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Fluorine in PDB 7lzu: Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B

Enzymatic activity of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B

All present enzymatic activity of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B:
3.4.22.69;

Protein crystallography data

The structure of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B, PDB code: 7lzu was solved by S.Lovell, M.M.Kashipathy, K.P.Battaile, S.D.Chamandi, A.D.Rathnayake, Y.Kim, K.D.Perera, A.R.M.Jesri, H.N.Nguyen, M.A.Baird, M.J.Miller, W.C.Groutas, K.O.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.12 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.397, 98.967, 59.152, 90, 108.34, 90
R / Rfree (%) 17.8 / 20.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B (pdb code 7lzu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B, PDB code: 7lzu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7lzu

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Fluorine binding site 1 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:47.5
occ:0.50
 F29 A:YKM401 0.0 47.5 0.5
F29 A:YKP402 0.0 47.4 0.5
C28 A:YKP402 1.4 44.5 0.5
C28 A:YKM401 1.4 44.5 0.5
F30 A:YKP402 2.1 49.2 0.5
F30 A:YKM401 2.1 49.2 0.5
C27 A:YKP402 2.4 42.2 0.5
C27 A:YKM401 2.4 42.2 0.5
C31 A:YKM401 2.4 38.4 0.5
C31 A:YKP402 2.4 38.4 0.5
C26 A:YKM401 3.0 38.8 0.5
C26 A:YKP402 3.0 38.8 0.5
C32 A:YKM401 3.1 31.9 0.5
C32 A:YKP402 3.1 31.9 0.5
CG A:PRO168 3.1 35.3 1.0
CD A:PRO168 3.4 29.5 1.0
CB A:ALA191 3.6 28.6 1.0
C25 A:YKM401 3.7 29.7 0.5
C25 A:YKP402 3.7 29.7 0.5
CB A:PRO168 3.7 30.1 1.0
CA A:ALA191 3.7 25.6 1.0
N A:PRO168 3.8 25.9 1.0
CA A:PRO168 3.8 28.8 1.0
O A:HOH583 4.3 26.6 1.0
N A:ALA191 4.4 26.5 1.0
C A:LEU167 4.5 28.9 1.0
O A:THR190 4.9 28.1 1.0
C A:ALA191 4.9 26.8 1.0
C02 A:YKM401 5.0 25.2 0.5
C A:THR190 5.0 24.3 1.0
C02 A:YKP402 5.0 25.2 0.5

Fluorine binding site 2 out of 8 in 7lzu

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Fluorine binding site 2 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:49.2
occ:0.50
 F30 A:YKM401 0.0 49.2 0.5
F30 A:YKP402 0.0 49.2 0.5
C28 A:YKM401 1.4 44.5 0.5
C28 A:YKP402 1.4 44.5 0.5
F29 A:YKM401 2.1 47.5 0.5
F29 A:YKP402 2.1 47.4 0.5
C31 A:YKM401 2.4 38.4 0.5
C31 A:YKP402 2.4 38.4 0.5
C27 A:YKM401 2.4 42.2 0.5
C27 A:YKP402 2.5 42.2 0.5
C26 A:YKM401 3.8 38.8 0.5
C32 A:YKM401 3.8 31.9 0.5
C26 A:YKP402 3.8 38.8 0.5
C32 A:YKP402 3.8 31.9 0.5
CB A:ALA191 3.8 28.6 1.0
C25 A:YKM401 4.2 29.7 0.5
C25 A:YKP402 4.2 29.7 0.5
CA A:ALA191 4.3 25.6 1.0
N A:ALA191 4.5 26.5 1.0
CG A:PRO168 4.7 35.3 1.0
O A:HOH574 4.8 33.4 1.0

Fluorine binding site 3 out of 8 in 7lzu

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Fluorine binding site 3 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:47.4
occ:0.50
 F29 A:YKP402 0.0 47.4 0.5
F29 A:YKM401 0.0 47.5 0.5
C28 A:YKP402 1.4 44.5 0.5
C28 A:YKM401 1.4 44.5 0.5
F30 A:YKP402 2.1 49.2 0.5
F30 A:YKM401 2.1 49.2 0.5
C27 A:YKP402 2.4 42.2 0.5
C27 A:YKM401 2.4 42.2 0.5
C31 A:YKM401 2.4 38.4 0.5
C31 A:YKP402 2.4 38.4 0.5
C26 A:YKM401 3.0 38.8 0.5
C26 A:YKP402 3.0 38.8 0.5
C32 A:YKM401 3.1 31.9 0.5
C32 A:YKP402 3.1 31.9 0.5
CG A:PRO168 3.1 35.3 1.0
CD A:PRO168 3.4 29.5 1.0
CB A:ALA191 3.6 28.6 1.0
C25 A:YKM401 3.7 29.7 0.5
C25 A:YKP402 3.7 29.7 0.5
CB A:PRO168 3.7 30.1 1.0
CA A:ALA191 3.7 25.6 1.0
N A:PRO168 3.8 25.9 1.0
CA A:PRO168 3.8 28.8 1.0
O A:HOH583 4.3 26.6 1.0
N A:ALA191 4.4 26.5 1.0
C A:LEU167 4.5 28.9 1.0
O A:THR190 4.9 28.1 1.0
C02 A:YKM401 4.9 25.2 0.5
C A:ALA191 4.9 26.8 1.0
C A:THR190 5.0 24.3 1.0
C02 A:YKP402 5.0 25.2 0.5

