Atomistry » Fluorine » PDB 7m8o-7mmh » 7maz
Atomistry »
  Fluorine »
    PDB 7m8o-7mmh »
      7maz »

Fluorine in PDB 7maz: Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139

Enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139

All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139:
3.4.22.69;

Protein crystallography data

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139, PDB code: 7maz was solved by G.J.Lockbaum, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.63 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.823, 105.273, 52.894, 90, 104.05, 90
R / Rfree (%) 16.4 / 20.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 (pdb code 7maz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139, PDB code: 7maz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7maz

Go back to Fluorine Binding Sites List in 7maz
Fluorine binding site 1 out of 6 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.5
occ:0.61
F30 A:YVD401 0.0 35.5 0.6
F30 A:YVD401 0.2 35.1 0.4
C24 A:YVD401 1.3 28.3 0.6
C24 A:YVD401 1.4 28.2 0.4
C29 A:YVD401 2.4 29.5 0.4
C25 A:YVD401 2.4 28.7 0.6
C29 A:YVD401 2.5 29.9 0.6
C25 A:YVD401 2.5 28.4 0.4
H291 A:YVD401 2.6 35.5 0.4
H251 A:YVD401 2.6 34.5 0.6
HA A:ASP187 2.6 22.4 1.0
H291 A:YVD401 2.7 35.9 0.6
H251 A:YVD401 2.8 34.1 0.4
N A:ARG188 2.8 21.9 1.0
C A:ASP187 2.8 21.7 1.0
C A:ARG188 2.9 22.8 1.0
O A:ARG188 3.0 21.4 1.0
H A:ARG188 3.1 26.3 1.0
CA A:ASP187 3.2 18.7 1.0
CA A:ARG188 3.2 30.0 1.0
HA A:ARG188 3.3 36.0 1.0
H391 A:YVD401 3.3 25.3 0.4
O A:ASP187 3.3 19.1 1.0
H391 A:YVD401 3.3 24.7 0.6
N A:GLN189 3.4 19.9 1.0
HA A:GLN189 3.5 28.1 1.0
O A:VAL186 3.8 20.2 1.0
C26 A:YVD401 3.8 25.4 0.6
C28 A:YVD401 3.8 26.8 0.4
C28 A:YVD401 3.8 27.0 0.6
HB2 A:ASP187 3.8 27.3 1.0
H A:GLN189 3.9 23.9 1.0
H381 A:YVD401 3.9 23.9 0.4
C26 A:YVD401 3.9 25.3 0.4
CA A:GLN189 3.9 23.4 1.0
HB2 A:GLN189 3.9 25.7 1.0
H381 A:YVD401 4.0 23.6 0.6
C39 A:YVD401 4.0 21.1 0.4
C39 A:YVD401 4.1 20.5 0.6
CB A:ASP187 4.1 22.8 1.0
HE22 A:GLN192 4.1 27.5 1.0
C27 A:YVD401 4.3 21.4 0.6
N A:ASP187 4.3 16.3 1.0
C27 A:YVD401 4.3 21.5 0.4
C38 A:YVD401 4.3 19.9 0.4
C38 A:YVD401 4.4 19.7 0.6
SD A:MET165 4.4 25.9 1.0
CB A:GLN189 4.4 21.4 1.0
C A:VAL186 4.5 16.9 1.0
HB3 A:ASP187 4.5 27.3 1.0
H281 A:YVD401 4.5 32.2 0.4
H261 A:YVD401 4.5 30.4 0.6
H281 A:YVD401 4.6 32.5 0.6
HE21 A:GLN192 4.6 27.5 1.0
HG3 A:GLN189 4.6 22.7 1.0
H261 A:YVD401 4.7 30.4 0.4
NE2 A:GLN192 4.7 22.9 1.0
CB A:ARG188 4.7 26.2 1.0
HH A:TYR54 4.8 31.5 1.0
HB2 A:ARG188 5.0 31.4 1.0
H A:ASP187 5.0 19.6 1.0

Fluorine binding site 2 out of 6 in 7maz

Go back to Fluorine Binding Sites List in 7maz
Fluorine binding site 2 out of 6 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.1
occ:0.39
F30 A:YVD401 0.0 35.1 0.4
F30 A:YVD401 0.2 35.5 0.6
C24 A:YVD401 1.3 28.3 0.6
C24 A:YVD401 1.3 28.2 0.4
C25 A:YVD401 2.3 28.7 0.6
C25 A:YVD401 2.4 28.4 0.4
C29 A:YVD401 2.4 29.5 0.4
H251 A:YVD401 2.5 34.5 0.6
C29 A:YVD401 2.5 29.9 0.6
H251 A:YVD401 2.6 34.1 0.4
H291 A:YVD401 2.7 35.5 0.4
HA A:ASP187 2.8 22.4 1.0
H291 A:YVD401 2.8 35.9 0.6
N A:ARG188 2.8 21.9 1.0
C A:ASP187 2.8 21.7 1.0
C A:ARG188 2.9 22.8 1.0
O A:ARG188 3.0 21.4 1.0
H A:ARG188 3.1 26.3 1.0
CA A:ARG188 3.2 30.0 1.0
HA A:ARG188 3.2 36.0 1.0
O A:ASP187 3.3 19.1 1.0
CA A:ASP187 3.3 18.7 1.0
N A:GLN189 3.3 19.9 1.0
H391 A:YVD401 3.4 25.3 0.4
H391 A:YVD401 3.5 24.7 0.6
HA A:GLN189 3.5 28.1 1.0
C26 A:YVD401 3.7 25.4 0.6
H A:GLN189 3.8 23.9 1.0
C26 A:YVD401 3.8 25.3 0.4
C28 A:YVD401 3.8 26.8 0.4
C28 A:YVD401 3.8 27.0 0.6
HB2 A:GLN189 3.8 25.7 1.0
HB2 A:ASP187 3.8 27.3 1.0
CA A:GLN189 3.9 23.4 1.0
H381 A:YVD401 3.9 23.9 0.4
O A:VAL186 3.9 20.2 1.0
H381 A:YVD401 4.0 23.6 0.6
C39 A:YVD401 4.1 21.1 0.4
CB A:ASP187 4.2 22.8 1.0
C39 A:YVD401 4.2 20.5 0.6
C27 A:YVD401 4.2 21.4 0.6
C27 A:YVD401 4.3 21.5 0.4
HE22 A:GLN192 4.3 27.5 1.0
CB A:GLN189 4.3 21.4 1.0
C38 A:YVD401 4.4 19.9 0.4
N A:ASP187 4.4 16.3 1.0
H261 A:YVD401 4.4 30.4 0.6
C38 A:YVD401 4.4 19.7 0.6
H261 A:YVD401 4.5 30.4 0.4
H281 A:YVD401 4.6 32.2 0.4
HG3 A:GLN189 4.6 22.7 1.0
H281 A:YVD401 4.6 32.5 0.6
SD A:MET165 4.6 25.9 1.0
C A:VAL186 4.6 16.9 1.0
HB3 A:ASP187 4.6 27.3 1.0
HE21 A:GLN192 4.7 27.5 1.0
CB A:ARG188 4.7 26.2 1.0
HH A:TYR54 4.7 31.5 1.0
NE2 A:GLN192 4.8 22.9 1.0
HB2 A:ARG188 5.0 31.4 1.0
O A:MET49 5.0 29.6 1.0

Fluorine binding site 3 out of 6 in 7maz

Go back to Fluorine Binding Sites List in 7maz
Fluorine binding site 3 out of 6 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:28.3
occ:0.61
F40 A:YVD401 0.0 28.3 0.6
F40 A:YVD401 0.0 25.9 0.4
C34 A:YVD401 1.3 21.9 0.4
C34 A:YVD401 1.3 22.1 0.6
C35 A:YVD401 2.4 21.5 0.4
C35 A:YVD401 2.5 21.6 0.6
C39 A:YVD401 2.5 20.5 0.6
C39 A:YVD401 2.5 21.1 0.4
HB2 A:GLN192 2.6 21.6 1.0
H351 A:YVD401 2.6 25.8 0.4
H351 A:YVD401 2.7 25.9 0.6
HE3 A:MET165 2.7 31.6 1.0
H391 A:YVD401 2.7 24.7 0.6
H391 A:YVD401 2.7 25.3 0.4
HE21 A:GLN192 3.1 27.5 1.0
HD23 A:LEU167 3.1 25.2 1.0
NE2 A:GLN192 3.1 22.9 1.0
HD22 A:LEU167 3.1 25.2 1.0
HD21 A:LEU167 3.2 25.2 1.0
CD A:GLN192 3.3 19.7 1.0
CD2 A:LEU167 3.3 21.0 1.0
HG3 A:GLN192 3.4 24.9 1.0
CB A:GLN192 3.4 17.9 1.0
CE A:MET165 3.4 26.3 1.0
HE1 A:MET165 3.4 31.6 1.0
HE22 A:GLN192 3.4 27.5 1.0
CG A:GLN192 3.5 20.7 1.0
C36 A:YVD401 3.8 20.0 0.4
C36 A:YVD401 3.8 20.2 0.6
C38 A:YVD401 3.8 19.7 0.6
C38 A:YVD401 3.8 19.9 0.4
H A:GLN192 3.9 21.3 1.0
OE1 A:GLN192 3.9 20.9 1.0
HB3 A:GLN192 3.9 21.6 1.0
SD A:MET165 4.1 25.9 1.0
HG3 A:MET165 4.2 26.0 1.0
HE2 A:MET165 4.2 31.6 1.0
O A:THR190 4.2 20.0 1.0
C37 A:YVD401 4.4 19.5 0.4
C37 A:YVD401 4.4 19.4 0.6
HD1 A:PHE185 4.4 25.0 1.0
N A:GLN192 4.4 17.7 1.0
CA A:GLN192 4.4 25.2 1.0
HA A:LEU167 4.5 20.9 1.0
HG2 A:GLN192 4.5 24.9 1.0
O A:HOH596 4.5 23.4 1.0
H361 A:YVD401 4.6 24.1 0.4
H361 A:YVD401 4.6 24.3 0.6
H381 A:YVD401 4.6 23.6 0.6
H381 A:YVD401 4.6 23.9 0.4
O A:GLN192 4.6 25.7 1.0
CG A:MET165 4.7 21.7 1.0
HB2 A:MET165 4.7 17.1 1.0
CG A:LEU167 4.8 19.3 1.0
C A:GLN192 4.9 21.5 1.0
HB3 A:PHE185 5.0 22.2 1.0
HA A:GLN189 5.0 28.1 1.0
HD3 A:PRO168 5.0 21.6 1.0

Fluorine binding site 4 out of 6 in 7maz

Go back to Fluorine Binding Sites List in 7maz
Fluorine binding site 4 out of 6 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:25.9
occ:0.39
F40 A:YVD401 0.0 25.9 0.4
F40 A:YVD401 0.0 28.3 0.6
C34 A:YVD401 1.3 21.9 0.4
C34 A:YVD401 1.4 22.1 0.6
C35 A:YVD401 2.5 21.5 0.4
C39 A:YVD401 2.5 20.5 0.6
C39 A:YVD401 2.5 21.1 0.4
C35 A:YVD401 2.5 21.6 0.6
HB2 A:GLN192 2.6 21.6 1.0
HE3 A:MET165 2.7 31.6 1.0
H351 A:YVD401 2.7 25.8 0.4
H391 A:YVD401 2.7 24.7 0.6
H351 A:YVD401 2.7 25.9 0.6
H391 A:YVD401 2.7 25.3 0.4
HE21 A:GLN192 3.1 27.5 1.0
NE2 A:GLN192 3.1 22.9 1.0
HD23 A:LEU167 3.1 25.2 1.0
HD22 A:LEU167 3.2 25.2 1.0
HD21 A:LEU167 3.2 25.2 1.0
CD A:GLN192 3.3 19.7 1.0
CD2 A:LEU167 3.3 21.0 1.0
HG3 A:GLN192 3.4 24.9 1.0
CE A:MET165 3.4 26.3 1.0
HE1 A:MET165 3.4 31.6 1.0
HE22 A:GLN192 3.4 27.5 1.0
CB A:GLN192 3.4 17.9 1.0
CG A:GLN192 3.5 20.7 1.0
C36 A:YVD401 3.8 20.0 0.4
C38 A:YVD401 3.8 19.7 0.6
C38 A:YVD401 3.8 19.9 0.4
C36 A:YVD401 3.9 20.2 0.6
OE1 A:GLN192 3.9 20.9 1.0
H A:GLN192 3.9 21.3 1.0
HB3 A:GLN192 3.9 21.6 1.0
SD A:MET165 4.1 25.9 1.0
HG3 A:MET165 4.2 26.0 1.0
HE2 A:MET165 4.2 31.6 1.0
O A:THR190 4.2 20.0 1.0
C37 A:YVD401 4.4 19.5 0.4
HD1 A:PHE185 4.4 25.0 1.0
C37 A:YVD401 4.4 19.4 0.6
CA A:GLN192 4.4 25.2 1.0
N A:GLN192 4.4 17.7 1.0
HG2 A:GLN192 4.5 24.9 1.0
HA A:LEU167 4.5 20.9 1.0
O A:HOH596 4.5 23.4 1.0
H361 A:YVD401 4.6 24.1 0.4
H381 A:YVD401 4.6 23.6 0.6
H381 A:YVD401 4.6 23.9 0.4
H361 A:YVD401 4.6 24.3 0.6
O A:GLN192 4.6 25.7 1.0
CG A:MET165 4.7 21.7 1.0
HB2 A:MET165 4.7 17.1 1.0
CG A:LEU167 4.8 19.3 1.0
C A:GLN192 4.9 21.5 1.0
HB3 A:PHE185 4.9 22.2 1.0
HA A:GLN189 5.0 28.1 1.0

Fluorine binding site 5 out of 6 in 7maz

Go back to Fluorine Binding Sites List in 7maz
Fluorine binding site 5 out of 6 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:46.6
occ:1.00
F30 B:YVD401 0.0 46.6 1.0
C24 B:YVD401 1.4 41.2 1.0
N B:ARG188 2.4 34.4 1.0
C25 B:YVD401 2.5 39.1 1.0
C29 B:YVD401 2.5 35.7 1.0
HA B:ASP187 2.6 28.7 1.0
H B:ARG188 2.6 41.3 1.0
C B:ASP187 2.7 30.2 1.0
H291 B:YVD401 2.7 42.9 1.0
H251 B:YVD401 2.7 46.9 1.0
C B:ARG188 2.8 38.8 1.0
HA B:ARG188 2.8 42.9 1.0
CA B:ARG188 2.9 35.7 1.0
O B:ARG188 3.0 32.9 1.0
CA B:ASP187 3.1 23.9 1.0
O B:ASP187 3.2 28.3 1.0
HE3 B:MET49 3.3 59.1 1.0
H391 B:YVD401 3.3 32.9 1.0
N B:GLN189 3.4 35.7 1.0
HA B:GLN189 3.6 45.4 1.0
HB2 B:ASP187 3.7 32.8 1.0
H B:GLN189 3.8 42.9 1.0
O B:VAL186 3.8 24.4 1.0
C26 B:YVD401 3.8 33.2 1.0
C28 B:YVD401 3.9 32.4 1.0
HE2 B:MET49 3.9 59.1 1.0
CE B:MET49 3.9 49.3 1.0
CB B:ASP187 4.0 27.3 1.0
CA B:GLN189 4.0 37.9 1.0
HE1 B:MET49 4.1 59.1 1.0
C39 B:YVD401 4.1 27.4 1.0
H381 B:YVD401 4.1 36.3 1.0
HB2 B:GLN189 4.1 36.5 1.0
N B:ASP187 4.2 19.8 1.0
HE22 B:GLN192 4.3 37.7 1.0
C27 B:YVD401 4.3 22.5 1.0
SD B:MET165 4.4 30.1 1.0
CB B:ARG188 4.4 38.7 1.0
C B:VAL186 4.4 23.0 1.0
HB3 B:ASP187 4.4 32.8 1.0
HH B:TYR54 4.5 32.6 1.0
C38 B:YVD401 4.5 30.2 1.0
H261 B:YVD401 4.6 39.8 1.0
H281 B:YVD401 4.6 38.9 1.0
CB B:GLN189 4.6 30.4 1.0
HB3 B:ARG188 4.7 46.5 1.0
HE21 B:GLN192 4.8 37.7 1.0
HE2 B:MET165 4.8 29.4 1.0
H B:THR190 4.8 43.8 1.0
NE2 B:GLN192 4.9 31.4 1.0
HG2 B:ARG188 4.9 51.5 1.0
HB2 B:ARG188 4.9 46.5 1.0
H B:ASP187 4.9 23.8 1.0

