Chlorine in PDB 8v8e: Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv)

Enzymatic activity of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv)

All present enzymatic activity of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv):
3.4.22.69;

Protein crystallography data

The structure of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv), PDB code: 8v8e was solved by A.Kovalevsky, L.Coates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.83 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.476, 62.641, 58.583, 90, 100.23, 90
R / Rfree (%) 14.9 / 19.3

Other elements in 8v8e:

The structure of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv) also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv) (pdb code 8v8e). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv), PDB code: 8v8e:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8v8e

Go back to Chlorine Binding Sites List in 8v8e
Chlorine binding site 1 out of 2 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:16.3
occ:0.98
 CL2 A:7YY301 0.0 16.3 1.0
C22 A:7YY301 1.8 20.9 1.0
C21 A:7YY301 2.7 16.3 1.0
C13 A:7YY301 2.8 22.5 1.0
N12 A:7YY301 3.0 17.5 1.0
C11 A:7YY301 3.2 20.1 1.0
N10 A:7YY301 3.3 15.0 1.0
SG A:CYS145 3.5 14.1 1.0
CB A:CYS145 3.6 9.6 1.0
C34 A:7YY301 3.8 22.5 1.0
O A:HOH444 3.8 33.3 1.0
CD2 A:HIS41 3.8 15.0 1.0
C20 A:7YY301 4.0 24.9 1.0
C14 A:7YY301 4.1 22.4 1.0
CD2 A:LEU27 4.1 10.3 1.0
N24 A:7YY301 4.1 18.7 1.0
C08 A:7YY301 4.2 16.3 1.0
F33 A:7YY301 4.3 18.8 1.0
C32 A:7YY301 4.4 20.8 1.0
CB A:LEU27 4.5 11.6 1.0
C15 A:7YY301 4.5 18.3 1.0
C26 A:7YY301 4.6 17.7 1.0
O A:HOH425 4.6 21.2 1.0
CG A:HIS41 4.7 21.2 1.0
O A:HOH448 4.7 28.7 1.0
O09 A:7YY301 4.7 22.8 1.0
O A:THR26 4.7 18.6 1.0
C25 A:7YY301 4.8 17.7 1.0
CG A:LEU27 4.8 15.8 1.0
N07 A:7YY301 4.8 21.3 1.0
CB A:HIS41 4.8 17.3 1.0
NE2 A:HIS41 4.8 21.1 1.0
C35 A:7YY301 4.9 17.6 1.0

Chlorine binding site 2 out of 2 in 8v8e

Go back to Chlorine Binding Sites List in 8v8e
Chlorine binding site 2 out of 2 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:23.8
occ:0.75
 CL2 B:7YY301 0.0 23.8 0.8
C22 B:7YY301 1.8 27.2 0.8
C21 B:7YY301 2.7 31.9 0.8
C13 B:7YY301 2.8 26.8 0.8
N12 B:7YY301 3.0 20.5 0.8
C11 B:7YY301 3.2 19.4 0.8
N10 B:7YY301 3.2 20.7 0.8
SG B:CYS145 3.5 23.0 1.0
CB B:CYS145 3.6 18.5 1.0
CD2 B:LEU27 3.8 21.9 1.0
C34 B:7YY301 3.9 22.5 0.8
C20 B:7YY301 4.0 26.8 0.8
C14 B:7YY301 4.0 26.0 0.8
N24 B:7YY301 4.1 22.4 0.8
C08 B:7YY301 4.1 25.1 0.8
CD2 B:HIS41 4.1 36.0 1.0
F33 B:7YY301 4.4 28.8 0.8
CB B:LEU27 4.5 14.2 1.0
C15 B:7YY301 4.5 27.1 0.8
C32 B:7YY301 4.6 31.0 0.8
CG B:LEU27 4.6 22.7 1.0
O09 B:7YY301 4.6 22.8 0.8
C26 B:7YY301 4.7 27.6 0.8
N07 B:7YY301 4.8 21.1 0.8
O B:THR26 4.8 23.0 1.0
C25 B:7YY301 4.8 26.5 0.8
C35 B:7YY301 4.8 24.0 0.8
CG B:HIS41 4.8 28.0 1.0
CB B:HIS41 4.9 21.8 1.0
O B:HOH435 4.9 31.9 1.0
CG2 B:THR25 4.9 23.9 1.0

Reference:

A.Kovalevsky, A.Aniana, L.Coates, R.Ghirlando, N.T.Nashed, J.M.Louis. Visualizing the Active Site Oxyanion Loop Transition Upon Ensitrelvir Binding and Transient Dimerization of Sars-Cov-2 Main Protease. J.Mol.Biol. 68616 2024.
ISSN: ESSN 1089-8638
PubMed: 38762033
DOI: 10.1016/J.JMB.2024.168616
Page generated: Tue Jul 30 13:32:27 2024

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