HB1 A:ALA129 3.2 13.6 0.7
HA2 A:GLY130 3.2 14.3 0.3
O A:HOH458 3.2 22.5 0.7
C2 A:RDN201 3.4 13.0 0.1
CD2 A:LEU160 3.5 18.0 0.3
HA2 A:GLY130 3.5 13.3 0.7
HD22 A:LEU160 3.5 21.6 0.3
N A:GLY130 3.5 11.8 0.3
OXT A:TFA202 3.5 5.0 0.1
HD21 A:LEU160 3.6 21.6 0.3
N A:GLY130 3.6 10.6 0.7
HA3 A:GLY130 3.6 14.3 0.3
CA A:GLY130 3.6 11.9 0.3
HB1 A:ALA129 3.7 11.5 0.3
CA A:GLY130 4.0 11.1 0.7
CB A:ALA129 4.0 11.3 0.7
O1 A:RDN201 4.1 13.0 0.1
HB3 A:PRO136 4.1 18.8 0.7
HB3 A:ALA129 4.1 13.6 0.7
HB3 A:PRO136 4.1 19.1 0.3
HA3 A:GLY130 4.1 13.3 0.7
HG3 A:PRO136 4.1 20.3 0.7
O A:HOH536 4.1 30.3 0.7
H3 A:RDN201 4.2 15.3 0.1
HB3 A:ALA129 4.2 11.5 0.3
H13 A:RDN201 4.3 15.9 0.1
HB2 A:ASP157 4.4 17.9 0.3
CB A:ALA129 4.4 9.6 0.3
C3 A:RDN201 4.4 12.8 0.1
HB3 A:ASP157 4.5 17.9 0.3
O A:HOH515 4.5 31.9 0.7
CG A:LEU160 4.5 19.6 0.7
O A:HOH542 4.5 27.6 0.9
H A:ASP157 4.5 16.6 0.3
C A:ALA129 4.6 11.6 0.3
C A:ALA129 4.6 9.8 0.7
O A:HOH472 4.6 38.8 0.7
HB2 A:ALA129 4.7 13.6 0.7
HG13 A:VAL155 4.7 18.9 0.7
HB3 A:LEU160 4.7 21.2 0.3
C15 A:RDN201 4.7 12.6 0.1
HG3 A:PRO136 4.7 19.3 0.3
CB A:PRO136 4.8 15.6 0.7
CG A:LEU160 4.8 17.8 0.3
HB2 A:LEU160 4.9 22.6 0.7
CA A:ALA129 4.9 9.8 0.7
CG A:PRO136 4.9 16.9 0.7
HB3 A:LEU160 4.9 22.6 0.7
CB A:ASP157 4.9 14.9 0.3
HB3 A:ASP157 4.9 25.9 0.7
HB3 A:PHE156 5.0 14.1 0.3
C16 A:RDN201 5.0 13.3 0.1
HB2 A:LEU160 5.0 21.2 0.3
HG A:LEU160 5.0 23.5 0.7

Fluorine binding site 2 out of 3 in 5srp

Go back to Fluorine Binding Sites List in 5srp
Fluorine binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer


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 Z5340019182 - (R) Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:8.8
occ:0.14
F2 A:TFA202 0.0 8.8 0.1
H1 A:RDN201 1.2 15.6 0.1
C2 A:TFA202 1.4 8.3 0.1
O A:HOH543 2.0 39.8 0.7
C2 A:RDN201 2.0 13.0 0.1
O A:HOH536 2.1 30.3 0.7
F1 A:TFA202 2.2 9.3 0.1
F3 A:TFA202 2.2 8.9 0.1
H13 A:RDN201 2.3 15.9 0.1
C1 A:TFA202 2.4 6.4 0.1
C1 A:RDN201 2.5 13.3 0.1
O2 A:RDN201 2.8 13.6 0.1
C15 A:RDN201 2.8 12.6 0.1
OXT A:TFA202 2.8 5.0 0.1
C16 A:RDN201 2.9 13.3 0.1
HB3 A:ALA129 2.9 13.6 0.7
HB1 A:ALA129 2.9 13.6 0.7
HA3 A:GLY130 3.0 14.3 0.3
H A:GLY130 3.1 12.7 0.7
O A:HOH542 3.2 27.6 0.9
N A:GLY130 3.2 10.6 0.7
HA3 A:GLY130 3.3 13.3 0.7
C3 A:RDN201 3.3 12.8 0.1
O A:TFA202 3.3 7.1 0.1
O1 A:RDN201 3.3 13.0 0.1
CB A:ALA129 3.4 11.3 0.7
O A:HOH472 3.4 38.8 0.7
HB3 A:ALA129 3.4 11.5 0.3
H A:GLY130 3.5 14.2 0.3
N A:GLY130 3.5 11.8 0.3
O A:HOH344 3.5 16.4 0.9
C14 A:RDN201 3.5 12.3 0.1
H3 A:RDN201 3.6 15.3 0.1
H12 A:RDN201 3.6 15.9 0.1
CA A:GLY130 3.6 11.9 0.3
H10 A:RDN201 3.6 14.7 0.1
CA A:GLY130 3.6 11.1 0.7
O A:HOH458 3.6 22.5 0.7
HA2 A:GLY130 3.6 13.3 0.7
HA2 A:GLY130 3.7 14.3 0.3
H15 A:RDN201 3.7 16.4 0.1
O A:HOH419 3.8 23.6 0.7
N1 A:RDN201 3.8 11.6 0.1
C A:ALA129 3.8 9.8 0.7
HB1 A:ALA129 3.8 11.5 0.3
C17 A:RDN201 3.9 13.6 0.1
H2 A:RDN201 4.0 15.3 0.1
CB A:ALA129 4.1 9.6 0.3
C A:ALA129 4.1 11.6 0.3
C18 A:RDN201 4.1 13.3 0.1
HB2 A:ALA129 4.1 13.6 0.7
CA A:ALA129 4.2 9.8 0.7
HB2 A:LEU126 4.2 16.3 0.3
O A:HOH412 4.3 27.8 0.3
O A:HOH383 4.3 14.2 0.9
O A:HOH310 4.3 16.6 0.3
HD23 A:LEU160 4.3 23.3 0.7
H11 A:RDN201 4.4 14.7 0.1
H16 A:RDN201 4.4 15.9 0.1
HB2 A:LEU126 4.5 13.1 0.7
O A:HOH544 4.5 57.3 0.9
O A:ALA129 4.5 9.4 0.7
O A:LEU126 4.5 11.1 0.3
HD21 A:LEU160 4.6 23.3 0.7
O A:ALA129 4.6 12.3 0.3
HD23 A:LEU160 4.6 21.6 0.3
O A:HOH500 4.7 16.9 0.3
HB3 A:PHE156 4.7 14.1 0.3
HD22 A:LEU160 4.7 23.3 0.7
CA A:ALA129 4.7 10.0 0.3
H A:PHE156 4.7 14.9 0.3
H14 A:RDN201 4.7 16.4 0.1
CD2 A:LEU160 4.7 19.4 0.7
H A:LEU126 4.8 15.1 0.3
HA A:ALA129 4.8 11.8 0.7
O A:HOH443 4.8 13.9 0.7
HB2 A:ALA129 4.9 11.5 0.3
H17 A:RDN201 4.9 15.9 0.1
HB3 A:PRO136 4.9 18.8 0.7
O A:LEU126 5.0 11.1 0.7

Fluorine binding site 3 out of 3 in 5srp

Go back to Fluorine Binding Sites List in 5srp
Fluorine binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:8.9
occ:0.14
F3 A:TFA202 0.0 8.9 0.1
O A:HOH543 1.3 39.8 0.7
C2 A:TFA202 1.4 8.3 0.1
F1 A:TFA202 2.2 9.3 0.1
F2 A:TFA202 2.2 8.8 0.1
C1 A:TFA202 2.3 6.4 0.1
HB1 A:ALA129 2.5 13.6 0.7
HD21 A:LEU160 2.7 23.3 0.7
OXT A:TFA202 2.9 5.0 0.1
HD23 A:LEU160 2.9 23.3 0.7
HB3 A:ALA129 2.9 13.6 0.7
O2 A:RDN201 3.0 13.6 0.1
HB2 A:LEU126 3.0 16.3 0.3
C1 A:RDN201 3.0 13.3 0.1
CB A:ALA129 3.1 11.3 0.7
H13 A:RDN201 3.1 15.9 0.1
HB3 A:ALA129 3.1 11.5 0.3
HD21 A:LEU160 3.1 21.6 0.3
HB3 A:PRO136 3.2 18.8 0.7
CD2 A:LEU160 3.2 19.4 0.7
HD23 A:LEU160 3.2 21.6 0.3
HB1 A:ALA129 3.2 11.5 0.3
H1 A:RDN201 3.2 15.6 0.1
HD12 A:LEU126 3.2 17.0 0.7
O A:TFA202 3.3 7.1 0.1
HB2 A:LEU126 3.3 13.1 0.7
O1 A:RDN201 3.4 13.0 0.1
HB3 A:PRO136 3.4 19.1 0.3
HD12 A:LEU126 3.4 18.3 0.3
HB2 A:ALA129 3.4 13.6 0.7
HD22 A:LEU160 3.5 23.3 0.7
O A:HOH419 3.6 23.6 0.7
CB A:ALA129 3.6 9.6 0.3
CD2 A:LEU160 3.6 18.0 0.3
C2 A:RDN201 3.6 13.0 0.1
O A:HOH383 3.7 14.2 0.9
O A:HOH536 3.7 30.3 0.7
H15 A:RDN201 3.7 16.4 0.1
O A:HOH458 3.8 22.5 0.7
H A:GLY130 3.8 12.7 0.7
HG13 A:VAL155 3.8 18.9 0.7
H A:GLY130 3.8 14.2 0.3
CB A:LEU126 3.9 13.6 0.3
C16 A:RDN201 3.9 13.3 0.1
HB3 A:LEU126 3.9 16.3 0.3
CB A:PRO136 4.0 15.6 0.7
HG13 A:VAL155 4.0 15.7 0.3
HD22 A:LEU160 4.1 21.6 0.3
HB2 A:PRO136 4.1 18.8 0.7
O A:HOH310 4.1 16.6 0.3
CD1 A:LEU126 4.1 14.2 0.7
HD13 A:LEU126 4.1 18.3 0.3
HB2 A:ALA129 4.1 11.5 0.3
CD1 A:LEU126 4.1 15.3 0.3
O A:HOH472 4.2 38.8 0.7
HD13 A:LEU126 4.2 17.0 0.7
CB A:LEU126 4.2 10.9 0.7
N A:GLY130 4.3 11.8 0.3
CB A:PRO136 4.3 15.9 0.3
C15 A:RDN201 4.3 12.6 0.1
C17 A:RDN201 4.3 13.6 0.1
HG3 A:PRO136 4.3 20.3 0.7
N A:GLY130 4.3 10.6 0.7
H A:LEU126 4.4 15.1 0.3
HB2 A:PRO136 4.4 19.1 0.3
HB3 A:LEU126 4.4 13.1 0.7
CA A:ALA129 4.5 9.8 0.7
HD11 A:LEU164 4.5 19.9 1.0
HG22 A:VAL155 4.5 18.6 0.7
CG A:LEU160 4.5 19.6 0.7
CG A:LEU126 4.6 14.6 0.3
O A:LEU126 4.6 11.1 0.3
H A:LEU126 4.6 12.3 0.7
HG A:LEU160 4.6 23.5 0.7
O A:HOH344 4.7 16.4 0.9
H A:PHE156 4.7 14.9 0.3
CG A:LEU126 4.7 12.6 0.7
CG1 A:VAL155 4.7 15.7 0.7
H12 A:RDN201 4.7 15.9 0.1
CG A:PRO136 4.8 16.9 0.7
HG A:LEU160 4.8 21.4 0.3
HA3 A:GLY130 4.8 14.3 0.3
HA A:PRO136 4.8 18.7 0.3
C A:ALA129 4.8 9.8 0.7
HG11 A:VAL155 4.8 18.9 0.7
HD11 A:LEU126 4.8 17.0 0.7
HA A:ALA129 4.8 11.8 0.7
C A:ALA129 4.8 11.6 0.3
CA A:ALA129 4.8 10.0 0.3
CG A:LEU160 4.8 17.8 0.3
HG A:LEU126 4.9 17.5 0.3
HA2 A:GLY130 4.9 14.3 0.3
HA A:VAL155 4.9 17.9 0.7
HA A:VAL155 4.9 15.3 0.3
HG A:LEU126 4.9 15.1 0.7
HD11 A:LEU126 4.9 18.3 0.3
CA A:GLY130 4.9 11.9 0.3
CA A:LEU126 4.9 12.1 0.3
HA A:PRO136 4.9 17.6 0.7
HG3 A:PRO136 5.0 19.3 0.3
HD11 A:LEU160 5.0 24.6 0.7

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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