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

Go back to Fluorine Binding Sites List in 7m01
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

Go back to Fluorine Binding Sites List in 7m01
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

Go back to Fluorine Binding Sites List in 7m01
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

Go back to Fluorine Binding Sites List in 7m01
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

Go back to Fluorine Binding Sites List in 7m01
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

Go back to Fluorine Binding Sites List in 7m01
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

Go back to Fluorine Binding Sites List in 7m01
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy