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Fluorine in PDB 5rmf: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006:
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 Z54226006, PDB code: 5rmf 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) 81.49 / 2.23
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.190, 70.107, 85.386, 102.60, 96.01, 112.56
R / Rfree (%) 20.8 / 27

Other elements in 5rmf:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006 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 Z54226006 (pdb code 5rmf). 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 Z54226006, PDB code: 5rmf:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5rmf

Go back to Fluorine Binding Sites List in 5rmf
Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006


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 Z54226006 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:50.6
occ:0.60
F A:NX7701 0.0 50.6 0.6
C A:NX7701 1.4 48.8 0.6
C1 A:NX7701 2.3 47.6 0.6
C5 A:NX7701 2.4 47.3 0.6
C6 A:NX7701 2.9 47.5 0.6
O A:NX7701 3.2 49.2 0.6
CG A:LYS460 3.5 54.7 1.0
C2 A:NX7701 3.6 46.1 0.6
C4 A:NX7701 3.6 48.0 0.6
CB A:LYS460 3.6 48.7 1.0
CD A:LYS460 3.6 62.4 1.0
N A:NX7701 3.7 45.9 0.6
CD1 A:PHE437 3.9 55.6 1.0
C10 A:NX7701 4.1 46.3 0.6
C3 A:NX7701 4.1 46.7 0.6
CE1 A:PHE437 4.1 55.5 1.0
CE A:LYS460 4.2 70.5 1.0
CG A:PHE437 4.7 55.2 1.0
F1 A:NX7701 4.7 50.9 0.6
CA A:LYS460 4.9 45.3 1.0
C7 A:NX7701 4.9 45.3 0.6

Fluorine binding site 2 out of 2 in 5rmf

Go back to Fluorine Binding Sites List in 5rmf
Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006


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 Z54226006 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:50.9
occ:0.60
F1 A:NX7701 0.0 50.9 0.6
C4 A:NX7701 1.4 48.0 0.6
C3 A:NX7701 2.3 46.7 0.6
C5 A:NX7701 2.4 47.3 0.6
C6 A:NX7701 2.8 47.5 0.6
CD A:PRO434 3.0 49.9 1.0
N A:NX7701 3.2 45.9 0.6
C10 A:NX7701 3.6 46.3 0.6
O A:NX7701 3.6 49.2 0.6
C2 A:NX7701 3.6 46.1 0.6
C A:NX7701 3.6 48.8 0.6
CG A:PRO434 3.7 48.3 1.0
C1 A:NX7701 4.1 47.6 0.6
C7 A:NX7701 4.1 45.3 0.6
CA A:GLY433 4.2 49.1 1.0
N A:PRO434 4.2 49.0 1.0
O A:HOH863 4.5 51.4 1.0
OE1 A:GLN281 4.7 41.8 1.0
C A:GLY433 4.7 46.3 1.0
F A:NX7701 4.7 50.6 0.6
C8 A:NX7701 4.8 45.7 0.6
C9 A:NX7701 4.8 46.7 0.6

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: Sun Dec 13 12:34:47 2020

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