Fluorine binding site 4 out of 8 in 7lzu

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Fluorine binding site 4 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:49.2
occ:0.50
 F30 A:YKP402 0.0 49.2 0.5
F30 A:YKM401 0.0 49.2 0.5
C28 A:YKM401 1.4 44.5 0.5
C28 A:YKP402 1.4 44.5 0.5
F29 A:YKM401 2.1 47.5 0.5
F29 A:YKP402 2.1 47.4 0.5
C31 A:YKM401 2.4 38.4 0.5
C31 A:YKP402 2.4 38.4 0.5
C27 A:YKM401 2.4 42.2 0.5
C27 A:YKP402 2.4 42.2 0.5
C26 A:YKM401 3.8 38.8 0.5
C32 A:YKM401 3.8 31.9 0.5
C26 A:YKP402 3.8 38.8 0.5
C32 A:YKP402 3.8 31.9 0.5
CB A:ALA191 3.8 28.6 1.0
C25 A:YKM401 4.2 29.7 0.5
C25 A:YKP402 4.2 29.7 0.5
CA A:ALA191 4.3 25.6 1.0
N A:ALA191 4.5 26.5 1.0
CG A:PRO168 4.7 35.3 1.0
O A:HOH574 4.8 33.4 1.0

Fluorine binding site 5 out of 8 in 7lzu

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Fluorine binding site 5 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:51.4
occ:0.50
 F29 B:YKP401 0.0 51.4 0.5
F29 B:YKM402 0.1 51.4 0.5
C28 B:YKM402 1.4 50.7 0.5
C28 B:YKP401 1.4 50.6 0.5
F30 B:YKP401 2.1 59.4 0.5
F30 B:YKM402 2.1 59.4 0.5
C31 B:YKM402 2.4 48.4 0.5
C31 B:YKP401 2.4 48.4 0.5
C27 B:YKM402 2.4 46.4 0.5
C27 B:YKP401 2.4 46.4 0.5
C32 B:YKM402 3.0 38.6 0.5
C26 B:YKM402 3.0 43.7 0.5
C26 B:YKP401 3.0 43.6 0.5
C32 B:YKP401 3.0 38.5 0.5
CG B:PRO168 3.2 42.7 1.0
O B:HOH626 3.3 36.8 1.0
N B:PRO168 3.3 42.9 1.0
CD B:PRO168 3.4 47.0 1.0
C25 B:YKM402 3.6 36.3 0.5
CA B:PRO168 3.6 41.5 1.0
C25 B:YKP401 3.6 36.3 0.5
CA B:ALA191 3.7 46.2 1.0
CB B:PRO168 3.8 41.9 1.0
C B:LEU167 3.9 32.5 1.0
CB B:ALA191 4.0 46.8 1.0
O B:GLU166 4.2 26.1 1.0
O B:THR190 4.3 40.6 1.0
N B:ALA191 4.4 55.3 1.0
CA B:LEU167 4.4 31.1 1.0
N B:GLN192 4.5 36.4 1.0
O B:LEU167 4.5 32.7 1.0
C B:THR190 4.6 41.6 1.0
C02 B:YKM402 4.6 36.2 0.5
C B:ALA191 4.7 38.3 1.0
C02 B:YKP401 4.8 36.2 0.5

Fluorine binding site 6 out of 8 in 7lzu

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Fluorine binding site 6 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:59.4
occ:0.50
 F30 B:YKP401 0.0 59.4 0.5
F30 B:YKM402 0.1 59.4 0.5
C28 B:YKM402 1.3 50.7 0.5
C28 B:YKP401 1.4 50.6 0.5
F29 B:YKM402 2.1 51.4 0.5
F29 B:YKP401 2.1 51.4 0.5
C31 B:YKM402 2.4 48.4 0.5
C27 B:YKM402 2.4 46.4 0.5
C31 B:YKP401 2.4 48.4 0.5
C27 B:YKP401 2.4 46.4 0.5
CB B:ALA191 3.4 46.8 1.0
C32 B:YKM402 3.7 38.6 0.5
CA B:ALA191 3.7 46.2 1.0
C26 B:YKM402 3.7 43.7 0.5
C32 B:YKP401 3.8 38.5 0.5
C26 B:YKP401 3.8 43.6 0.5
CG B:PRO168 4.1 42.7 1.0
N B:ALA191 4.2 55.3 1.0
C25 B:YKM402 4.2 36.3 0.5
C25 B:YKP401 4.3 36.3 0.5
CB B:PRO168 4.4 41.9 1.0
CA B:PRO168 4.7 41.5 1.0
C B:THR190 4.8 41.6 1.0
CD B:PRO168 4.9 47.0 1.0
N B:PRO168 4.9 42.9 1.0
O B:THR190 5.0 40.6 1.0

Fluorine binding site 7 out of 8 in 7lzu

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Fluorine binding site 7 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:51.4
occ:0.50
 F29 B:YKM402 0.0 51.4 0.5
F29 B:YKP401 0.1 51.4 0.5
C28 B:YKM402 1.4 50.7 0.5
C28 B:YKP401 1.4 50.6 0.5
F30 B:YKP401 2.1 59.4 0.5
F30 B:YKM402 2.1 59.4 0.5
C31 B:YKM402 2.4 48.4 0.5
C27 B:YKM402 2.4 46.4 0.5
C27 B:YKP401 2.4 46.4 0.5
C31 B:YKP401 2.4 48.4 0.5
C26 B:YKM402 3.0 43.7 0.5
C32 B:YKM402 3.0 38.6 0.5
C26 B:YKP401 3.0 43.6 0.5
C32 B:YKP401 3.1 38.5 0.5
CG B:PRO168 3.2 42.7 1.0
N B:PRO168 3.3 42.9 1.0
O B:HOH626 3.3 36.8 1.0
CD B:PRO168 3.4 47.0 1.0
CA B:PRO168 3.6 41.5 1.0
C25 B:YKM402 3.6 36.3 0.5
C25 B:YKP401 3.7 36.3 0.5
CA B:ALA191 3.7 46.2 1.0
CB B:PRO168 3.7 41.9 1.0
C B:LEU167 3.9 32.5 1.0
CB B:ALA191 4.0 46.8 1.0
O B:GLU166 4.2 26.1 1.0
O B:THR190 4.3 40.6 1.0
CA B:LEU167 4.4 31.1 1.0
N B:ALA191 4.4 55.3 1.0
O B:LEU167 4.5 32.7 1.0
N B:GLN192 4.5 36.4 1.0
C B:THR190 4.6 41.6 1.0
C02 B:YKM402 4.7 36.2 0.5
C B:ALA191 4.7 38.3 1.0
C02 B:YKP401 4.8 36.2 0.5

Fluorine binding site 8 out of 8 in 7lzu

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Fluorine binding site 8 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:59.4
occ:0.50
 F30 B:YKM402 0.0 59.4 0.5
F30 B:YKP401 0.1 59.4 0.5
C28 B:YKM402 1.4 50.7 0.5
C28 B:YKP401 1.4 50.6 0.5
F29 B:YKM402 2.1 51.4 0.5
F29 B:YKP401 2.1 51.4 0.5
C31 B:YKM402 2.4 48.4 0.5
C27 B:YKM402 2.4 46.4 0.5
C27 B:YKP401 2.5 46.4 0.5
C31 B:YKP401 2.5 48.4 0.5
CB B:ALA191 3.4 46.8 1.0
CA B:ALA191 3.7 46.2 1.0
C32 B:YKM402 3.8 38.6 0.5
C26 B:YKM402 3.8 43.7 0.5
C26 B:YKP401 3.8 43.6 0.5
C32 B:YKP401 3.8 38.5 0.5
CG B:PRO168 4.1 42.7 1.0
N B:ALA191 4.2 55.3 1.0
C25 B:YKM402 4.3 36.3 0.5
CB B:PRO168 4.3 41.9 1.0
C25 B:YKP401 4.4 36.3 0.5
CA B:PRO168 4.6 41.5 1.0
C B:THR190 4.8 41.6 1.0
CD B:PRO168 4.9 47.0 1.0
N B:PRO168 4.9 42.9 1.0

Reference:

S.D.Chamandi, A.D.Rathnayake, J.Zhang, Y.Kim, K.D.Perera, A.R.M.Jesri, H.N.Nguyen, M.A.Baird, S.Makin, D.K.Meyerholz, M.M.Kashipathy, K.P.Battaile, S.Lovell, S.Perlman, K.O.Chang, W.C.Groutas. Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 12B To Be Published.
Page generated: Tue Jul 15 21:24:36 2025

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