Fluorine binding site 6 out of 6 in 7maz

Go back to Fluorine Binding Sites List in 7maz
Fluorine binding site 6 out of 6 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:34.6
occ:1.00
F40 B:YVD401 0.0 34.6 1.0
C34 B:YVD401 1.3 31.4 1.0
C39 B:YVD401 2.5 27.4 1.0
C35 B:YVD401 2.5 26.0 1.0
HE21 B:GLN192 2.6 37.7 1.0
H391 B:YVD401 2.7 32.9 1.0
H351 B:YVD401 2.7 31.2 1.0
NE2 B:GLN192 2.9 31.4 1.0
HB2 B:GLN192 2.9 38.0 1.0
HE3 B:MET165 3.0 29.4 1.0
HD23 B:LEU167 3.1 38.9 1.0
HE22 B:GLN192 3.1 37.7 1.0
HD22 B:LEU167 3.2 38.9 1.0
HD21 B:LEU167 3.4 38.9 1.0
CD2 B:LEU167 3.4 32.4 1.0
CD B:GLN192 3.5 29.0 1.0
HG3 B:GLN192 3.6 40.5 1.0
CB B:GLN192 3.8 31.6 1.0
C38 B:YVD401 3.8 30.2 1.0
CG B:GLN192 3.9 33.7 1.0
C36 B:YVD401 3.9 29.8 1.0
CE B:MET165 3.9 24.5 1.0
O B:THR190 4.0 34.1 1.0
HE2 B:MET165 4.1 29.4 1.0
HG3 B:MET165 4.1 24.1 1.0
H B:GLN192 4.1 38.7 1.0
OE1 B:GLN192 4.3 27.2 1.0
C37 B:YVD401 4.4 23.7 1.0
HB3 B:GLN192 4.4 38.0 1.0
HA B:LEU167 4.4 27.8 1.0
SD B:MET165 4.5 30.1 1.0
N B:GLN192 4.6 32.3 1.0
H381 B:YVD401 4.6 36.3 1.0
HE1 B:MET165 4.6 29.4 1.0
H361 B:YVD401 4.6 35.8 1.0
CA B:GLN192 4.7 27.6 1.0
CG B:MET165 4.7 20.0 1.0
O B:GLN192 4.7 36.8 1.0
HA B:GLN189 4.8 45.4 1.0
O B:ARG188 4.8 32.9 1.0
HB2 B:MET165 4.8 24.4 1.0
HG2 B:GLN192 4.8 40.5 1.0
HD3 B:PRO168 4.8 37.1 1.0
HD1 B:PHE185 4.9 33.4 1.0
CG B:LEU167 4.9 23.2 1.0
H B:THR190 4.9 43.8 1.0

Reference:

G.J.Lockbaum, C.A.Schiffer. Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 To Be Published.
Page generated: Tue Jul 15 21:36:41 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy