Fluorine in PDB 7grx: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20, PDB code: 7grx was solved by C.-Y.Huang, A.Metz, M.Sharpe, A.Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.08 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.87, 99.57, 103.83, 90, 90, 90
R / Rfree (%) 18.7 / 21.9

Other elements in 7grx:

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20 (pdb code 7grx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20, PDB code: 7grx:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7grx

Go back to Fluorine Binding Sites List in 7grx
Fluorine binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:52.6
occ:0.46
 F12 B:XZT403 0.0 52.6 0.5
F12 B:XZT403 0.2 52.6 0.5
C11 B:XZT403 1.3 46.4 0.5
C11 B:XZT403 1.4 46.3 0.5
C13 B:XZT403 2.2 41.8 0.5
C10 B:XZT403 2.4 41.8 0.5
C13 B:XZT403 2.4 40.6 0.5
C10 B:XZT403 2.4 40.8 0.5
C14 B:XZT403 3.5 40.8 0.5
C09 B:XZT403 3.6 40.3 0.5
C14 B:XZT403 3.6 39.0 0.5
C09 B:XZT403 3.6 38.7 0.5
C08 B:XZT403 4.1 39.1 0.5
C08 B:XZT403 4.1 39.0 0.5
F15 B:XZT403 4.6 34.5 0.5
F15 B:XZT403 4.8 34.0 0.5

Fluorine binding site 2 out of 4 in 7grx

Go back to Fluorine Binding Sites List in 7grx
Fluorine binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:52.6
occ:0.54
 F12 B:XZT403 0.0 52.6 0.5
F12 B:XZT403 0.2 52.6 0.5
C11 B:XZT403 1.4 46.4 0.5
C11 B:XZT403 1.4 46.3 0.5
C13 B:XZT403 2.3 40.6 0.5
C10 B:XZT403 2.4 40.8 0.5
C13 B:XZT403 2.4 41.8 0.5
C10 B:XZT403 2.5 41.8 0.5
C14 B:XZT403 3.6 39.0 0.5
C09 B:XZT403 3.6 38.7 0.5
C14 B:XZT403 3.6 40.8 0.5
C09 B:XZT403 3.8 40.3 0.5
C08 B:XZT403 4.1 39.1 0.5
C08 B:XZT403 4.2 39.0 0.5
F15 B:XZT403 4.7 34.0 0.5
F15 B:XZT403 4.8 34.5 0.5

Fluorine binding site 3 out of 4 in 7grx

Go back to Fluorine Binding Sites List in 7grx
Fluorine binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:34.0
occ:0.46
 F15 B:XZT403 0.0 34.0 0.5
C09 B:XZT403 1.3 38.7 0.5
C14 B:XZT403 1.4 39.0 0.5
C08 B:XZT403 2.3 39.1 0.5
C10 B:XZT403 2.4 40.8 0.5
C13 B:XZT403 2.4 40.6 0.5
C08 B:XZT403 2.4 39.0 0.5
N07 B:XZT403 2.7 39.1 0.5
OE1 B:GLN189 2.7 67.2 1.0
N07 B:XZT403 2.8 39.0 0.5
O01 B:XZT403 2.8 36.9 0.5
C02 B:XZT403 2.9 40.6 0.5
C B:THR190 3.0 37.7 1.0
O06 B:XZT403 3.0 36.6 0.5
C05 B:XZT403 3.1 40.5 0.5
N B:ALA191 3.2 33.0 1.0
O B:THR190 3.2 29.8 1.0
CD B:GLN189 3.2 62.9 1.0
N B:THR190 3.3 34.7 1.0
CA B:THR190 3.4 42.1 1.0
C14 B:XZT403 3.6 40.8 0.5
C11 B:XZT403 3.6 46.4 0.5
C11 B:XZT403 3.6 46.3 0.5
C09 B:XZT403 3.7 40.3 0.5
C B:GLN189 3.8 44.5 1.0
CA B:ALA191 3.8 32.2 1.0
NE2 B:GLN189 3.9 62.3 1.0
C05 B:XZT403 3.9 30.9 0.5
C02 B:XZT403 3.9 31.0 0.5
CG B:GLN189 4.0 44.7 1.0
C13 B:XZT403 4.1 41.8 0.5
C10 B:XZT403 4.1 41.8 0.5
C03 B:XZT403 4.2 31.8 0.5
CA B:GLN189 4.3 34.5 1.0
O B:HOH592 4.4 38.3 1.0
O06 B:XZT403 4.4 32.4 0.5
C04 B:XZT403 4.4 33.2 0.5
O B:GLN189 4.5 47.1 1.0
O01 B:XZT403 4.5 32.3 0.5
CB B:ALA191 4.6 35.4 1.0
F15 B:XZT403 4.7 34.5 0.5
CB B:GLN189 4.7 35.9 1.0
C03 B:XZT403 4.7 28.8 0.5
F12 B:XZT403 4.7 52.6 0.5
C04 B:XZT403 4.7 28.4 0.5
F12 B:XZT403 4.8 52.6 0.5
CB B:THR190 4.9 35.7 1.0

