Chlorine in PDB 8v8g: Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-196) in Complex with Ensitrelvir (Esv)

Enzymatic activity of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-196) in Complex with Ensitrelvir (Esv)

All present enzymatic activity of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-196) 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 1-196) in Complex with Ensitrelvir (Esv), PDB code: 8v8g 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) 28.57 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.538, 62.479, 58.091, 90, 100.38, 90
R / Rfree (%) 15.9 / 20.1

Other elements in 8v8g:

The structure of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-196) 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 1-196) in Complex with Ensitrelvir (Esv) (pdb code 8v8g). 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 1-196) in Complex with Ensitrelvir (Esv), PDB code: 8v8g:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8v8g

Go back to Chlorine Binding Sites List in 8v8g
Chlorine binding site 1 out of 2 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-196) 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 1-196) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:21.5
occ:1.00
 CL2 A:7YY201 0.0 21.5 1.0
C22 A:7YY201 1.8 25.8 1.0
C21 A:7YY201 2.7 22.6 1.0
C13 A:7YY201 2.8 24.9 1.0
N12 A:7YY201 3.0 22.9 1.0
C11 A:7YY201 3.2 24.2 1.0
N10 A:7YY201 3.2 18.4 1.0
SG A:CYS145 3.5 19.8 1.0
CB A:CYS145 3.6 15.3 1.0
C34 A:7YY201 3.8 25.8 1.0
CD2 A:HIS41 3.9 19.4 1.0
CD2 A:LEU27 4.0 15.2 1.0
C20 A:7YY201 4.0 26.8 1.0
C14 A:7YY201 4.0 27.1 1.0
N24 A:7YY201 4.1 22.3 1.0
C08 A:7YY201 4.1 20.6 1.0
F33 A:7YY201 4.3 24.3 1.0
CB A:LEU27 4.5 17.4 1.0
C32 A:7YY201 4.5 27.9 1.0
C15 A:7YY201 4.5 26.1 1.0
O A:HOH309 4.7 36.3 1.0
C26 A:7YY201 4.7 21.1 1.0
CG A:LEU27 4.7 17.9 1.0
O09 A:7YY201 4.7 27.7 1.0
O A:THR26 4.7 22.1 1.0
CG A:HIS41 4.8 26.3 1.0
O A:HOH335 4.8 27.4 1.0
N07 A:7YY201 4.8 22.3 1.0
C25 A:7YY201 4.8 24.6 1.0
C35 A:7YY201 4.9 23.1 1.0
CB A:HIS41 4.9 22.1 1.0
NE2 A:HIS41 4.9 25.1 1.0

Chlorine binding site 2 out of 2 in 8v8g

Go back to Chlorine Binding Sites List in 8v8g
Chlorine binding site 2 out of 2 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-196) 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 1-196) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:35.2
occ:0.60
 CL2 B:7YY201 0.0 35.2 0.6
C22 B:7YY201 1.8 34.3 0.6
NE2 B:HIS41 2.3 33.8 0.4
C21 B:7YY201 2.7 35.7 0.6
C13 B:7YY201 2.8 31.2 0.6
CE1 B:HIS41 2.9 29.4 0.4
N12 B:7YY201 3.0 31.4 0.6
N10 B:7YY201 3.1 34.3 0.6
C11 B:7YY201 3.1 29.7 0.6
SG B:CYS145 3.3 27.4 0.4
CD2 B:HIS41 3.4 30.4 0.4
SG B:CYS145 3.5 28.6 0.6
CB B:CYS145 3.6 26.7 0.4
CB B:CYS145 3.6 26.7 0.6
CD2 B:LEU27 3.7 25.2 1.0
C08 B:7YY201 4.0 34.5 0.6
C20 B:7YY201 4.0 34.4 0.6
C14 B:7YY201 4.0 36.3 0.6
ND1 B:HIS41 4.1 32.2 0.4
N24 B:7YY201 4.1 33.2 0.6
C34 B:7YY201 4.2 32.8 0.6
CG B:HIS41 4.4 29.4 0.4
O09 B:7YY201 4.5 32.2 0.6
CB B:LEU27 4.5 18.8 1.0
CG B:LEU27 4.5 25.9 1.0
C15 B:7YY201 4.5 33.6 0.6
CD2 B:HIS41 4.7 34.2 0.6
O B:THR26 4.7 32.2 1.0
CG2 B:THR25 4.7 35.1 1.0
N07 B:7YY201 4.7 30.9 0.6
F33 B:7YY201 4.8 35.9 0.6
C32 B:7YY201 4.9 40.3 0.6
C26 B:7YY201 4.9 35.4 0.6
C35 B:7YY201 4.9 31.4 0.6
C25 B:7YY201 4.9 35.0 0.6
O B:HOH350 5.0 44.5 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 13:33:18 2024

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