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Fluorine in PDB 7m00: Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 13C

Enzymatic activity of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 13C

All present enzymatic activity of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 13C:
3.4.22.69;

Protein crystallography data

The structure of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 13C, PDB code: 7m00 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) 39.05 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.744, 53.544, 113.423, 90, 101.25, 90
R / Rfree (%) 21.1 / 26.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 13C (pdb code 7m00). 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 13C, PDB code: 7m00:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7m00

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Fluorine binding site 1 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 13C


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 13C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:39.5
occ:0.50
 F30 A:YKA401 0.0 39.5 0.5
F30 A:YKD402 0.0 39.5 0.5
C29 A:YKD402 1.4 42.3 0.5
C29 A:YKA401 1.4 42.3 0.5
F31 A:YKA401 2.1 45.8 0.5
F31 A:YKD402 2.1 45.8 0.5
C28 A:YKA401 2.4 35.3 0.5
C28 A:YKD402 2.4 35.3 0.5
C32 A:YKD402 2.4 41.0 0.5
C32 A:YKA401 2.4 41.0 0.5
O A:THR190 3.2 39.1 1.0
CD A:PRO168 3.3 33.3 1.0
CA A:ALA191 3.4 42.8 1.0
N A:GLN192 3.4 32.2 1.0
CG A:PRO168 3.5 34.0 1.0
C27 A:YKA401 3.7 36.0 0.5
C27 A:YKD402 3.7 36.0 0.5
C33 A:YKD402 3.7 35.2 0.5
C33 A:YKA401 3.7 35.2 0.5
N A:PRO168 3.8 29.1 1.0
CA A:LEU167 3.8 28.3 1.0
O A:GLU166 3.9 27.1 1.0
C A:ALA191 3.9 43.2 1.0
C A:THR190 3.9 42.9 1.0
N A:ALA191 4.0 38.6 1.0
C A:LEU167 4.1 29.7 1.0
CD2 A:LEU167 4.1 30.2 1.0
C26 A:YKD402 4.3 31.2 0.5
C26 A:YKA401 4.3 31.2 0.5
CB A:GLN192 4.4 30.7 1.0
CA A:GLN192 4.5 32.6 1.0
CB A:ALA191 4.5 60.1 1.0
O A:GLN192 4.5 33.5 1.0
CA A:PRO168 4.6 37.3 1.0
CB A:PRO168 4.6 45.0 1.0
C A:GLU166 4.7 30.5 1.0
N A:LEU167 4.7 26.0 1.0
CB A:LEU167 4.7 33.8 1.0
CG A:GLN192 4.9 28.8 1.0
C A:GLN192 5.0 27.6 1.0

Fluorine binding site 2 out of 8 in 7m00

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Fluorine binding site 2 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 13C


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 13C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:45.8
occ:0.50
 F31 A:YKA401 0.0 45.8 0.5
F31 A:YKD402 0.0 45.8 0.5
C29 A:YKD402 1.3 42.3 0.5
C29 A:YKA401 1.4 42.3 0.5
F30 A:YKD402 2.1 39.5 0.5
F30 A:YKA401 2.1 39.5 0.5
C32 A:YKD402 2.4 41.0 0.5
C32 A:YKA401 2.4 41.0 0.5
C28 A:YKA401 2.4 35.3 0.5
C28 A:YKD402 2.4 35.3 0.5
O A:THR190 3.0 39.1 1.0
C33 A:YKD402 3.0 35.2 0.5
C33 A:YKA401 3.0 35.2 0.5
C27 A:YKD402 3.0 36.0 0.5
C27 A:YKA401 3.0 36.0 0.5
C A:THR190 3.1 42.9 1.0
CA A:ALA191 3.1 42.8 1.0
N A:ALA191 3.1 38.6 1.0
C26 A:YKD402 3.7 31.2 0.5
C26 A:YKA401 3.7 31.2 0.5
CB A:ALA191 4.0 60.1 1.0
CA A:THR190 4.1 38.3 1.0
C A:ALA191 4.2 43.2 1.0
N A:THR190 4.2 30.2 1.0
N A:GLN192 4.4 32.2 1.0
CG A:PRO168 4.7 34.0 1.0
C A:GLN189 4.8 38.1 1.0
CD A:PRO168 5.0 33.3 1.0
C02 A:YKD402 5.0 35.0 0.5
O A:GLU166 5.0 27.1 1.0
C02 A:YKA401 5.0 35.0 0.5

Fluorine binding site 3 out of 8 in 7m00

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Fluorine binding site 3 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 13C


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 13C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:39.5
occ:0.50
 F30 A:YKD402 0.0 39.5 0.5
F30 A:YKA401 0.0 39.5 0.5
C29 A:YKD402 1.4 42.3 0.5
C29 A:YKA401 1.4 42.3 0.5
F31 A:YKA401 2.1 45.8 0.5
F31 A:YKD402 2.1 45.8 0.5
C28 A:YKA401 2.4 35.3 0.5
C28 A:YKD402 2.4 35.3 0.5
C32 A:YKD402 2.4 41.0 0.5
C32 A:YKA401 2.4 41.0 0.5
O A:THR190 3.2 39.1 1.0
CD A:PRO168 3.3 33.3 1.0
CA A:ALA191 3.4 42.8 1.0
N A:GLN192 3.4 32.2 1.0
CG A:PRO168 3.5 34.0 1.0
C27 A:YKA401 3.7 36.0 0.5
C27 A:YKD402 3.7 36.0 0.5
C33 A:YKD402 3.7 35.2 0.5
C33 A:YKA401 3.7 35.2 0.5
N A:PRO168 3.8 29.1 1.0
CA A:LEU167 3.8 28.3 1.0
O A:GLU166 3.9 27.1 1.0
C A:ALA191 3.9 43.2 1.0
C A:THR190 3.9 42.9 1.0
N A:ALA191 4.0 38.6 1.0
C A:LEU167 4.1 29.7 1.0
CD2 A:LEU167 4.1 30.2 1.0
C26 A:YKD402 4.3 31.2 0.5
C26 A:YKA401 4.3 31.2 0.5
CB A:GLN192 4.4 30.7 1.0
CA A:GLN192 4.5 32.6 1.0
CB A:ALA191 4.5 60.1 1.0
O A:GLN192 4.5 33.5 1.0
CA A:PRO168 4.5 37.3 1.0
CB A:PRO168 4.6 45.0 1.0
C A:GLU166 4.7 30.5 1.0
N A:LEU167 4.7 26.0 1.0
CB A:LEU167 4.7 33.8 1.0
CG A:GLN192 4.9 28.8 1.0
C A:GLN192 5.0 27.6 1.0

Fluorine binding site 4 out of 8 in 7m00

Go back to Fluorine Binding Sites List in 7m00
Fluorine binding site 4 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 13C


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 13C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:45.8
occ:0.50
 F31 A:YKD402 0.0 45.8 0.5
F31 A:YKA401 0.0 45.8 0.5
C29 A:YKD402 1.4 42.3 0.5
C29 A:YKA401 1.4 42.3 0.5
F30 A:YKD402 2.1 39.5 0.5
F30 A:YKA401 2.1 39.5 0.5
C32 A:YKD402 2.4 41.0 0.5
C32 A:YKA401 2.4 41.0 0.5
C28 A:YKA401 2.4 35.3 0.5
C28 A:YKD402 2.4 35.3 0.5
O A:THR190 3.0 39.1 1.0
C33 A:YKD402 3.0 35.2 0.5
C33 A:YKA401 3.0 35.2 0.5
C27 A:YKD402 3.0 36.0 0.5
C27 A:YKA401 3.0 36.0 0.5
C A:THR190 3.1 42.9 1.0
CA A:ALA191 3.1 42.8 1.0
N A:ALA191 3.1 38.6 1.0
C26 A:YKD402 3.7 31.2 0.5
C26 A:YKA401 3.7 31.2 0.5
CB A:ALA191 3.9 60.1 1.0
CA A:THR190 4.1 38.3 1.0
C A:ALA191 4.2 43.2 1.0
N A:THR190 4.3 30.2 1.0
N A:GLN192 4.4 32.2 1.0
CG A:PRO168 4.7 34.0 1.0
C A:GLN189 4.8 38.1 1.0
CD A:PRO168 5.0 33.3 1.0
C02 A:YKD402 5.0 35.0 0.5
O A:GLU166 5.0 27.1 1.0
C02 A:YKA401 5.0 35.0 0.5

Fluorine binding site 5 out of 8 in 7m00

Go back to Fluorine Binding Sites List in 7m00
Fluorine binding site 5 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 13C


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 13C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:36.8
occ:0.50
 F30 B:YKA401 0.0 36.8 0.5
F30 B:YKD402 0.0 36.8 0.5
C29 B:YKA401 1.4 40.8 0.5
C29 B:YKD402 1.4 40.8 0.5
F31 B:YKA401 2.1 41.4 0.5
F31 B:YKD402 2.1 41.4 0.5
C28 B:YKA401 2.4 33.5 0.5
C28 B:YKD402 2.4 33.5 0.5
C32 B:YKD402 2.4 41.2 0.5
C32 B:YKA401 2.4 41.2 0.5
O B:THR190 3.2 37.0 1.0
CD B:PRO168 3.3 35.4 1.0
CG B:PRO168 3.4 45.0 1.0
N B:GLN192 3.4 30.4 1.0
CA B:ALA191 3.5 41.2 1.0
C27 B:YKA401 3.7 31.9 0.5
C27 B:YKD402 3.7 31.9 0.5
C33 B:YKD402 3.7 35.3 0.5
C33 B:YKA401 3.7 35.3 0.5
N B:PRO168 3.8 26.0 1.0
CA B:LEU167 3.8 25.1 1.0
O B:GLU166 3.9 28.4 1.0
C B:ALA191 3.9 40.7 1.0
C B:THR190 3.9 39.7 1.0
N B:ALA191 4.1 41.7 1.0
C B:LEU167 4.1 23.3 1.0
CD2 B:LEU167 4.2 33.6 1.0
C26 B:YKA401 4.3 30.2 0.5
C26 B:YKD402 4.3 30.2 0.5
CA B:GLN192 4.5 29.4 1.0
CB B:GLN192 4.5 31.9 1.0
O B:GLN192 4.5 33.6 1.0
CA B:PRO168 4.5 38.6 1.0
CB B:ALA191 4.6 52.5 1.0
CB B:PRO168 4.6 44.9 1.0
CB B:LEU167 4.7 25.6 1.0
C B:GLU166 4.7 31.4 1.0
N B:LEU167 4.8 25.8 1.0
CG B:GLN192 4.9 26.3 1.0

Fluorine binding site 6 out of 8 in 7m00

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Fluorine binding site 6 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 13C


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 13C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:41.4
occ:0.50
 F31 B:YKA401 0.0 41.4 0.5
F31 B:YKD402 0.0 41.4 0.5
C29 B:YKA401 1.3 40.8 0.5
C29 B:YKD402 1.4 40.8 0.5
F30 B:YKD402 2.1 36.8 0.5
F30 B:YKA401 2.1 36.8 0.5
C32 B:YKD402 2.4 41.2 0.5
C32 B:YKA401 2.4 41.2 0.5
C28 B:YKA401 2.4 33.5 0.5
C28 B:YKD402 2.4 33.5 0.5
O B:THR190 3.0 37.0 1.0
C33 B:YKD402 3.0 35.3 0.5
C33 B:YKA401 3.0 35.3 0.5
C27 B:YKA401 3.0 31.9 0.5
C27 B:YKD402 3.0 31.9 0.5
C B:THR190 3.1 39.7 1.0
N B:ALA191 3.2 41.7 1.0
CA B:ALA191 3.2 41.2 1.0
C26 B:YKA401 3.7 30.2 0.5
C26 B:YKD402 3.7 30.2 0.5
CB B:ALA191 4.1 52.5 1.0
CA B:THR190 4.1 34.1 1.0
N B:THR190 4.2 29.1 1.0
C B:ALA191 4.3 40.7 1.0
N B:GLN192 4.5 30.4 1.0
CG B:PRO168 4.6 45.0 1.0
C B:GLN189 4.8 33.8 1.0
C02 B:YKA401 5.0 32.5 0.5
C02 B:YKD402 5.0 32.5 0.5
CD B:PRO168 5.0 35.4 1.0
C25 B:YKA401 5.0 34.9 0.5
C25 B:YKD402 5.0 34.9 0.5
O B:GLU166 5.0 28.4 1.0

Fluorine binding site 7 out of 8 in 7m00

Go back to Fluorine Binding Sites List in 7m00
Fluorine binding site 7 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 13C


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 13C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:36.8
occ:0.50
 F30 B:YKD402 0.0 36.8 0.5
F30 B:YKA401 0.0 36.8 0.5
C29 B:YKA401 1.4 40.8 0.5
C29 B:YKD402 1.4 40.8 0.5
F31 B:YKD402 2.1 41.4 0.5
F31 B:YKA401 2.1 41.4 0.5
C28 B:YKA401 2.4 33.5 0.5
C28 B:YKD402 2.4 33.5 0.5
C32 B:YKD402 2.4 41.2 0.5
C32 B:YKA401 2.4 41.2 0.5
O B:THR190 3.2 37.0 1.0
CD B:PRO168 3.3 35.4 1.0
CG B:PRO168 3.4 45.0 1.0
N B:GLN192 3.5 30.4 1.0
CA B:ALA191 3.5 41.2 1.0
C27 B:YKA401 3.7 31.9 0.5
C27 B:YKD402 3.7 31.9 0.5
C33 B:YKD402 3.7 35.3 0.5
C33 B:YKA401 3.7 35.3 0.5
N B:PRO168 3.7 26.0 1.0
CA B:LEU167 3.8 25.1 1.0
O B:GLU166 3.9 28.4 1.0
C B:ALA191 3.9 40.7 1.0
C B:THR190 3.9 39.7 1.0
N B:ALA191 4.1 41.7 1.0
C B:LEU167 4.1 23.3 1.0
CD2 B:LEU167 4.2 33.6 1.0
C26 B:YKA401 4.3 30.2 0.5
C26 B:YKD402 4.3 30.2 0.5
CA B:GLN192 4.5 29.4 1.0
CB B:GLN192 4.5 31.9 1.0
CA B:PRO168 4.5 38.6 1.0
O B:GLN192 4.5 33.6 1.0
CB B:PRO168 4.6 44.9 1.0
CB B:ALA191 4.6 52.5 1.0
CB B:LEU167 4.7 25.6 1.0
C B:GLU166 4.7 31.4 1.0
N B:LEU167 4.8 25.8 1.0
CG B:GLN192 4.9 26.3 1.0

Fluorine binding site 8 out of 8 in 7m00

Go back to Fluorine Binding Sites List in 7m00
Fluorine binding site 8 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 13C


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 13C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:41.4
occ:0.50
 F31 B:YKD402 0.0 41.4 0.5
F31 B:YKA401 0.0 41.4 0.5
C29 B:YKA401 1.3 40.8 0.5
C29 B:YKD402 1.3 40.8 0.5
F30 B:YKD402 2.1 36.8 0.5
F30 B:YKA401 2.1 36.8 0.5
C32 B:YKD402 2.4 41.2 0.5
C32 B:YKA401 2.4 41.2 0.5
C28 B:YKA401 2.4 33.5 0.5
C28 B:YKD402 2.4 33.5 0.5
O B:THR190 3.0 37.0 1.0
C33 B:YKD402 3.0 35.3 0.5
C27 B:YKA401 3.0 31.9 0.5
C33 B:YKA401 3.0 35.3 0.5
C27 B:YKD402 3.0 31.9 0.5
C B:THR190 3.1 39.7 1.0
N B:ALA191 3.2 41.7 1.0
CA B:ALA191 3.2 41.2 1.0
C26 B:YKA401 3.7 30.2 0.5
C26 B:YKD402 3.7 30.2 0.5
CB B:ALA191 4.1 52.5 1.0
CA B:THR190 4.1 34.1 1.0
N B:THR190 4.3 29.1 1.0
C B:ALA191 4.3 40.7 1.0
N B:GLN192 4.5 30.4 1.0
CG B:PRO168 4.6 45.0 1.0
C B:GLN189 4.8 33.8 1.0
C02 B:YKA401 5.0 32.5 0.5
C02 B:YKD402 5.0 32.5 0.5
CD B:PRO168 5.0 35.4 1.0
C25 B:YKA401 5.0 34.9 0.5
C25 B:YKD402 5.0 34.9 0.5
O B:GLU166 5.0 28.4 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 13C To Be Published.
Page generated: Fri Aug 2 09:09:18 2024

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