Chlorine in PDB 8p5a: Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 5 Millimolar X77 Enantiomer R.

Enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 5 Millimolar X77 Enantiomer R.

All present enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 5 Millimolar X77 Enantiomer R.:
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 5 Millimolar X77 Enantiomer R., PDB code: 8p5a 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) 49.32 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.568, 100.247, 103.919, 90, 90, 90
R / Rfree (%) 16.6 / 18.9

Other elements in 8p5a:

The structure of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 5 Millimolar X77 Enantiomer R. also contains other interesting chemical elements:

Sodium (Na) 1 atom

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 5 Millimolar X77 Enantiomer R. (pdb code 8p5a). 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 5 Millimolar X77 Enantiomer R., PDB code: 8p5a:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8p5a

Go back to Chlorine Binding Sites List in 8p5a
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 5 Millimolar X77 Enantiomer R.


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 5 Millimolar X77 Enantiomer R. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:21.7
occ:1.00
 HE21 A:GLN110 2.5 25.9 1.0
H A:GLN107 2.5 26.7 1.0
HA A:ILE106 3.0 22.8 1.0
HB2 A:GLN110 3.2 22.4 1.0
NE2 A:GLN110 3.3 21.6 1.0
N A:GLN107 3.3 22.2 1.0
O A:HOH739 3.3 34.6 1.0
HB A:ILE106 3.3 20.2 1.0
HG2 A:GLN110 3.3 22.5 1.0
HG2 A:GLN107 3.4 37.0 1.0
HB2 A:GLN107 3.4 33.1 1.0
HG22 A:ILE106 3.5 28.1 1.0
CA A:ILE106 3.7 18.9 1.0
HE22 A:GLN110 3.8 25.9 1.0
CB A:ILE106 3.9 16.8 1.0
CG A:GLN110 3.9 18.7 1.0
CB A:GLN110 4.0 18.7 1.0
CB A:GLN107 4.0 27.6 1.0
C A:ILE106 4.0 24.8 1.0
CG A:GLN107 4.1 30.9 1.0
CD A:GLN110 4.1 21.9 1.0
CG2 A:ILE106 4.2 23.4 1.0
CA A:GLN107 4.2 21.9 1.0
HB3 A:GLN110 4.2 22.4 1.0
HG3 A:GLN107 4.3 37.0 1.0
O A:GLN107 4.6 21.8 1.0
HG21 A:ILE106 4.6 28.1 1.0
HG3 A:GLN110 4.8 22.5 1.0
O A:ARG105 4.9 23.8 1.0
HB3 A:GLN107 4.9 33.1 1.0
C A:GLN107 4.9 22.2 1.0
HG23 A:ILE106 5.0 28.1 1.0

Chlorine binding site 2 out of 2 in 8p5a

Go back to Chlorine Binding Sites List in 8p5a
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 5 Millimolar X77 Enantiomer R.


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 5 Millimolar X77 Enantiomer R. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:52.1
occ:1.00
 H B:TYR54 2.5 45.8 1.0
HD2 B:TYR54 3.2 47.2 1.0
HA B:ASN53 3.2 51.9 1.0
HB2 B:TYR54 3.3 42.9 1.0
O B:PRO52 3.3 46.1 1.0
N B:TYR54 3.3 38.1 1.0
CD2 B:TYR54 4.0 39.3 1.0
CA B:ASN53 4.0 43.2 1.0
H B:GLU55 4.0 51.9 1.0
CB B:TYR54 4.0 35.7 1.0
HH22 B:ARG40 4.1 31.4 1.0
C B:ASN53 4.1 37.7 1.0
C B:PRO52 4.2 46.1 1.0
CA B:TYR54 4.3 36.9 1.0
HH12 B:ARG40 4.3 33.9 1.0
CG B:TYR54 4.5 32.7 1.0
O B:HOH680 4.5 42.7 1.0
N B:ASN53 4.6 43.0 1.0
NH2 B:ARG40 4.6 26.1 1.0
OD1 B:ASN53 4.7 44.8 1.0
NH1 B:ARG40 4.7 28.2 1.0
HG2 B:PRO52 4.7 51.4 1.0
N B:GLU55 4.7 43.3 1.0
HB3 B:TYR54 4.8 42.9 1.0
CZ B:ARG40 5.0 27.0 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 11:26:31 2024

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