Atomistry » Fluorine » PDB 8eew-8f0s » 8ezz
Atomistry »
  Fluorine »
    PDB 8eew-8f0s »
      8ezz »

Fluorine in PDB 8ezz: Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2

Enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2

All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2:
3.4.22.69;

Protein crystallography data

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2, PDB code: 8ezz was solved by M.Westberg, D.Fernandez, M.Z.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.10 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 45.494, 63.18, 103.655, 90, 90, 90
R / Rfree (%) 19 / 25.4

Other elements in 8ezz:

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2 (pdb code 8ezz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2, PDB code: 8ezz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 8ezz

Go back to Fluorine Binding Sites List in 8ezz
Fluorine binding site 1 out of 5 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2


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 ML2006A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:55.4
occ:1.00
 F1 A:X70401 0.0 55.4 1.0
C16 A:X70401 1.3 52.0 1.0
F3 A:X70401 2.0 58.9 1.0
F2 A:X70401 2.1 67.0 1.0
C15 A:X70401 2.4 43.5 1.0
N2 A:X70401 2.7 33.0 1.0
O A:GLU166 2.7 33.5 1.0
CD2 A:LEU167 3.2 34.2 1.0
CE A:MET165 3.3 49.4 1.0
O2 A:X70401 3.4 38.7 1.0
CA A:LEU167 3.5 34.4 1.0
C A:GLU166 3.5 30.8 1.0
N A:LEU167 3.9 33.6 1.0
CG A:LEU167 3.9 37.4 1.0
C10 A:X70401 4.1 32.5 1.0
CB A:LEU167 4.1 34.0 1.0
N A:GLU166 4.6 29.4 1.0
CD A:PRO168 4.6 43.3 1.0
SD A:MET165 4.6 47.7 1.0
C A:LEU167 4.7 39.6 1.0
CA A:GLU166 4.7 28.4 1.0
C9 A:X70401 4.7 27.9 1.0
O A:GLN192 4.7 46.7 1.0
NE2 A:GLN192 4.7 33.3 1.0
CB A:MET165 4.7 34.5 1.0
O3 A:X70401 4.8 31.6 1.0
CG A:MET165 4.8 37.6 1.0
CB A:GLN192 4.8 41.7 1.0
O A:THR190 4.9 45.1 1.0

Fluorine binding site 2 out of 5 in 8ezz

Go back to Fluorine Binding Sites List in 8ezz
Fluorine binding site 2 out of 5 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2


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 ML2006A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:67.0
occ:1.00
 F2 A:X70401 0.0 67.0 1.0
C16 A:X70401 1.3 52.0 1.0
F1 A:X70401 2.1 55.4 1.0
F3 A:X70401 2.2 58.9 1.0
C15 A:X70401 2.4 43.5 1.0
O2 A:X70401 3.1 38.7 1.0
N2 A:X70401 3.1 33.0 1.0
O A:GLU166 3.7 33.5 1.0
CD A:PRO168 3.9 43.3 1.0
O A:GLN192 4.1 46.7 1.0
O A:THR190 4.1 45.1 1.0
O A:HOH601 4.1 38.4 1.0
CA A:LEU167 4.1 34.4 1.0
C12 A:X70401 4.4 35.2 1.0
N A:GLN192 4.4 42.8 1.0
C10 A:X70401 4.4 32.5 1.0
CG A:PRO168 4.4 45.0 1.0
CD2 A:LEU167 4.5 34.2 1.0
N A:PRO168 4.6 41.8 1.0
C A:GLU166 4.6 30.8 1.0
C A:LEU167 4.7 39.6 1.0
N A:LEU167 4.9 33.6 1.0
C11 A:X70401 4.9 30.7 1.0
C A:GLN192 4.9 40.8 1.0
C A:THR190 5.0 52.2 1.0
CB A:LEU167 5.0 34.0 1.0
CB A:GLN192 5.0 41.7 1.0

Fluorine binding site 3 out of 5 in 8ezz

Go back to Fluorine Binding Sites List in 8ezz
Fluorine binding site 3 out of 5 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2


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 ML2006A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:58.9
occ:1.00
 F3 A:X70401 0.0 58.9 1.0
C16 A:X70401 1.3 52.0 1.0
F1 A:X70401 2.0 55.4 1.0
F2 A:X70401 2.2 67.0 1.0
C15 A:X70401 2.3 43.5 1.0
O2 A:X70401 2.7 38.7 1.0
O A:THR190 2.9 45.1 1.0
NE2 A:GLN192 3.3 33.3 1.0
N2 A:X70401 3.4 33.0 1.0
CE A:MET165 3.4 49.4 1.0
CD A:GLN192 3.7 38.1 1.0
CB A:GLN192 3.8 41.7 1.0
CG A:GLN192 3.8 39.7 1.0
N A:GLN192 4.0 42.8 1.0
C A:THR190 4.1 52.2 1.0
CD2 A:LEU167 4.2 34.2 1.0
O A:ARG188 4.2 35.7 1.0
CA A:GLN192 4.4 42.9 1.0
N A:THR190 4.4 41.8 1.0
O A:GLN192 4.5 46.7 1.0
OE1 A:GLN192 4.6 37.6 1.0
O A:GLU166 4.6 33.5 1.0
O A:HOH601 4.6 38.4 1.0
C10 A:X70401 4.7 32.5 1.0
C A:ALA191 4.7 46.4 1.0
C A:GLN192 4.8 40.8 1.0
CA A:THR190 5.0 49.7 1.0
N A:ALA191 5.0 49.4 1.0

Fluorine binding site 4 out of 5 in 8ezz

Go back to Fluorine Binding Sites List in 8ezz
Fluorine binding site 4 out of 5 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2


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 ML2006A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:86.2
occ:1.00
 F4 A:X70401 0.0 86.2 1.0
C21 A:X70401 1.4 79.6 1.0
F5 A:X70401 2.2 86.1 1.0
C22 A:X70401 2.4 71.9 1.0
C20 A:X70401 2.5 71.9 1.0
O A:HOH583 2.9 43.6 1.0
CG2 A:THR25 3.1 33.1 1.0
N4 A:X70401 3.2 71.4 1.0
O A:THR26 3.3 35.7 1.0
N A:THR26 3.7 38.4 1.0
C A:THR26 4.1 37.0 1.0
CA A:THR25 4.1 35.0 1.0
CB A:THR25 4.2 33.2 1.0
C A:THR25 4.3 37.6 1.0
C19 A:X70401 4.5 48.9 1.0
CA A:THR26 4.6 36.2 1.0
OD1 A:ASN142 4.7 31.5 0.5
OG1 A:THR25 4.8 35.4 1.0

Fluorine binding site 5 out of 5 in 8ezz

Go back to Fluorine Binding Sites List in 8ezz
Fluorine binding site 5 out of 5 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2


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 ML2006A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:86.1
occ:1.00
 F5 A:X70401 0.0 86.1 1.0
C21 A:X70401 1.4 79.6 1.0
F4 A:X70401 2.2 86.2 1.0
C22 A:X70401 2.5 71.9 1.0
C20 A:X70401 2.5 71.9 1.0
OD1 A:ASN142 2.9 31.5 0.5
N4 A:X70401 2.9 71.4 1.0
ND2 A:ASN142 3.0 37.1 0.5
CG A:ASN142 3.2 35.6 0.5
C19 A:X70401 4.0 48.9 1.0
O A:HOH583 4.2 43.6 1.0
CB A:ASN142 4.6 33.3 0.5
O4 A:X70401 4.6 44.3 1.0
O5 A:X70401 4.6 49.7 1.0
N A:GLY143 4.8 29.4 1.0
OD1 A:ASN142 4.9 35.0 0.5
CG2 A:THR25 4.9 33.1 1.0
C18 A:X70401 4.9 42.8 1.0

Reference:

M.Westberg, D.Fernandez, M.Z.Lin. Rational Design of A New Class of Protease Inhibitors For the Potential Treatment of Coronavirus Diseases To Be Published.
Page generated: Fri Aug 2 18:26:47 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy