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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

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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

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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

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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

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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: Wed Jul 16 01:03:51 2025

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