Chlorine in PDB 8p56: Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar X77.

Enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar X77.

All present enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar X77.:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar X77., PDB code: 8p56 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) 45.45 / 1.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.941, 101.009, 104.201, 90, 90, 90
R / Rfree (%) 16.3 / 18.4

Other elements in 8p56:

The structure of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar X77. also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar X77. (pdb code 8p56). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar X77., PDB code: 8p56:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8p56

Go back to Chlorine Binding Sites List in 8p56
Chlorine binding site 1 out of 2 in the Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar X77.


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 the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar X77. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:20.9
occ:1.00
 HE21 A:GLN110 2.4 27.4 1.0
H A:GLN107 2.5 23.1 1.0
HA A:ILE106 3.1 23.9 1.0
HB2 A:GLN110 3.2 21.8 1.0
NE2 A:GLN110 3.3 22.8 1.0
N A:GLN107 3.3 19.2 1.0
HG2 A:GLN110 3.3 23.1 1.0
HB2 A:GLN107 3.4 28.5 1.0
HB A:ILE106 3.4 22.0 1.0
HG2 A:GLN107 3.6 32.7 1.0
HG22 A:ILE106 3.6 23.2 1.0
CA A:ILE106 3.8 19.9 1.0
HE22 A:GLN110 3.8 27.4 1.0
O A:HOH517 3.8 37.7 1.0
CB A:ILE106 3.9 18.3 1.0
CG A:GLN110 3.9 19.2 1.0
CB A:GLN110 3.9 18.1 1.0
CB A:GLN107 4.0 23.7 1.0
C A:ILE106 4.0 22.1 1.0
CD A:GLN110 4.1 20.1 1.0
CG A:GLN107 4.2 27.2 1.0
HB3 A:GLN110 4.2 21.8 1.0
CG2 A:ILE106 4.2 19.4 1.0
CA A:GLN107 4.2 20.6 1.0
HG3 A:GLN107 4.5 32.7 1.0
O A:GLN107 4.6 20.2 1.0
HG21 A:ILE106 4.6 23.2 1.0
HG3 A:GLN110 4.8 23.1 1.0
O A:ARG105 4.9 25.3 1.0
HB3 A:GLN107 4.9 28.5 1.0
C A:GLN107 4.9 20.3 1.0
HG23 A:ILE106 5.0 23.2 1.0

Chlorine binding site 2 out of 2 in 8p56

Go back to Chlorine Binding Sites List in 8p56
Chlorine binding site 2 out of 2 in the Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar X77.


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 the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar X77. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl508

b:47.9
occ:1.00
 H B:TYR54 2.4 38.7 1.0
HD2 B:TYR54 3.0 33.2 1.0
HA B:ASN53 3.1 47.1 1.0
HB2 B:TYR54 3.2 36.1 1.0
N B:TYR54 3.2 32.2 1.0
O B:PRO52 3.3 41.9 1.0
CD2 B:TYR54 3.8 27.7 1.0
H B:GLU55 3.8 44.3 1.0
CA B:ASN53 3.9 39.3 1.0
CB B:TYR54 3.9 30.1 1.0
C B:ASN53 4.0 33.4 1.0
CA B:TYR54 4.1 28.4 1.0
O B:HOH829 4.2 50.0 1.0
C B:PRO52 4.2 40.5 1.0
CG B:TYR54 4.3 29.0 1.0
HH22 B:ARG40 4.4 28.8 1.0
HH12 B:ARG40 4.4 29.3 1.0
N B:ASN53 4.5 38.5 1.0
OD1 B:ASN53 4.6 44.5 1.0
N B:GLU55 4.6 36.9 1.0
HB3 B:TYR54 4.7 36.1 1.0
HG2 B:PRO52 4.7 45.4 1.0
NH2 B:ARG40 4.9 23.9 1.0
HA B:TYR54 4.9 34.1 1.0
CE2 B:TYR54 4.9 24.4 1.0
NH1 B:ARG40 4.9 24.4 1.0
HE2 B:TYR54 4.9 29.3 1.0
C B:TYR54 5.0 39.5 1.0

Reference:

S.Albani, E.Costanzi, G.L.Hoang, M.Kuzikov, M.Frings, N.Ansari, N.Demitri, T.T.Nguyen, V.Rizzi, J.B.Schulz, C.Bolm, A.Zaliani, P.Carloni, P.Storici, G.Rossetti. Unexpected Single-Ligand Occupancy and Negative Cooperativity in the Sars-Cov-2 Main Protease. J.Chem.Inf.Model. V. 64 892 2024.
ISSN: ESSN 1549-960X
PubMed: 38051605
DOI: 10.1021/ACS.JCIM.3C01497
Page generated: Tue Jul 30 11:25:57 2024

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