Fluorine in PDB 7lzw: Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 20B (Deuterated Analog of 19B)

Enzymatic activity of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 20B (Deuterated Analog of 19B)

All present enzymatic activity of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 20B (Deuterated Analog of 19B):
3.4.22.69;

Protein crystallography data

The structure of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 20B (Deuterated Analog of 19B), PDB code: 7lzw 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) 36.78 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55, 98.274, 58.173, 90, 107.5, 90
R / Rfree (%) 18.4 / 25.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 20B (Deuterated Analog of 19B) (pdb code 7lzw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 20B (Deuterated Analog of 19B), PDB code: 7lzw:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7lzw

Go back to Fluorine Binding Sites List in 7lzw
Fluorine binding site 1 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 20B (Deuterated Analog of 19B)


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 20B (Deuterated Analog of 19B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:93.1
occ:0.50
 F28 A:YLM401 0.0 93.1 0.5
F28 A:YLS402 0.0 93.2 0.5
C27 A:YLS402 1.3 75.2 0.5
C27 A:YLM401 1.3 75.2 0.5
C26 A:YLS402 2.3 70.8 0.5
C29 A:YLS402 2.4 74.8 0.5
C29 A:YLM401 2.4 70.8 0.5
C26 A:YLM401 2.4 74.8 0.5
CB A:ALA191 3.4 30.5 1.0
C25 A:YLS402 3.6 67.2 0.5
C30 A:YLS402 3.6 72.6 0.5
C30 A:YLM401 3.6 67.2 0.5
C25 A:YLM401 3.6 72.6 0.5
N A:ALA191 3.7 46.9 1.0
CA A:ALA191 3.8 41.7 1.0
C24 A:YLS402 4.2 72.0 0.5
C24 A:YLM401 4.2 72.0 0.5
C A:THR190 4.5 39.2 1.0
CA A:THR190 5.0 50.5 1.0

Fluorine binding site 2 out of 4 in 7lzw

Go back to Fluorine Binding Sites List in 7lzw
Fluorine binding site 2 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 20B (Deuterated Analog of 19B)


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 20B (Deuterated Analog of 19B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:93.2
occ:0.50
 F28 A:YLS402 0.0 93.2 0.5
F28 A:YLM401 0.0 93.1 0.5
C27 A:YLS402 1.3 75.2 0.5
C27 A:YLM401 1.4 75.2 0.5
C29 A:YLS402 2.4 74.8 0.5
C26 A:YLS402 2.4 70.8 0.5
C26 A:YLM401 2.4 74.8 0.5
C29 A:YLM401 2.4 70.8 0.5
CB A:ALA191 3.4 30.5 1.0
C25 A:YLS402 3.6 67.2 0.5
C30 A:YLS402 3.6 72.6 0.5
C25 A:YLM401 3.6 72.6 0.5
C30 A:YLM401 3.6 67.2 0.5
N A:ALA191 3.7 46.9 1.0
CA A:ALA191 3.9 41.7 1.0
C24 A:YLS402 4.2 72.0 0.5
C24 A:YLM401 4.2 72.0 0.5
C A:THR190 4.5 39.2 1.0

Fluorine binding site 3 out of 4 in 7lzw

Go back to Fluorine Binding Sites List in 7lzw
Fluorine binding site 3 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 20B (Deuterated Analog of 19B)


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 20B (Deuterated Analog of 19B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:52.9
occ:0.50
 F28 B:YLM401 0.0 52.9 0.5
F28 B:YLS402 0.0 52.9 0.5
C27 B:YLS402 1.3 49.6 0.5
C27 B:YLM401 1.3 49.6 0.5
C29 B:YLS402 2.3 52.6 0.5
C29 B:YLM401 2.4 52.6 0.5
C26 B:YLM401 2.4 49.1 0.5
C26 B:YLS402 2.4 49.1 0.5
C30 B:YLS402 3.6 52.5 0.5
C30 B:YLM401 3.6 52.5 0.5
C25 B:YLS402 3.6 51.3 0.5
C25 B:YLM401 3.6 51.3 0.5
C16 B:YLM401 3.9 49.1 0.5
C16 B:YLS402 4.0 48.9 0.5
C24 B:YLS402 4.2 54.3 0.5
C24 B:YLM401 4.2 54.3 0.5
OD1 B:ASN142 4.3 48.3 1.0
ND2 B:ASN142 4.4 40.2 1.0
CG B:ASN142 4.7 55.4 1.0
C17 B:YLS402 4.8 44.6 0.5
C17 B:YLM401 4.8 44.6 0.5

Fluorine binding site 4 out of 4 in 7lzw

Go back to Fluorine Binding Sites List in 7lzw
Fluorine binding site 4 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 20B (Deuterated Analog of 19B)


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 20B (Deuterated Analog of 19B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:52.9
occ:0.50
 F28 B:YLS402 0.0 52.9 0.5
F28 B:YLM401 0.0 52.9 0.5
C27 B:YLS402 1.3 49.6 0.5
C27 B:YLM401 1.4 49.6 0.5
C29 B:YLS402 2.4 52.6 0.5
C26 B:YLM401 2.4 49.1 0.5
C26 B:YLS402 2.4 49.1 0.5
C29 B:YLM401 2.4 52.6 0.5
C30 B:YLS402 3.6 52.5 0.5
C25 B:YLS402 3.6 51.3 0.5
C25 B:YLM401 3.6 51.3 0.5
C30 B:YLM401 3.6 52.5 0.5
C16 B:YLM401 3.9 49.1 0.5
C16 B:YLS402 4.0 48.9 0.5
C24 B:YLS402 4.2 54.3 0.5
C24 B:YLM401 4.2 54.3 0.5
OD1 B:ASN142 4.2 48.3 1.0
ND2 B:ASN142 4.4 40.2 1.0
CG B:ASN142 4.7 55.4 1.0
C17 B:YLS402 4.8 44.6 0.5
C17 B:YLM401 4.8 44.6 0.5

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 20B (Deuterated Analog of 19B) To Be Published.
Page generated: Sat Apr 3 15:13:25 2021

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