Fluorine in PDB 7uju: Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) in Complex with Nirmatrelvir

Enzymatic activity of Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) in Complex with Nirmatrelvir

All present enzymatic activity of Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) in Complex with Nirmatrelvir:
3.4.22.69;

Protein crystallography data

The structure of Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) in Complex with Nirmatrelvir, PDB code: 7uju was solved by A.Kovalevsky, D.W.Kneller, L.Coates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.03 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.726, 62.605, 58.965, 90, 99.08, 90
R / Rfree (%) 15.4 / 17.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) in Complex with Nirmatrelvir (pdb code 7uju). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) in Complex with Nirmatrelvir, PDB code: 7uju:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7uju

Go back to Fluorine Binding Sites List in 7uju
Fluorine binding site 1 out of 6 in the Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) 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 Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:36.1
occ:1.00
 F1 A:4WI401 0.0 36.1 1.0
C22 A:4WI401 1.3 33.6 1.0
F2 A:4WI401 2.2 35.3 1.0
F3 A:4WI401 2.2 42.6 1.0
C21 A:4WI401 2.4 29.6 1.0
N4 A:4WI401 2.8 23.7 1.0
O A:GLU166 3.0 23.1 1.0
CE A:MET165 3.2 37.4 1.0
O4 A:4WI401 3.4 36.3 1.0
CD2 A:LEU167 3.5 39.9 1.0
C A:GLU166 3.7 23.4 1.0
CA A:LEU167 3.9 26.9 1.0
N A:LEU167 4.1 22.2 1.0
C14 A:4WI401 4.2 23.7 1.0
CB A:MET165 4.3 19.9 1.0
CG A:LEU167 4.3 27.7 1.0
CG A:MET165 4.4 29.4 1.0
N A:GLU166 4.5 19.2 1.0
O3 A:4WI401 4.5 23.5 1.0
C13 A:4WI401 4.6 24.8 1.0
O A:HOH570 4.6 34.9 1.0
CD A:PRO168 4.6 30.5 1.0
SD A:MET165 4.6 37.1 1.0
CB A:LEU167 4.7 26.0 1.0
CB A:GLN192 4.7 51.3 1.0
CA A:GLU166 4.7 20.6 1.0
C A:LEU167 4.9 32.6 1.0
NE2 A:GLN192 4.9 34.6 1.0

Fluorine binding site 2 out of 6 in 7uju

Go back to Fluorine Binding Sites List in 7uju
Fluorine binding site 2 out of 6 in the Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) 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 Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.3
occ:1.00
 F2 A:4WI401 0.0 35.3 1.0
C22 A:4WI401 1.3 33.6 1.0
F3 A:4WI401 2.2 42.6 1.0
F1 A:4WI401 2.2 36.1 1.0
C21 A:4WI401 2.4 29.6 1.0
N4 A:4WI401 2.9 23.7 1.0
O4 A:4WI401 3.2 36.3 1.0
O A:HOH570 3.3 34.9 1.0
O A:GLU166 3.4 23.1 1.0
CD A:PRO168 3.4 30.5 1.0
CG A:PRO168 3.9 32.6 1.0
CA A:LEU167 4.1 26.9 1.0
N A:PRO168 4.1 31.7 1.0
O A:GLN192 4.3 63.6 1.0
C14 A:4WI401 4.3 23.7 1.0
C A:GLU166 4.4 23.4 1.0
C A:LEU167 4.4 32.6 1.0
CD2 A:LEU167 4.5 39.9 1.0
O A:THR190 4.5 58.7 1.0
N A:LEU167 4.7 22.2 1.0
C16 A:4WI401 4.7 25.7 1.0
CB A:GLN192 5.0 51.3 1.0

Fluorine binding site 3 out of 6 in 7uju

Go back to Fluorine Binding Sites List in 7uju
Fluorine binding site 3 out of 6 in the Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) 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 Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:42.6
occ:1.00
 F3 A:4WI401 0.0 42.6 1.0
C22 A:4WI401 1.3 33.6 1.0
F2 A:4WI401 2.2 35.3 1.0
F1 A:4WI401 2.2 36.1 1.0
C21 A:4WI401 2.4 29.6 1.0
O4 A:4WI401 2.6 36.3 1.0
O A:THR190 2.9 58.7 1.0
N4 A:4WI401 3.6 23.7 1.0
CB A:GLN192 3.7 51.3 1.0
NE2 A:GLN192 3.8 34.6 1.0
CE A:MET165 3.9 37.4 1.0
C A:THR190 4.1 60.8 1.0
N A:THR190 4.2 45.0 1.0
N A:GLN192 4.2 64.6 1.0
CD A:GLN192 4.2 38.9 1.0
O A:ARG188 4.3 28.8 1.0
CG A:GLN192 4.3 60.7 1.0
O A:GLN192 4.5 63.6 1.0
CA A:GLN192 4.5 65.0 1.0
CD2 A:LEU167 4.7 39.9 1.0
C14 A:4WI401 4.8 23.7 1.0
CA A:THR190 4.8 52.2 1.0
O A:GLU166 4.8 23.1 1.0
C A:GLN192 4.9 69.7 1.0
CA A:GLN189 5.0 37.8 1.0

Fluorine binding site 4 out of 6 in 7uju

Go back to Fluorine Binding Sites List in 7uju
Fluorine binding site 4 out of 6 in the Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) 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 Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:45.4
occ:1.00
 F1 B:4WI401 0.0 45.4 1.0
C22 B:4WI401 1.3 43.5 1.0
F3 B:4WI401 2.2 47.7 1.0
F2 B:4WI401 2.2 49.4 1.0
C21 B:4WI401 2.4 35.8 1.0
O4 B:4WI401 2.7 34.4 1.0
O B:THR190 2.9 48.9 1.0
NE2 B:GLN192 3.5 33.1 1.0
N4 B:4WI401 3.6 28.0 1.0
CE B:MET165 3.6 40.3 1.0
CB B:GLN192 3.7 46.6 1.0
C B:THR190 4.1 52.8 1.0
N B:GLN192 4.2 45.4 1.0
CD B:GLN192 4.3 35.6 1.0
O B:ARG188 4.3 31.3 1.0
CD2 B:LEU167 4.3 38.0 1.0
CG B:GLN192 4.4 42.7 1.0
N B:THR190 4.4 42.3 1.0
CA B:GLN192 4.6 43.3 1.0
O B:GLU166 4.7 23.1 1.0
C B:ALA191 4.8 51.0 1.0
CA B:ALA191 4.8 46.5 1.0
C14 B:4WI401 4.8 28.4 1.0
CA B:GLN189 4.9 39.4 1.0
N B:ALA191 4.9 45.9 1.0
O B:GLN192 4.9 47.6 1.0
CA B:THR190 4.9 49.4 1.0

Fluorine binding site 5 out of 6 in 7uju

Go back to Fluorine Binding Sites List in 7uju
Fluorine binding site 5 out of 6 in the Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) 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 Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:49.4
occ:1.00
 F2 B:4WI401 0.0 49.4 1.0
C22 B:4WI401 1.3 43.5 1.0
F3 B:4WI401 2.2 47.7 1.0
F1 B:4WI401 2.2 45.4 1.0
C21 B:4WI401 2.4 35.8 1.0
N4 B:4WI401 3.0 28.0 1.0
O4 B:4WI401 3.2 34.4 1.0
O B:GLU166 3.4 23.1 1.0
CD B:PRO168 3.5 39.1 1.0
CA B:LEU167 3.9 31.2 1.0
N B:PRO168 4.0 43.0 1.0
CG B:PRO168 4.2 43.5 1.0
C B:LEU167 4.3 39.1 1.0
CD2 B:LEU167 4.3 38.0 1.0
C14 B:4WI401 4.3 28.4 1.0
C B:GLU166 4.4 27.0 1.0
O B:THR190 4.5 48.9 1.0
N B:LEU167 4.6 27.1 1.0
C17 B:4WI401 4.7 31.6 1.0
O B:GLN192 4.7 47.6 1.0
N B:GLN192 4.8 45.4 1.0
CA B:PRO168 4.9 48.8 1.0
CB B:GLN192 4.9 46.6 1.0
C15 B:4WI401 4.9 30.1 1.0
CB B:LEU167 5.0 27.3 1.0

Fluorine binding site 6 out of 6 in 7uju

Go back to Fluorine Binding Sites List in 7uju
Fluorine binding site 6 out of 6 in the Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) 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 Room-Temperature X-Ray Structure of Monomeric Sars-Cov-2 Main Protease Catalytic Domain (MPRO1-196) in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:47.7
occ:1.00
 F3 B:4WI401 0.0 47.7 1.0
C22 B:4WI401 1.3 43.5 1.0
F2 B:4WI401 2.2 49.4 1.0
F1 B:4WI401 2.2 45.4 1.0
C21 B:4WI401 2.4 35.8 1.0
N4 B:4WI401 2.7 28.0 1.0
O B:GLU166 2.7 23.1 1.0
CE B:MET165 3.1 40.3 1.0
CD2 B:LEU167 3.2 38.0 1.0
O4 B:4WI401 3.4 34.4 1.0
C B:GLU166 3.5 27.0 1.0
CA B:LEU167 3.7 31.2 1.0
N B:LEU167 3.9 27.1 1.0
C14 B:4WI401 4.1 28.4 1.0
CG B:LEU167 4.2 34.3 1.0
CB B:MET165 4.3 23.9 1.0
N B:GLU166 4.5 20.1 1.0
CB B:LEU167 4.5 27.3 1.0
CG B:MET165 4.5 30.7 1.0
O3 B:4WI401 4.6 25.8 1.0
C13 B:4WI401 4.6 29.0 1.0
SD B:MET165 4.6 39.7 1.0
CD B:PRO168 4.6 39.1 1.0
NE2 B:GLN192 4.6 33.1 1.0
CA B:GLU166 4.6 22.2 1.0
C B:LEU167 4.7 39.1 1.0
CB B:GLN192 4.8 46.6 1.0
N B:PRO168 5.0 43.0 1.0

Reference:

N.T.Nashed, D.W.Kneller, L.Coates, R.Ghirlando, A.Aniana, A.Kovalevsky, J.M.Louis. Autoprocessing and Oxyanion Loop Reorganization Upon GC373 and Nirmatrelvir Binding of Monomeric Sars-Cov-2 Main Protease Catalytic Domain. Commun Biol V. 5 976 2022.
ISSN: ESSN 2399-3642
PubMed: 36114420
DOI: 10.1038/S42003-022-03910-Y
Page generated: Fri Aug 2 14:14:05 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy