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Chlorine in PDB 8okm: Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

Enzymatic activity of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

All present enzymatic activity of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 8okm was solved by E.Costanzi, N.Demitri, P.Storici, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.33 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.025, 100.036, 104.065, 90, 90, 90
R / Rfree (%) 16.3 / 18.7

Other elements in 8okm:

The structure of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. (pdb code 8okm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 8okm:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8okm

Go back to Chlorine Binding Sites List in 8okm
Chlorine binding site 1 out of 4 in the Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:37.5
occ:1.00
 O A:HOH576 3.4 24.9 1.0
HZ1 A:LYS102 3.5 80.6 1.0
O A:HOH616 3.5 33.6 1.0
HB2 A:ASP153 3.7 37.8 1.0
HD2 A:LYS102 3.7 53.8 1.0
HD2 A:TYR154 3.8 79.9 1.0
HE3 A:LYS102 4.1 61.7 1.0
HB3 A:SER158 4.1 30.9 1.0
NZ A:LYS102 4.3 67.2 1.0
HB3 A:CYS156 4.4 52.5 1.0
HE2 A:TYR154 4.4 84.9 1.0
CE A:LYS102 4.5 51.4 1.0
O A:ASP153 4.5 41.9 1.0
CD A:LYS102 4.6 44.9 1.0
CB A:ASP153 4.6 31.5 1.0
CD2 A:TYR154 4.6 66.6 1.0
HZ3 A:LYS102 4.7 80.6 1.0
HZ2 A:LYS102 4.8 80.6 1.0
OD2 A:ASP153 4.8 28.1 1.0
CE2 A:TYR154 4.9 70.7 1.0
OG A:SER158 5.0 30.9 1.0
CB A:SER158 5.0 25.7 1.0

Chlorine binding site 2 out of 4 in 8okm

Go back to Chlorine Binding Sites List in 8okm
Chlorine binding site 2 out of 4 in the Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:31.2
occ:0.49
 BR A:BR406 0.0 31.1 0.5
H B:ALA285 2.5 31.6 1.0
H A:ALA285 2.6 29.4 1.0
O B:HOH668 3.2 46.2 1.0
H A:LEU286 3.2 29.5 1.0
H B:LEU286 3.3 28.6 1.0
N B:ALA285 3.3 26.3 1.0
HA B:SER284 3.3 28.0 1.0
N A:ALA285 3.4 24.5 1.0
OG B:SER284 3.4 36.2 1.0
OG A:SER284 3.4 38.9 1.0
HG B:LEU286 3.4 37.6 1.0
HA A:SER284 3.4 30.9 1.0
HB3 A:ALA285 3.4 32.0 1.0
HG A:LEU286 3.5 37.1 1.0
HB3 B:ALA285 3.5 32.0 1.0
HD12 A:LEU286 3.6 36.1 1.0
HD12 B:LEU286 3.7 41.8 1.0
HG A:SER284 3.8 46.7 1.0
HB2 A:LEU286 3.8 31.3 1.0
N A:LEU286 3.8 24.6 1.0
HG B:SER284 3.8 43.4 1.0
N B:LEU286 3.9 23.8 1.0
HB2 B:LEU286 3.9 29.5 1.0
CA B:SER284 4.0 23.4 1.0
CA A:SER284 4.1 25.7 1.0
CA A:ALA285 4.1 24.5 1.0
CG B:LEU286 4.1 31.3 1.0
CA B:ALA285 4.1 23.9 1.0
C B:SER284 4.1 23.4 1.0
CG A:LEU286 4.2 30.9 1.0
CB A:ALA285 4.2 26.6 1.0
C A:SER284 4.2 26.9 1.0
CB B:SER284 4.2 23.4 1.0
C A:ALA285 4.2 24.2 1.0
CB B:ALA285 4.2 26.6 1.0
CB A:SER284 4.3 28.4 1.0
CD1 B:LEU286 4.3 34.9 1.0
CB A:LEU286 4.3 26.1 1.0
CD1 A:LEU286 4.3 30.1 1.0
C B:ALA285 4.4 27.4 1.0
CB B:LEU286 4.4 24.6 1.0
HB2 B:SER284 4.5 28.1 1.0
HB2 A:SER284 4.5 34.1 1.0
HB2 B:ALA285 4.6 32.0 1.0
HD11 B:LEU286 4.6 41.8 1.0
HB2 A:ALA285 4.6 32.0 1.0
CA A:LEU286 4.7 21.7 1.0
HD11 A:LEU286 4.8 36.1 1.0
CA B:LEU286 4.8 24.0 1.0
O A:HOH669 4.8 48.9 1.0
HB1 A:ALA285 4.9 32.0 1.0

Chlorine binding site 3 out of 4 in 8okm

Go back to Chlorine Binding Sites List in 8okm
Chlorine binding site 3 out of 4 in the Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:24.0
occ:0.47
 BR A:BR407 0.0 24.3 0.5
H A:GLN107 2.5 23.3 1.0
HE21 A:GLN110 2.5 24.3 1.0
HA A:ILE106 3.1 22.0 1.0
HB2 A:GLN110 3.2 20.9 1.0
O A:HOH731 3.2 39.6 1.0
N A:GLN107 3.3 19.4 1.0
HB A:ILE106 3.3 20.7 1.0
NE2 A:GLN110 3.4 20.3 1.0
HB2 A:GLN107 3.4 29.8 1.0
HG2 A:GLN110 3.4 21.2 1.0
HG2 A:GLN107 3.5 35.0 1.0
HG22 A:ILE106 3.6 25.2 1.0
CA A:ILE106 3.8 18.3 1.0
HE22 A:GLN110 3.9 24.3 1.0
CB A:ILE106 3.9 17.3 1.0
CB A:GLN110 3.9 17.5 1.0
CG A:GLN110 3.9 17.6 1.0
CB A:GLN107 4.0 24.8 1.0
C A:ILE106 4.0 22.7 1.0
CG A:GLN107 4.1 29.2 1.0
CD A:GLN110 4.1 20.1 1.0
HB3 A:GLN110 4.2 20.9 1.0
CA A:GLN107 4.2 22.4 1.0
CG2 A:ILE106 4.2 20.9 1.0
O A:HOH519 4.4 36.2 1.0
HG3 A:GLN107 4.4 35.0 1.0
O A:GLN107 4.5 20.1 1.0
HG21 A:ILE106 4.6 25.2 1.0
HG3 A:GLN110 4.9 21.2 1.0
C A:GLN107 4.9 20.5 1.0
O A:ARG105 4.9 24.2 1.0
HB3 A:GLN107 4.9 29.8 1.0
O A:HOH718 4.9 37.1 1.0
O A:HOH567 5.0 41.2 1.0

Chlorine binding site 4 out of 4 in 8okm

Go back to Chlorine Binding Sites List in 8okm
Chlorine binding site 4 out of 4 in the Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:65.5
occ:1.00
 HB1 A:ALA70 3.2 46.7 1.0
O A:MET17 3.3 23.9 1.0
O A:HOH502 3.5 42.2 1.0
HG12 A:VAL18 3.7 32.1 1.0
HA A:ALA70 3.8 42.0 1.0
H A:GLY71 3.9 47.6 1.0
HE3 A:TRP31 4.0 33.9 1.0
CB A:ALA70 4.0 38.9 1.0
HZ3 A:TRP31 4.0 37.3 1.0
CA A:ALA70 4.2 35.0 1.0
O A:GLY15 4.2 24.3 1.0
N A:GLY71 4.2 39.7 1.0
HG13 A:VAL18 4.3 32.1 1.0
C A:ALA70 4.3 41.2 1.0
HB2 A:ALA70 4.4 46.7 1.0
C A:MET17 4.4 23.9 1.0
O A:HOH580 4.4 44.9 1.0
CG1 A:VAL18 4.4 26.7 1.0
O A:HOH518 4.5 41.9 1.0
HA2 A:GLY15 4.5 27.6 1.0
H A:MET17 4.6 24.3 1.0
C A:GLY15 4.7 23.6 1.0
CE3 A:TRP31 4.7 28.2 1.0
CZ3 A:TRP31 4.7 31.1 1.0
HA A:VAL18 4.7 28.5 1.0
HB3 A:ALA70 4.7 46.7 1.0
HZ3 A:LYS97 4.7 96.4 1.0
O A:GLU14 4.8 22.6 1.0
N A:MET17 4.8 20.2 1.0
HZ2 A:LYS97 4.9 96.4 1.0
HG11 A:VAL18 4.9 32.1 1.0
HA3 A:GLY71 5.0 50.6 1.0

Reference:

I.Stefanelli, A.Corona, C.Cerchia, E.Cassese, S.Improta, E.Costanzi, S.Pelliccia, S.Morasso, F.Esposito, A.Paulis, S.Scognamiglio, F.S.Di Leva, P.Storici, M.Brindisi, E.Tramontano, R.Cannalire, V.Summa. Broad-Spectrum Coronavirus 3C-Like Protease Peptidomimetic Inhibitors Effectively Block Sars-Cov-2 Replication in Cells: Design, Synthesis, Biological Evaluation, and X-Ray Structure Determination. Eur.J.Med.Chem. V. 253 15311 2023.
ISSN: ISSN 0223-5234
PubMed: 37043904
DOI: 10.1016/J.EJMECH.2023.115311
Page generated: Sun Jul 13 12:50:49 2025

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