Atomistry » Fluorine » PDB 5rb5-5rmf » 5rm3
Atomistry »
  Fluorine »
    PDB 5rb5-5rmf »
      5rm3 »

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: Tue Jul 15 06:57:16 2025

Last articles

Mg in 6HWJ
Mg in 6HWE
Mg in 6HWD
Mg in 6HWC
Mg in 6HWB
Mg in 6HW9
Mg in 6HWA
Mg in 6HW8
Mg in 6HW7
Mg in 6HW5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy