Fluorine in PDB 7m01: Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 14C

Enzymatic activity of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 14C

All present enzymatic activity of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 14C:
3.4.22.69;

Protein crystallography data

The structure of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 14C, PDB code: 7m01 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) 48.77 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.093, 98.55, 59.007, 90, 108, 90
R / Rfree (%) 17.8 / 22.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 14C (pdb code 7m01). 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 14C, PDB code: 7m01:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7m01

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Fluorine binding site 1 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 14C


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 14C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:61.9
occ:0.50
 F35 A:YKV401 0.0 61.9 0.5
F35 A:YKS402 0.0 61.9 0.5
C34 A:YKS402 1.3 57.2 0.5
C34 A:YKV401 1.3 57.2 0.5
F36 A:YKS402 2.1 62.7 0.5
F36 A:YKV401 2.1 62.7 0.5
C37 A:YKV401 2.4 49.3 0.5
C33 A:YKS402 2.4 59.0 0.5
C33 A:YKV401 2.4 59.0 0.5
C37 A:YKS402 2.4 49.3 0.5
CB A:ALA191 3.4 30.9 1.0
C32 A:YKS402 3.7 54.8 0.5
C32 A:YKV401 3.7 54.8 0.5
C38 A:YKV401 3.7 43.9 0.5
C38 A:YKS402 3.7 43.9 0.5
CA A:ALA191 4.0 31.2 1.0
C31 A:YKV401 4.2 44.5 0.5
C31 A:YKS402 4.2 44.5 0.5
N A:ALA191 4.2 31.5 1.0
CG A:PRO168 4.6 37.5 1.0
O A:HOH558 4.8 36.5 1.0
C A:THR190 5.0 26.1 1.0

Fluorine binding site 2 out of 8 in 7m01

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Fluorine binding site 2 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 14C


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 14C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:62.7
occ:0.50
 F36 A:YKV401 0.0 62.7 0.5
F36 A:YKS402 0.0 62.7 0.5
C34 A:YKV401 1.3 57.2 0.5
C34 A:YKS402 1.3 57.2 0.5
F35 A:YKV401 2.1 61.9 0.5
F35 A:YKS402 2.1 61.9 0.5
C33 A:YKS402 2.4 59.0 0.5
C33 A:YKV401 2.4 59.0 0.5
C37 A:YKV401 2.4 49.3 0.5
C37 A:YKS402 2.4 49.3 0.5
C32 A:YKS402 3.0 54.8 0.5
C32 A:YKV401 3.0 54.8 0.5
C38 A:YKV401 3.1 43.9 0.5
C38 A:YKS402 3.1 43.9 0.5
CG A:PRO168 3.1 37.5 1.0
CD A:PRO168 3.2 34.0 1.0
CA A:ALA191 3.2 31.2 1.0
CB A:ALA191 3.3 30.9 1.0
C31 A:YKV401 3.6 44.5 0.5
C31 A:YKS402 3.6 44.5 0.5
N A:PRO168 3.8 30.1 1.0
CB A:PRO168 3.9 37.0 1.0
O A:HOH551 4.0 28.9 1.0
CA A:PRO168 4.0 30.8 1.0
N A:ALA191 4.0 31.5 1.0
C A:ALA191 4.4 26.8 1.0
O A:THR190 4.4 32.1 1.0
C A:THR190 4.5 26.1 1.0
N A:GLN192 4.5 23.9 1.0
C A:LEU167 4.6 32.6 1.0
C23 A:YKV401 4.9 39.3 0.5
C23 A:YKS402 4.9 39.3 0.5
O A:GLU166 5.0 29.5 1.0

Fluorine binding site 3 out of 8 in 7m01

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Fluorine binding site 3 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 14C


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 14C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:61.9
occ:0.50
 F35 A:YKS402 0.0 61.9 0.5
F35 A:YKV401 0.0 61.9 0.5
C34 A:YKS402 1.3 57.2 0.5
C34 A:YKV401 1.3 57.2 0.5
F36 A:YKS402 2.1 62.7 0.5
F36 A:YKV401 2.1 62.7 0.5
C37 A:YKV401 2.4 49.3 0.5
C37 A:YKS402 2.4 49.3 0.5
C33 A:YKS402 2.4 59.0 0.5
C33 A:YKV401 2.4 59.0 0.5
CB A:ALA191 3.4 30.9 1.0
C32 A:YKS402 3.7 54.8 0.5
C32 A:YKV401 3.7 54.8 0.5
C38 A:YKV401 3.7 43.9 0.5
C38 A:YKS402 3.7 43.9 0.5
CA A:ALA191 4.0 31.2 1.0
C31 A:YKV401 4.2 44.5 0.5
C31 A:YKS402 4.2 44.5 0.5
N A:ALA191 4.2 31.5 1.0
CG A:PRO168 4.6 37.5 1.0
O A:HOH558 4.8 36.5 1.0
C A:THR190 5.0 26.1 1.0

Fluorine binding site 4 out of 8 in 7m01

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Fluorine binding site 4 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 14C


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 14C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:62.7
occ:0.50
 F36 A:YKS402 0.0 62.7 0.5
F36 A:YKV401 0.0 62.7 0.5
C34 A:YKV401 1.3 57.2 0.5
C34 A:YKS402 1.3 57.2 0.5
F35 A:YKV401 2.1 61.9 0.5
F35 A:YKS402 2.1 61.9 0.5
C33 A:YKS402 2.4 59.0 0.5
C33 A:YKV401 2.4 59.0 0.5
C37 A:YKV401 2.4 49.3 0.5
C37 A:YKS402 2.4 49.3 0.5
C32 A:YKS402 3.0 54.8 0.5
C32 A:YKV401 3.0 54.8 0.5
C38 A:YKV401 3.1 43.9 0.5
C38 A:YKS402 3.1 43.9 0.5
CG A:PRO168 3.1 37.5 1.0
CA A:ALA191 3.2 31.2 1.0
CD A:PRO168 3.2 34.0 1.0
CB A:ALA191 3.3 30.9 1.0
C31 A:YKV401 3.6 44.5 0.5
C31 A:YKS402 3.6 44.5 0.5
N A:PRO168 3.8 30.1 1.0
CB A:PRO168 3.9 37.0 1.0
O A:HOH551 4.0 28.9 1.0
N A:ALA191 4.0 31.5 1.0
CA A:PRO168 4.0 30.8 1.0
C A:ALA191 4.4 26.8 1.0
O A:THR190 4.4 32.1 1.0
C A:THR190 4.5 26.1 1.0
N A:GLN192 4.5 23.9 1.0
C A:LEU167 4.6 32.6 1.0
C23 A:YKV401 4.9 39.3 0.5
C23 A:YKS402 4.9 39.3 0.5
O A:GLU166 5.0 29.5 1.0

Fluorine binding site 5 out of 8 in 7m01

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Fluorine binding site 5 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 14C


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 14C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:67.0
occ:0.50
 F35 B:YKS401 0.0 67.0 0.5
F35 B:YKV402 0.0 67.0 0.5
C34 B:YKS401 1.3 60.8 0.5
C34 B:YKV402 1.3 60.8 0.5
F36 B:YKS401 2.1 60.4 0.5
F36 B:YKV402 2.1 60.4 0.5
C33 B:YKS401 2.4 56.2 0.5
C37 B:YKS401 2.4 54.1 0.5
C33 B:YKV402 2.4 56.3 0.5
C37 B:YKV402 2.4 54.1 0.5
CA B:ALA191 3.1 55.2 1.0
CB B:ALA191 3.2 63.3 1.0
CG B:PRO168 3.6 52.1 1.0
N B:ALA191 3.7 63.1 1.0
C32 B:YKS401 3.7 53.4 0.5
C32 B:YKV402 3.7 53.4 0.5
C38 B:YKS401 3.7 44.9 0.5
C38 B:YKV402 3.7 44.9 0.5
C B:THR190 4.2 48.3 1.0
O B:HOH645 4.2 42.3 1.0
O B:THR190 4.2 48.1 1.0
CB B:PRO168 4.2 38.7 1.0
C31 B:YKS401 4.3 44.2 0.5
C31 B:YKV402 4.3 44.2 0.5
CD B:PRO168 4.3 51.8 1.0
C B:ALA191 4.4 40.3 1.0
N B:GLN192 4.6 40.8 1.0
N B:PRO168 4.7 50.0 1.0
CA B:PRO168 4.7 47.2 1.0

Fluorine binding site 6 out of 8 in 7m01

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Fluorine binding site 6 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 14C


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 14C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:60.4
occ:0.50
 F36 B:YKS401 0.0 60.4 0.5
F36 B:YKV402 0.0 60.4 0.5
C34 B:YKV402 1.3 60.8 0.5
C34 B:YKS401 1.3 60.8 0.5
F35 B:YKV402 2.1 67.0 0.5
F35 B:YKS401 2.1 67.0 0.5
C37 B:YKV402 2.4 54.1 0.5
C33 B:YKV402 2.4 56.3 0.5
C37 B:YKS401 2.4 54.1 0.5
C33 B:YKS401 2.4 56.2 0.5
O B:HOH645 2.6 42.3 1.0
C32 B:YKV402 2.9 53.4 0.5
C32 B:YKS401 2.9 53.4 0.5
C38 B:YKV402 3.0 44.9 0.5
C38 B:YKS401 3.0 44.9 0.5
CD B:PRO168 3.1 51.8 1.0
CG B:PRO168 3.2 52.1 1.0
N B:PRO168 3.3 50.0 1.0
C31 B:YKS401 3.5 44.2 0.5
C31 B:YKV402 3.5 44.2 0.5
C B:LEU167 3.8 36.1 1.0
CA B:PRO168 3.9 47.2 1.0
O B:GLU166 3.9 30.9 1.0
CA B:ALA191 4.0 55.2 1.0
CB B:PRO168 4.0 38.7 1.0
CA B:LEU167 4.1 34.4 1.0
O B:THR190 4.1 48.1 1.0
N B:GLN192 4.4 40.8 1.0
C23 B:YKS401 4.4 43.3 0.5
C23 B:YKV402 4.5 43.3 0.5
CB B:ALA191 4.6 63.3 1.0
N B:ALA191 4.6 63.1 1.0
C B:THR190 4.6 48.3 1.0
O B:LEU167 4.7 37.2 1.0
C B:ALA191 4.7 40.3 1.0
C B:GLU166 4.8 31.6 1.0
N B:LEU167 4.9 29.8 1.0
O B:GLN192 5.0 47.6 1.0

Fluorine binding site 7 out of 8 in 7m01

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Fluorine binding site 7 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 14C


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 14C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:67.0
occ:0.50
 F35 B:YKV402 0.0 67.0 0.5
F35 B:YKS401 0.0 67.0 0.5
C34 B:YKS401 1.3 60.8 0.5
C34 B:YKV402 1.3 60.8 0.5
F36 B:YKS401 2.1 60.4 0.5
F36 B:YKV402 2.1 60.4 0.5
C33 B:YKS401 2.4 56.2 0.5
C37 B:YKS401 2.4 54.1 0.5
C33 B:YKV402 2.4 56.3 0.5
C37 B:YKV402 2.4 54.1 0.5
CA B:ALA191 3.1 55.2 1.0
CB B:ALA191 3.2 63.3 1.0
CG B:PRO168 3.6 52.1 1.0
N B:ALA191 3.7 63.1 1.0
C32 B:YKS401 3.7 53.4 0.5
C32 B:YKV402 3.7 53.4 0.5
C38 B:YKS401 3.7 44.9 0.5
C38 B:YKV402 3.7 44.9 0.5
C B:THR190 4.2 48.3 1.0
O B:HOH645 4.2 42.3 1.0
O B:THR190 4.2 48.1 1.0
CB B:PRO168 4.2 38.7 1.0
C31 B:YKS401 4.3 44.2 0.5
C31 B:YKV402 4.3 44.2 0.5
CD B:PRO168 4.3 51.8 1.0
C B:ALA191 4.4 40.3 1.0
N B:GLN192 4.6 40.8 1.0
N B:PRO168 4.7 50.0 1.0
CA B:PRO168 4.7 47.2 1.0

Fluorine binding site 8 out of 8 in 7m01

Go back to Fluorine Binding Sites List in 7m01
Fluorine binding site 8 out of 8 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 14C


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 14C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:60.4
occ:0.50
 F36 B:YKV402 0.0 60.4 0.5
F36 B:YKS401 0.0 60.4 0.5
C34 B:YKV402 1.3 60.8 0.5
C34 B:YKS401 1.3 60.8 0.5
F35 B:YKV402 2.1 67.0 0.5
F35 B:YKS401 2.1 67.0 0.5
C37 B:YKV402 2.4 54.1 0.5
C33 B:YKV402 2.4 56.3 0.5
C37 B:YKS401 2.4 54.1 0.5
C33 B:YKS401 2.4 56.2 0.5
O B:HOH645 2.6 42.3 1.0
C32 B:YKV402 2.9 53.4 0.5
C32 B:YKS401 2.9 53.4 0.5
C38 B:YKV402 3.0 44.9 0.5
C38 B:YKS401 3.0 44.9 0.5
CD B:PRO168 3.1 51.8 1.0
CG B:PRO168 3.2 52.1 1.0
N B:PRO168 3.3 50.0 1.0
C31 B:YKS401 3.5 44.2 0.5
C31 B:YKV402 3.5 44.2 0.5
C B:LEU167 3.8 36.1 1.0
CA B:PRO168 3.9 47.2 1.0
O B:GLU166 3.9 30.9 1.0
CA B:ALA191 4.0 55.2 1.0
CB B:PRO168 4.0 38.7 1.0
CA B:LEU167 4.0 34.4 1.0
O B:THR190 4.1 48.1 1.0
N B:GLN192 4.4 40.8 1.0
C23 B:YKS401 4.4 43.3 0.5
C23 B:YKV402 4.5 43.3 0.5
CB B:ALA191 4.6 63.3 1.0
N B:ALA191 4.6 63.1 1.0
C B:THR190 4.6 48.3 1.0
O B:LEU167 4.7 37.2 1.0
C B:ALA191 4.7 40.3 1.0
C B:GLU166 4.8 31.6 1.0
N B:LEU167 4.9 29.8 1.0
O B:GLN192 5.0 47.6 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 14C To Be Published.
Page generated: Fri Aug 2 09:09:27 2024

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