Fluorine binding site 4 out of 4 in 7grx

Go back to Fluorine Binding Sites List in 7grx
Fluorine binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:34.5
occ:0.54
 F15 B:XZT403 0.0 34.5 0.5
C09 B:XZT403 1.3 40.3 0.5
C14 B:XZT403 1.4 40.8 0.5
C10 B:XZT403 2.3 41.8 0.5
C08 B:XZT403 2.3 39.0 0.5
C13 B:XZT403 2.4 41.8 0.5
C08 B:XZT403 2.4 39.1 0.5
N07 B:XZT403 2.8 39.0 0.5
N07 B:XZT403 2.8 39.1 0.5
O B:GLU166 3.0 22.8 1.0
C05 B:XZT403 3.2 30.9 0.5
C02 B:XZT403 3.2 31.0 0.5
C B:LEU167 3.3 25.8 1.0
O01 B:XZT403 3.3 32.3 0.5
N B:PRO168 3.3 23.8 1.0
O06 B:XZT403 3.3 32.4 0.5
C11 B:XZT403 3.5 46.3 0.5
C14 B:XZT403 3.5 39.0 0.5
C11 B:XZT403 3.6 46.4 0.5
O B:LEU167 3.7 22.7 1.0
C09 B:XZT403 3.7 38.7 0.5
CA B:PRO168 3.7 24.0 1.0
CA B:LEU167 3.7 15.4 1.0
O B:HOH559 3.7 35.7 1.0
C05 B:XZT403 3.8 40.5 0.5
CD B:PRO168 3.8 25.2 1.0
C B:GLU166 3.8 23.0 1.0
CG B:PRO168 3.9 26.9 1.0
C02 B:XZT403 3.9 40.6 0.5
C13 B:XZT403 4.0 40.6 0.5
C10 B:XZT403 4.1 40.8 0.5
N B:LEU167 4.2 17.6 1.0
C04 B:XZT403 4.2 28.4 0.5
CB B:PRO168 4.3 25.4 1.0
O06 B:XZT403 4.4 36.6 0.5
C03 B:XZT403 4.4 28.8 0.5
O01 B:XZT403 4.5 36.9 0.5
C04 B:XZT403 4.5 33.2 0.5
F12 B:XZT403 4.6 52.6 0.5
F15 B:XZT403 4.7 34.0 0.5
C03 B:XZT403 4.7 31.8 0.5
F12 B:XZT403 4.8 52.6 0.5
C B:PRO168 5.0 27.2 1.0

Reference:

C.Y.Huang, A.Metz, R.Lange, N.Artico, C.Potot, J.Hazemann, M.Muller, M.Dos Santos, A.Chambovey, D.Ritz, D.Eris, S.Meyer, G.Bourquin, M.Sharpe, A.Mac Sweeney. Fragment-Based Screening Targeting An Open Form of the Sars-Cov-2 Main Protease Binding Pocket. Acta Crystallogr D Struct V. 80 123 2024BIOL.
ISSN: ISSN 2059-7983
PubMed: 38289714
DOI: 10.1107/S2059798324000329
Page generated: Fri Aug 2 07:45:07 2024

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