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Fluorine in PDB 5ssh: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINCPX000006MH4L - (S) Isomer

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINCPX000006MH4L - (S) Isomer

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINCPX000006MH4L - (S) 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 ZINCPX000006MH4L - (S) Isomer, PDB code: 5ssh 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) 36.02 / 1.15
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 88.703, 88.703, 39.412, 90, 90, 90
R / Rfree (%) 13.2 / 14.9

Other elements in 5ssh:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINCPX000006MH4L - (S) Isomer also contains other interesting chemical elements:

Bromine (Br) 1 atom

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 ZINCPX000006MH4L - (S) Isomer (pdb code 5ssh). 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 ZINCPX000006MH4L - (S) Isomer, PDB code: 5ssh:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5ssh

Go back to Fluorine Binding Sites List in 5ssh
Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINCPX000006MH4L - (S) 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 ZINCPX000006MH4L - (S) Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:25.6
occ:0.20
 F03 A:RQ8201 0.0 25.6 0.2
C02 A:RQ8201 1.4 25.2 0.2
O A:HOH532 2.0 50.7 0.8
F25 A:RQ8201 2.2 25.6 0.2
C01 A:RQ8201 2.4 25.4 0.2
C04 A:RQ8201 2.4 24.1 0.2
O A:HOH539 2.4 43.0 0.8
O A:HOH544 2.5 41.7 0.8
H012 A:RQ8201 2.6 30.4 0.2
H011 A:RQ8201 2.7 30.4 0.2
H241 A:RQ8201 2.8 28.4 0.2
O A:HOH529 2.9 37.8 0.8
C24 A:RQ8201 2.9 23.7 0.2
O A:HOH503 3.2 37.7 0.8
H013 A:RQ8201 3.3 30.4 0.2
C05 A:RQ8201 3.5 23.2 0.2
H051 A:RQ8201 3.7 27.8 0.2
O A:HOH535 3.8 43.9 0.8
N23 A:RQ8201 4.2 23.2 0.2
C06 A:RQ8201 4.6 22.4 0.2
HD13 A:LEU160 4.7 26.9 0.8
HD13 A:LEU160 4.8 25.1 0.2
HD22 A:LEU160 4.9 26.0 0.8
C22 A:RQ8201 4.9 22.8 0.2
HG3 A:PRO136 4.9 24.0 0.8
O A:HOH405 5.0 27.8 0.8
HG3 A:PRO136 5.0 19.8 0.2
HB2 A:LEU160 5.0 25.8 0.8

Fluorine binding site 2 out of 2 in 5ssh

Go back to Fluorine Binding Sites List in 5ssh
Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINCPX000006MH4L - (S) 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 ZINCPX000006MH4L - (S) Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:25.6
occ:0.20
 F25 A:RQ8201 0.0 25.6 0.2
O A:HOH503 1.1 37.7 0.8
C02 A:RQ8201 1.4 25.2 0.2
O A:HOH539 1.7 43.0 0.8
F03 A:RQ8201 2.2 25.6 0.2
H051 A:RQ8201 2.3 27.8 0.2
C01 A:RQ8201 2.3 25.4 0.2
C04 A:RQ8201 2.4 24.1 0.2
H011 A:RQ8201 2.5 30.4 0.2
O A:HOH544 2.6 41.7 0.8
O A:HOH532 2.6 50.7 0.8
C05 A:RQ8201 2.7 23.2 0.2
H013 A:RQ8201 2.7 30.4 0.2
O A:HOH529 2.7 37.8 0.8
H012 A:RQ8201 3.3 30.4 0.2
O A:HOH405 3.3 27.8 0.8
HG3 A:PRO136 3.4 24.0 0.8
HD3 A:PRO136 3.5 22.0 0.8
HG3 A:PRO136 3.6 19.8 0.2
C24 A:RQ8201 3.7 23.7 0.2
HD3 A:PRO136 3.7 20.0 0.2
O A:HOH350 3.9 20.6 1.0
HD2 A:PRO136 3.9 22.0 0.8
CD A:PRO136 4.0 18.3 0.8
C06 A:RQ8201 4.0 22.4 0.2
CG A:PRO136 4.1 20.0 0.8
H241 A:RQ8201 4.1 28.4 0.2
HD22 A:LEU160 4.2 26.0 0.8
CG A:PRO136 4.4 16.5 0.2
CD A:PRO136 4.4 16.7 0.2
O A:HOH535 4.4 43.9 0.8
HG2 A:PRO136 4.4 24.0 0.8
HD13 A:LEU160 4.5 26.9 0.8
HD22 A:LEU160 4.6 25.4 0.2
HD13 A:LEU160 4.6 25.1 0.2
H A:GLY130 4.6 20.9 0.2
N23 A:RQ8201 4.7 23.2 0.2
H A:GLY130 4.7 16.6 0.8
HD11 A:LEU160 4.8 25.1 0.2
HD2 A:PRO136 4.8 20.0 0.2
HB3 A:PRO136 4.8 19.8 0.2
O21 A:RQ8201 4.8 20.6 0.2
HA2 A:GLY130 4.8 20.9 0.2
C22 A:RQ8201 4.9 22.8 0.2
C07 A:RQ8201 4.9 21.4 0.2

Reference:

G.J.Correy, J.S.Fraser. Ligand Screen Against Sars-Cov-2 NSP3 Macrodomain To Be Published.
Page generated: Tue Jul 15 07:41:17 2025

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