Atomistry » Chlorine » PDB 8oe2-8oq7 » 8okm
Atomistry »
  Chlorine »
    PDB 8oe2-8oq7 »
      8okm »

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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy