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Fluorine in PDB 5rm3: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1745658474

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1745658474

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1745658474:
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 Z1745658474, PDB code: 5rm3 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) 81.27 / 2.09
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.130, 70.161, 85.280, 102.81, 96.13, 112.39
R / Rfree (%) 21.6 / 27.4

Other elements in 5rm3:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1745658474 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 Z1745658474 (pdb code 5rm3). 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 Helicase in Complex with Z1745658474, PDB code: 5rm3:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5rm3

Go back to Fluorine Binding Sites List in 5rm3
Fluorine binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1745658474


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 Z1745658474 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:52.5
occ:0.61
 F B:S7J701 0.0 52.5 0.6
C5 B:S7J701 1.3 54.8 0.6
F2 B:S7J701 2.1 53.9 0.6
F1 B:S7J701 2.1 56.1 0.6
C3 B:S7J701 2.4 56.4 0.6
N2 B:S7J701 2.8 55.1 0.6
CB B:PHE499 3.1 34.6 1.0
CA B:PHE499 3.4 36.6 1.0
N1 B:S7J701 3.5 58.2 0.6
CD2 B:PHE499 3.5 33.6 1.0
N B:PHE499 3.7 37.6 1.0
CE B:MET474 3.7 44.4 0.3
CG B:PHE499 3.8 34.0 1.0
O B:VAL495 3.8 31.6 1.0
C4 B:S7J701 4.1 55.0 0.6
SD B:MET474 4.1 56.4 0.3
CG B:PRO593 4.4 89.7 1.0
C2 B:S7J701 4.5 56.9 0.6
CG1 B:VAL495 4.6 40.1 1.0
C B:GLU498 4.6 39.8 1.0
CD B:PRO593 4.7 89.0 1.0
CE2 B:PHE499 4.8 32.3 1.0
C B:VAL495 4.8 36.4 1.0
C1 B:S7J701 4.8 54.6 0.6
C B:PHE499 4.9 37.5 1.0

Fluorine binding site 2 out of 3 in 5rm3

Go back to Fluorine Binding Sites List in 5rm3
Fluorine binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1745658474


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 Z1745658474 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:56.1
occ:0.61
 F1 B:S7J701 0.0 56.1 0.6
C5 B:S7J701 1.3 54.8 0.6
F2 B:S7J701 2.1 53.9 0.6
F B:S7J701 2.1 52.5 0.6
C3 B:S7J701 2.4 56.4 0.6
N2 B:S7J701 3.0 55.1 0.6
CD B:ARG502 3.1 48.2 0.6
CA B:PHE499 3.2 36.6 1.0
N1 B:S7J701 3.2 58.2 0.6
N B:PHE499 3.3 37.6 1.0
NE B:ARG502 3.3 50.6 0.6
CZ B:ARG502 3.5 53.1 0.6
NH2 B:ARG502 3.5 54.6 0.6
C B:GLU498 3.7 39.8 1.0
CB B:PHE499 3.8 34.6 1.0
O B:GLU498 3.8 35.6 1.0
CG B:GLU498 4.0 57.4 1.0
CG B:ARG502 4.2 47.6 0.6
C4 B:S7J701 4.2 55.0 0.6
CB B:GLU498 4.3 46.2 1.0
CG B:PRO593 4.3 89.7 1.0
C2 B:S7J701 4.4 56.9 0.6
NH1 B:ARG502 4.4 52.6 0.6
C B:PHE499 4.4 37.5 1.0
CD2 B:PHE499 4.5 33.6 1.0
CB B:ARG502 4.6 46.9 0.6
O B:VAL495 4.6 31.6 1.0
CG B:PHE499 4.6 34.0 1.0
CA B:GLU498 4.6 39.4 1.0
O B:PHE499 4.7 40.5 1.0
C1 B:S7J701 4.8 54.6 0.6
ND2 B:ASN503 5.0 42.3 1.0

Fluorine binding site 3 out of 3 in 5rm3

Go back to Fluorine Binding Sites List in 5rm3
Fluorine binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1745658474


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 Helicase in Complex with Z1745658474 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:53.9
occ:0.61
 F2 B:S7J701 0.0 53.9 0.6
C5 B:S7J701 1.3 54.8 0.6
F B:S7J701 2.1 52.5 0.6
F1 B:S7J701 2.1 56.1 0.6
C3 B:S7J701 2.4 56.4 0.6
CG B:PRO593 2.4 89.7 1.0
N1 B:S7J701 2.7 58.2 0.6
CD B:PRO593 3.2 89.0 1.0
CB B:PRO593 3.5 93.2 1.0
N2 B:S7J701 3.5 55.1 0.6
CG B:GLU498 4.0 57.4 1.0
C2 B:S7J701 4.0 56.9 0.6
O B:VAL495 4.0 31.6 1.0
CB B:GLU498 4.1 46.2 1.0
N B:PRO593 4.1 92.2 1.0
CA B:PRO593 4.1 91.9 1.0
N B:PHE499 4.2 37.6 1.0
CZ B:ARG502 4.2 53.1 0.6
NH2 B:ARG502 4.2 54.6 0.6
CE B:MET474 4.4 44.4 0.3
NE B:ARG502 4.5 50.6 0.6
NH1 B:ARG502 4.5 52.6 0.6
CA B:PHE499 4.5 36.6 1.0
C4 B:S7J701 4.6 55.0 0.6
C B:GLU498 4.6 39.8 1.0
SD B:MET474 4.7 56.4 0.3
CB B:PHE499 4.7 34.6 1.0
CG1 B:VAL495 4.7 40.1 1.0
C1 B:S7J701 4.8 54.6 0.6
CD B:ARG502 4.9 48.2 0.6
C B:VAL495 4.9 36.4 1.0
O B:GLU591 5.0 71.5 1.0
CA B:GLU498 5.0 39.4 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: Thu Aug 1 13:57:09 2024

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