Fluorine in PDB 8dcz: Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir, PDB code: 8dcz was solved by E.M.Lewandowski, Y.Hu, H.Tan, J.Wang, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.28 / 2.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.566, 53.786, 114.76, 90, 100.53, 90
R / Rfree (%) 19.2 / 25.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir (pdb code 8dcz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir, PDB code: 8dcz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8dcz

Go back to Fluorine Binding Sites List in 8dcz
Fluorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:49.1
occ:1.00
 F1 A:4WI401 0.0 49.1 1.0
C22 A:4WI401 1.3 47.9 1.0
F2 A:4WI401 2.1 57.7 1.0
F3 A:4WI401 2.1 44.9 1.0
C21 A:4WI401 2.4 41.9 1.0
N4 A:4WI401 2.8 36.2 1.0
O A:GLU166 3.1 24.5 1.0
O4 A:4WI401 3.4 42.0 1.0
N A:PRO168 3.4 31.4 1.0
C A:LEU167 3.6 31.1 1.0
CD A:PRO168 3.7 30.6 1.0
C23 A:4WI401 3.8 31.7 1.0
CA A:PRO168 3.8 30.4 1.0
CG A:PRO168 3.9 30.6 1.0
O A:LEU167 3.9 32.3 1.0
C14 A:4WI401 4.0 31.5 1.0
C A:GLU166 4.2 26.5 1.0
CA A:LEU167 4.2 29.7 1.0
C15 A:4WI401 4.3 31.4 1.0
C17 A:4WI401 4.4 31.3 1.0
OH A:TYR165 4.4 35.9 1.0
CB A:PRO168 4.4 30.8 1.0
N A:LEU167 4.6 26.9 1.0
CZ A:TYR165 4.7 33.5 1.0
CE1 A:TYR165 4.9 31.8 1.0

Fluorine binding site 2 out of 6 in 8dcz

Go back to Fluorine Binding Sites List in 8dcz
Fluorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:57.7
occ:1.00
 F2 A:4WI401 0.0 57.7 1.0
C22 A:4WI401 1.3 47.9 1.0
F1 A:4WI401 2.1 49.1 1.0
F3 A:4WI401 2.1 44.9 1.0
OH A:TYR165 2.3 35.9 1.0
C21 A:4WI401 2.4 41.9 1.0
CZ A:TYR165 2.7 33.5 1.0
O A:GLU166 2.9 24.5 1.0
N4 A:4WI401 3.0 36.2 1.0
CE1 A:TYR165 3.1 31.8 1.0
O4 A:4WI401 3.2 42.0 1.0
CD A:PRO168 3.4 30.6 1.0
CE2 A:TYR165 3.5 32.8 1.0
O A:THR190 3.6 35.8 1.0
CA A:LEU167 3.6 29.7 1.0
N A:PRO168 3.8 31.4 1.0
C A:LEU167 3.8 31.1 1.0
C A:GLU166 3.9 26.5 1.0
CG A:PRO168 4.0 30.6 1.0
CD1 A:TYR165 4.2 30.1 1.0
N A:LEU167 4.2 26.9 1.0
C A:THR190 4.4 35.5 1.0
CA A:ALA191 4.4 36.5 1.0
C14 A:4WI401 4.4 31.5 1.0
CD2 A:TYR165 4.5 31.0 1.0
N A:GLN192 4.6 34.4 1.0
O A:LEU167 4.6 32.3 1.0
N A:ALA191 4.7 36.0 1.0
CA A:PRO168 4.8 30.4 1.0
CG A:TYR165 4.8 27.7 1.0
CB A:LEU167 4.8 30.0 1.0
C A:ALA191 5.0 36.5 1.0

Fluorine binding site 3 out of 6 in 8dcz

Go back to Fluorine Binding Sites List in 8dcz
Fluorine binding site 3 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:44.9
occ:1.00
 F3 A:4WI401 0.0 44.9 1.0
C22 A:4WI401 1.3 47.9 1.0
F1 A:4WI401 2.1 49.1 1.0
F2 A:4WI401 2.1 57.7 1.0
C21 A:4WI401 2.4 41.9 1.0
O4 A:4WI401 2.7 42.0 1.0
O A:THR190 3.3 35.8 1.0
C A:THR190 3.4 35.5 1.0
N A:ALA191 3.5 36.0 1.0
CA A:ALA191 3.5 36.5 1.0
N4 A:4WI401 3.6 36.2 1.0
OH A:TYR165 3.7 35.9 1.0
CG A:PRO168 3.8 30.6 1.0
CD A:PRO168 4.1 30.6 1.0
CB A:ALA191 4.3 37.2 1.0
N A:THR190 4.3 35.6 1.0
CA A:THR190 4.3 36.8 1.0
CZ A:TYR165 4.4 33.5 1.0
N A:PRO168 4.5 31.4 1.0
C A:ALA191 4.6 36.5 1.0
CE1 A:TYR165 4.6 31.8 1.0
O A:GLU166 4.6 24.5 1.0
C14 A:4WI401 4.8 31.5 1.0
C23 A:4WI401 4.8 31.7 1.0
N A:GLN192 4.8 34.4 1.0
CB A:PRO168 4.8 30.8 1.0
CA A:PRO168 4.9 30.4 1.0

Fluorine binding site 4 out of 6 in 8dcz

Go back to Fluorine Binding Sites List in 8dcz
Fluorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:44.1
occ:1.00
 F1 B:4WI401 0.0 44.1 1.0
C22 B:4WI401 1.3 41.7 1.0
F3 B:4WI401 2.1 40.3 1.0
F2 B:4WI401 2.1 49.5 1.0
C21 B:4WI401 2.4 39.9 1.0
N4 B:4WI401 2.8 35.4 1.0
O4 B:4WI401 3.3 38.9 1.0
O B:GLU166 3.3 24.4 1.0
N B:PRO168 3.6 33.0 1.0
C23 B:4WI401 3.7 31.8 1.0
C B:LEU167 3.8 32.5 1.0
CD B:PRO168 3.8 33.1 1.0
O B:HOH516 3.9 28.4 1.0
CA B:PRO168 3.9 33.3 1.0
CG B:PRO168 4.0 34.7 1.0
C14 B:4WI401 4.0 32.1 1.0
O B:LEU167 4.1 33.0 1.0
C15 B:4WI401 4.2 31.9 1.0
C17 B:4WI401 4.3 32.5 1.0
C B:GLU166 4.4 27.1 1.0
CA B:LEU167 4.4 30.6 1.0
CB B:PRO168 4.5 34.5 1.0
OH B:TYR165 4.6 30.3 1.0
N B:LEU167 4.9 29.8 1.0
CZ B:TYR165 4.9 30.9 1.0

Fluorine binding site 5 out of 6 in 8dcz

Go back to Fluorine Binding Sites List in 8dcz
Fluorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:49.5
occ:1.00
 F2 B:4WI401 0.0 49.5 1.0
C22 B:4WI401 1.3 41.7 1.0
F1 B:4WI401 2.1 44.1 1.0
F3 B:4WI401 2.1 40.3 1.0
C21 B:4WI401 2.4 39.9 1.0
OH B:TYR165 2.5 30.3 1.0
CZ B:TYR165 2.8 30.9 1.0
O B:GLU166 2.9 24.4 1.0
N4 B:4WI401 2.9 35.4 1.0
CE1 B:TYR165 3.2 30.3 1.0
O4 B:4WI401 3.3 38.9 1.0
CD B:PRO168 3.3 33.1 1.0
CA B:LEU167 3.6 30.6 1.0
N B:PRO168 3.6 33.0 1.0
CE2 B:TYR165 3.7 30.9 1.0
C B:LEU167 3.7 32.5 1.0
O B:THR190 3.8 37.8 1.0
C B:GLU166 3.8 27.1 1.0
CG B:PRO168 4.0 34.7 1.0
N B:LEU167 4.2 29.8 1.0
CD1 B:TYR165 4.3 29.8 1.0
C14 B:4WI401 4.3 32.1 1.0
C B:THR190 4.5 36.9 1.0
O B:LEU167 4.5 33.0 1.0
CA B:ALA191 4.5 38.2 1.0
CD2 B:TYR165 4.6 29.2 1.0
O B:HOH516 4.6 28.4 1.0
CA B:PRO168 4.6 33.3 1.0
N B:GLN192 4.8 34.4 1.0
N B:ALA191 4.8 37.2 1.0
CB B:LEU167 4.8 29.9 1.0
CG B:TYR165 4.9 28.2 1.0

Fluorine binding site 6 out of 6 in 8dcz

Go back to Fluorine Binding Sites List in 8dcz
Fluorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:40.3
occ:1.00
 F3 B:4WI401 0.0 40.3 1.0
C22 B:4WI401 1.3 41.7 1.0
F1 B:4WI401 2.1 44.1 1.0
F2 B:4WI401 2.1 49.5 1.0
C21 B:4WI401 2.4 39.9 1.0
O4 B:4WI401 2.7 38.9 1.0
O B:HOH516 2.7 28.4 1.0
O B:THR190 3.3 37.8 1.0
C B:THR190 3.4 36.9 1.0
N B:ALA191 3.4 37.2 1.0
CA B:ALA191 3.5 38.2 1.0
N4 B:4WI401 3.6 35.4 1.0
OH B:TYR165 3.7 30.3 1.0
CG B:PRO168 3.9 34.7 1.0
CD B:PRO168 4.1 33.1 1.0
CB B:ALA191 4.3 39.0 1.0
N B:THR190 4.3 35.0 1.0
CA B:THR190 4.3 36.6 1.0
CZ B:TYR165 4.5 30.9 1.0
N B:PRO168 4.5 33.0 1.0
CE1 B:TYR165 4.6 30.3 1.0
C B:ALA191 4.7 36.8 1.0
O B:GLU166 4.7 24.4 1.0
C14 B:4WI401 4.8 32.1 1.0
C23 B:4WI401 4.8 31.8 1.0
N B:GLN192 4.9 34.4 1.0
C B:GLN189 4.9 33.9 1.0
CB B:PRO168 4.9 34.5 1.0
CA B:PRO168 5.0 33.3 1.0

Reference:

Y.Hu, E.M.Lewandowski, H.Tan, X.Zhang, R.T.Morgan, X.Zhang, L.M.C.Jacobs, S.G.Butler, M.V.Gongora, J.Choy, X.Deng, Y.Chen, J.Wang. Naturally Occurring Mutations of Sars-Cov-2 Main Protease Confer Drug Resistance to Nirmatrelvir. Biorxiv 2022.
ISSN: ISSN 2692-8205
PubMed: 36119652
DOI: 10.1101/2022.06.28.497978
Page generated: Fri Aug 2 17:27:09 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