Fluorine in PDB 8e5c: Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States

Enzymatic activity of Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States

All present enzymatic activity of Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States, PDB code: 8e5c was solved by A.M.Shaqra, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.41 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 45.129, 63.693, 105.323, 90, 90, 90
R / Rfree (%) 19.6 / 25.4

Other elements in 8e5c:

The structure of Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Sodium (Na) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States (pdb code 8e5c). 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 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States, PDB code: 8e5c:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8e5c

Go back to Fluorine Binding Sites List in 8e5c
Fluorine binding site 1 out of 6 in the Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States


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 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:28.6
occ:0.50
 F1 A:4WI502 0.0 28.6 0.5
F1 A:4WI502 0.1 28.2 0.5
C22 A:4WI502 1.3 22.8 0.5
C22 A:4WI502 1.4 22.9 0.5
F3 A:4WI502 2.2 22.9 0.5
F3 A:4WI502 2.2 23.0 0.5
F2 A:4WI502 2.2 21.9 0.5
F2 A:4WI502 2.2 21.9 0.5
C21 A:4WI502 2.3 22.8 0.5
C21 A:4WI502 2.3 23.0 0.5
O A:HOH612 2.8 30.2 1.0
N4 A:4WI502 3.0 18.8 0.5
O A:HOH854 3.0 19.7 1.0
N4 A:4WI502 3.0 18.4 0.5
O A:HOH734 3.1 28.6 1.0
O4 A:4WI502 3.1 20.6 0.5
O4 A:4WI502 3.2 20.7 0.5
O A:GLU166 3.7 21.5 1.0
O A:THR190 3.7 25.8 1.0
CD A:PRO168 3.8 32.3 1.0
CG A:PRO168 4.1 36.2 1.0
O A:GLN192 4.3 29.0 1.0
C14 A:4WI502 4.3 18.6 0.5
CA A:LEU167 4.3 16.0 1.0
C14 A:4WI502 4.3 18.6 0.5
CD2 A:LEU167 4.3 20.5 1.0
CB A:GLN192 4.4 18.2 1.0
N A:PRO168 4.5 22.8 1.0
C16 A:4WI502 4.5 14.7 0.5
N A:GLN192 4.5 26.5 1.0
C16 A:4WI502 4.6 14.1 0.5
C A:GLU166 4.7 8.0 1.0
CE A:MET165 4.7 18.6 1.0
C A:LEU167 4.7 19.0 1.0
CA A:GLN192 4.9 14.5 1.0
N A:LEU167 5.0 16.0 1.0
C A:THR190 5.0 22.3 1.0
C15 A:4WI502 5.0 18.5 0.5
C A:GLN192 5.0 28.2 1.0

Fluorine binding site 2 out of 6 in 8e5c

Go back to Fluorine Binding Sites List in 8e5c
Fluorine binding site 2 out of 6 in the Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States


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 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:28.2
occ:0.50
 F1 A:4WI502 0.0 28.2 0.5
F1 A:4WI502 0.1 28.6 0.5
C22 A:4WI502 1.4 22.8 0.5
C22 A:4WI502 1.4 22.9 0.5
F3 A:4WI502 2.2 22.9 0.5
F2 A:4WI502 2.2 21.9 0.5
F2 A:4WI502 2.2 21.9 0.5
F3 A:4WI502 2.3 23.0 0.5
C21 A:4WI502 2.4 22.8 0.5
C21 A:4WI502 2.4 23.0 0.5
O A:HOH612 2.7 30.2 1.0
O A:HOH854 3.0 19.7 1.0
N4 A:4WI502 3.1 18.8 0.5
O A:HOH734 3.1 28.6 1.0
N4 A:4WI502 3.2 18.4 0.5
O4 A:4WI502 3.2 20.6 0.5
O4 A:4WI502 3.2 20.7 0.5
O A:THR190 3.7 25.8 1.0
CD A:PRO168 3.7 32.3 1.0
O A:GLU166 3.8 21.5 1.0
CG A:PRO168 4.0 36.2 1.0
O A:GLN192 4.2 29.0 1.0
CD2 A:LEU167 4.3 20.5 1.0
CA A:LEU167 4.3 16.0 1.0
CB A:GLN192 4.3 18.2 1.0
C14 A:4WI502 4.4 18.6 0.5
N A:GLN192 4.4 26.5 1.0
C14 A:4WI502 4.4 18.6 0.5
N A:PRO168 4.4 22.8 1.0
C16 A:4WI502 4.6 14.7 0.5
C16 A:4WI502 4.7 14.1 0.5
C A:LEU167 4.8 19.0 1.0
CE A:MET165 4.8 18.6 1.0
C A:GLU166 4.8 8.0 1.0
CA A:GLN192 4.8 14.5 1.0
C A:GLN192 4.9 28.2 1.0
C A:THR190 4.9 22.3 1.0

