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Fluorine in PDB 5rl8: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53825177

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53825177

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53825177:
3.6.4.12; 3.6.4.13;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53825177, PDB code: 5rl8 was solved by J.A.Newman, Y.Yosaatmadja, A.Douangamath, A.Aimon, A.J.Powell, A.Dias, D.Fearon, L.Dunnett, J.Brandao-Neto, T.Krojer, R.Skyner, T.Gorrie-Stone, W.Thompson, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, O.Gileadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.24 / 2.21
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.112, 70.206, 85.095, 102.61, 95.93, 112.44
R / Rfree (%) 20.9 / 27

Other elements in 5rl8:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53825177 also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53825177 (pdb code 5rl8). 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 Helicase in Complex with Z53825177, PDB code: 5rl8:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5rl8

Go back to Fluorine Binding Sites List in 5rl8
Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53825177


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 Helicase in Complex with Z53825177 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:36.8
occ:0.36
F1 B:VVG701 0.0 36.8 0.4
C8 B:VVG701 1.4 33.8 0.4
C7 B:VVG701 2.3 33.2 0.4
C3 B:VVG701 2.4 34.3 0.4
N1 B:VVG701 2.8 33.2 0.4
O2 B:VVG701 2.9 38.6 0.4
O B:ILE334 3.2 56.9 1.0
CA B:PRO335 3.4 68.0 1.0
S1 B:VVG701 3.5 36.5 0.4
C6 B:VVG701 3.6 33.3 0.4
C4 B:VVG701 3.6 34.1 0.4
ND2 B:ASN349 3.8 43.6 1.0
C B:ILE334 3.8 59.5 1.0
N B:PRO335 3.8 63.4 1.0
CG B:ASN349 4.1 48.1 1.0
C5 B:VVG701 4.1 32.8 0.4
CB B:PRO335 4.2 68.3 1.0
OD1 B:ASN349 4.2 52.5 1.0
CG2 B:ILE333 4.4 47.7 1.0
C B:PRO335 4.4 73.9 1.0
N B:ALA336 4.5 82.0 1.0
C2 B:VVG701 4.6 33.6 0.4
O1 B:VVG701 4.6 34.9 0.4
CB B:ASN349 4.9 50.1 1.0
N B:ILE334 4.9 52.0 1.0
CD B:PRO335 5.0 63.7 1.0

Fluorine binding site 2 out of 2 in 5rl8

Go back to Fluorine Binding Sites List in 5rl8
Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53825177


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 Helicase in Complex with Z53825177 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F702

b:36.8
occ:0.44
F1 B:VVG702 0.0 36.8 0.4
C8 B:VVG702 1.4 37.1 0.4
O1 B:VVG702 2.1 47.2 0.4
C7 B:VVG702 2.4 35.6 0.4
C3 B:VVG702 2.4 39.4 0.4
N1 B:VVG702 2.8 45.0 0.4
S1 B:VVG702 2.9 49.5 0.4
C1 B:VVG702 3.3 48.8 0.4
C6 B:VVG702 3.6 36.0 0.4
C4 B:VVG702 3.6 37.1 0.4
C2 B:VVG702 3.7 50.4 0.4
C5 B:VVG702 4.1 36.1 0.4
O2 B:VVG702 4.2 41.1 0.4
ND2 B:ASN86 4.6 65.0 1.0

Reference:

J.A.Newman, Y.Yosaatmadja, A.Douangamath, A.Aimon, A.J.Powell, A.Dias, D.Fearon, L.Dunnett, J.Brandao-Neto, T.Krojer, R.Skyner, T.Gorrie-Stone, W.Thompson, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, O.Gileadi. Pandda Analysis Group Deposition To Be Published.
Page generated: Tue Jul 15 06:56:31 2025

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