Fluorine binding site 3 out of 6 in 8e5c

Go back to Fluorine Binding Sites List in 8e5c
Fluorine binding site 3 out of 6 in the Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States


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 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:21.9
occ:0.50
 F2 A:4WI502 0.0 21.9 0.5
F2 A:4WI502 0.1 21.9 0.5
C22 A:4WI502 1.3 22.8 0.5
C22 A:4WI502 1.4 22.9 0.5
F3 A:4WI502 2.2 22.9 0.5
F3 A:4WI502 2.2 23.0 0.5
F1 A:4WI502 2.2 28.2 0.5
F1 A:4WI502 2.2 28.6 0.5
C21 A:4WI502 2.3 22.8 0.5
C21 A:4WI502 2.4 23.0 0.5
O4 A:4WI502 2.6 20.6 0.5
O4 A:4WI502 2.6 20.7 0.5
CE A:MET165 3.0 18.6 1.0
NE2 A:GLN192 3.2 17.8 1.0
O A:THR190 3.3 25.8 1.0
CB A:GLN192 3.6 18.2 1.0
N4 A:4WI502 3.7 18.8 0.5
CD A:GLN192 3.7 16.7 1.0
N4 A:4WI502 3.7 18.4 0.5
O A:ARG188 3.7 19.8 1.0
CG A:GLN192 3.8 13.7 1.0
O A:HOH612 3.9 30.2 1.0
N A:THR190 4.3 19.8 1.0
C A:THR190 4.4 22.3 1.0
N A:GLN192 4.4 26.5 1.0
OE1 A:GLN192 4.5 16.8 1.0
CA A:GLN192 4.6 14.5 1.0
CD2 A:LEU167 4.6 20.5 1.0
O A:HOH854 4.7 19.7 1.0
C14 A:4WI502 4.8 18.6 0.5
SD A:MET165 4.8 25.4 1.0
C14 A:4WI502 4.8 18.6 0.5
C A:ARG188 4.8 13.7 1.0
CA A:GLN189 4.9 25.1 1.0
O A:GLU166 4.9 21.5 1.0
O A:GLN192 5.0 29.0 1.0

Fluorine binding site 4 out of 6 in 8e5c

Go back to Fluorine Binding Sites List in 8e5c
Fluorine binding site 4 out of 6 in the Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States


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 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:21.9
occ:0.50
 F2 A:4WI502 0.0 21.9 0.5
F2 A:4WI502 0.1 21.9 0.5
C22 A:4WI502 1.4 22.8 0.5
C22 A:4WI502 1.4 22.9 0.5
F3 A:4WI502 2.2 22.9 0.5
F1 A:4WI502 2.2 28.2 0.5
F1 A:4WI502 2.2 28.6 0.5
F3 A:4WI502 2.3 23.0 0.5
C21 A:4WI502 2.4 22.8 0.5
C21 A:4WI502 2.4 23.0 0.5
O4 A:4WI502 2.6 20.6 0.5
O4 A:4WI502 2.7 20.7 0.5
CE A:MET165 3.1 18.6 1.0
NE2 A:GLN192 3.1 17.8 1.0
O A:THR190 3.3 25.8 1.0
CB A:GLN192 3.5 18.2 1.0
CD A:GLN192 3.6 16.7 1.0
O A:ARG188 3.7 19.8 1.0
N4 A:4WI502 3.7 18.8 0.5
N4 A:4WI502 3.8 18.4 0.5
CG A:GLN192 3.8 13.7 1.0
O A:HOH612 3.8 30.2 1.0
N A:THR190 4.3 19.8 1.0
C A:THR190 4.4 22.3 1.0
N A:GLN192 4.4 26.5 1.0
OE1 A:GLN192 4.5 16.8 1.0
CA A:GLN192 4.5 14.5 1.0
CD2 A:LEU167 4.5 20.5 1.0
O A:HOH854 4.7 19.7 1.0
SD A:MET165 4.8 25.4 1.0
C A:ARG188 4.8 13.7 1.0
C14 A:4WI502 4.9 18.6 0.5
C14 A:4WI502 4.9 18.6 0.5
CA A:GLN189 4.9 25.1 1.0
O A:GLU166 4.9 21.5 1.0
O A:GLN192 4.9 29.0 1.0

Fluorine binding site 5 out of 6 in 8e5c

Go back to Fluorine Binding Sites List in 8e5c
Fluorine binding site 5 out of 6 in the Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States


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 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:23.0
occ:0.50
 F3 A:4WI502 0.0 23.0 0.5
F3 A:4WI502 0.1 22.9 0.5
C22 A:4WI502 1.4 22.9 0.5
C22 A:4WI502 1.4 22.8 0.5
F1 A:4WI502 2.2 28.6 0.5
F2 A:4WI502 2.2 21.9 0.5
F2 A:4WI502 2.3 21.9 0.5
F1 A:4WI502 2.3 28.2 0.5
C21 A:4WI502 2.3 22.8 0.5
C21 A:4WI502 2.4 23.0 0.5
N4 A:4WI502 2.8 18.8 0.5
O A:GLU166 2.8 21.5 1.0
N4 A:4WI502 2.8 18.4 0.5
CE A:MET165 3.0 18.6 1.0
O4 A:4WI502 3.3 20.6 0.5
O4 A:4WI502 3.3 20.7 0.5
C A:GLU166 3.5 8.0 1.0
CD2 A:LEU167 3.6 20.5 1.0
CA A:LEU167 3.8 16.0 1.0
N A:LEU167 3.9 16.0 1.0
CB A:MET165 4.2 12.4 1.0
CG A:LEU167 4.2 13.2 1.0
C14 A:4WI502 4.2 18.6 0.5
C14 A:4WI502 4.2 18.6 0.5
O A:HOH734 4.2 28.6 1.0
CG A:MET165 4.3 13.9 1.0
N A:GLU166 4.3 13.2 1.0
SD A:MET165 4.4 25.4 1.0
CB A:LEU167 4.6 13.9 1.0
CA A:GLU166 4.6 17.1 1.0
C13 A:4WI502 4.6 17.1 0.5
C13 A:4WI502 4.6 17.0 0.5
O3 A:4WI502 4.7 15.7 0.5
O A:HOH612 4.7 30.2 1.0
O3 A:4WI502 4.7 15.5 0.5
CB A:GLN192 4.7 18.2 1.0
CD A:PRO168 4.7 32.3 1.0
C A:LEU167 4.8 19.0 1.0
NE2 A:GLN192 4.8 17.8 1.0
C A:MET165 4.9 14.3 1.0

Fluorine binding site 6 out of 6 in 8e5c

Go back to Fluorine Binding Sites List in 8e5c
Fluorine binding site 6 out of 6 in the Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States


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 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:22.9
occ:0.50
 F3 A:4WI502 0.0 22.9 0.5
F3 A:4WI502 0.1 23.0 0.5
C22 A:4WI502 1.4 22.9 0.5
C22 A:4WI502 1.4 22.8 0.5
F1 A:4WI502 2.2 28.6 0.5
F2 A:4WI502 2.2 21.9 0.5
F1 A:4WI502 2.2 28.2 0.5
F2 A:4WI502 2.2 21.9 0.5
C21 A:4WI502 2.4 22.8 0.5
C21 A:4WI502 2.4 23.0 0.5
O A:GLU166 2.9 21.5 1.0
N4 A:4WI502 2.9 18.8 0.5
N4 A:4WI502 2.9 18.4 0.5
CE A:MET165 3.0 18.6 1.0
O4 A:4WI502 3.4 20.6 0.5
O4 A:4WI502 3.4 20.7 0.5
CD2 A:LEU167 3.5 20.5 1.0
C A:GLU166 3.5 8.0 1.0
CA A:LEU167 3.7 16.0 1.0
N A:LEU167 3.9 16.0 1.0
CG A:LEU167 4.1 13.2 1.0
O A:HOH734 4.2 28.6 1.0
CB A:MET165 4.3 12.4 1.0
C14 A:4WI502 4.3 18.6 0.5
C14 A:4WI502 4.3 18.6 0.5
CG A:MET165 4.3 13.9 1.0
N A:GLU166 4.4 13.2 1.0
SD A:MET165 4.4 25.4 1.0
CB A:LEU167 4.5 13.9 1.0
CA A:GLU166 4.6 17.1 1.0
O A:HOH612 4.6 30.2 1.0
CB A:GLN192 4.6 18.2 1.0
CD A:PRO168 4.6 32.3 1.0
C13 A:4WI502 4.7 17.1 0.5
C13 A:4WI502 4.7 17.0 0.5
C A:LEU167 4.8 19.0 1.0
O3 A:4WI502 4.8 15.7 0.5
O3 A:4WI502 4.8 15.5 0.5
NE2 A:GLN192 4.8 17.8 1.0
C A:MET165 5.0 14.3 1.0

Reference:

A.M.Shaqra, C.A.Schiffer. Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States To Be Published.
Page generated: Fri Aug 2 17:49:07 2024

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