Chlorine in PDB 8p87: Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 5 Mm X77, From An "Old" Crystal.

Enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 5 Mm X77, From An "Old" Crystal.

All present enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 5 Mm X77, From An "Old" Crystal.:
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 Mm X77, From An "Old" Crystal., PDB code: 8p87 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) 50.57 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.848, 101.138, 104.258, 90, 90, 90
R / Rfree (%) 17 / 19.1

Other elements in 8p87:

The structure of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 5 Mm X77, From An "Old" Crystal. 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 Mm X77, From An "Old" Crystal. (pdb code 8p87). 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 Mm X77, From An "Old" Crystal., PDB code: 8p87:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8p87

Go back to Chlorine Binding Sites List in 8p87
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 Mm X77, From An "Old" Crystal.


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 Mm X77, From An "Old" Crystal. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:24.5
occ:1.00
 HE21 A:GLN110 2.4 29.9 1.0
H A:GLN107 2.5 28.4 1.0
HA A:ILE106 3.1 25.6 1.0
HB2 A:GLN110 3.2 25.9 1.0
NE2 A:GLN110 3.3 24.9 1.0
N A:GLN107 3.3 23.7 1.0
HB A:ILE106 3.3 25.6 1.0
HG2 A:GLN110 3.4 23.9 1.0
HB2 A:GLN107 3.4 29.4 1.0
HG2 A:GLN107 3.6 34.6 1.0
HG22 A:ILE106 3.6 28.2 1.0
CA A:ILE106 3.7 21.3 1.0
HE22 A:GLN110 3.7 29.9 1.0
CB A:ILE106 3.9 21.3 1.0
CG A:GLN110 3.9 19.9 1.0
CB A:GLN110 4.0 21.6 1.0
C A:ILE106 4.0 25.1 1.0
CB A:GLN107 4.1 24.5 1.0
CD A:GLN110 4.1 23.4 1.0
CG A:GLN107 4.2 28.8 1.0
CG2 A:ILE106 4.2 23.5 1.0
CA A:GLN107 4.2 24.3 1.0
HB3 A:GLN110 4.3 25.9 1.0
O A:HOH516 4.3 42.8 1.0
HG3 A:GLN107 4.5 34.6 1.0
O A:GLN107 4.6 22.6 1.0
HG21 A:ILE106 4.6 28.2 1.0
O A:ARG105 4.8 28.0 1.0
HG3 A:GLN110 4.8 23.9 1.0
C A:GLN107 4.9 22.3 1.0
HB3 A:GLN107 5.0 29.4 1.0

Chlorine binding site 2 out of 2 in 8p87

Go back to Chlorine Binding Sites List in 8p87
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 Mm X77, From An "Old" Crystal.


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 Mm X77, From An "Old" Crystal. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:62.1
occ:1.00
 O B:HOH666 2.4 46.7 1.0
H B:TYR54 2.5 46.7 1.0
HD2 B:TYR54 2.9 41.9 1.0
HH21 B:ARG188 3.2 91.1 1.0
HB2 B:TYR54 3.2 43.0 1.0
HA B:ASN53 3.2 53.0 1.0
N B:TYR54 3.4 38.9 1.0
O B:PRO52 3.4 49.0 1.0
HH22 B:ARG188 3.4 91.1 1.0
NH2 B:ARG188 3.6 75.9 1.0
CD2 B:TYR54 3.7 34.9 1.0
CB B:TYR54 4.0 35.8 1.0
H B:GLU55 4.0 52.1 1.0
CA B:ASN53 4.0 44.1 1.0
C B:ASN53 4.2 38.8 1.0
HH22 B:ARG40 4.2 28.8 1.0
CA B:TYR54 4.3 36.0 1.0
C B:PRO52 4.3 52.1 1.0
CG B:TYR54 4.3 33.4 1.0
HH12 B:ARG40 4.3 32.8 1.0
O B:HOH644 4.5 51.3 1.0
N B:ASN53 4.6 47.5 1.0
NH2 B:ARG40 4.6 23.9 1.0
OD1 B:ASN53 4.7 48.1 1.0
HG2 B:PRO52 4.7 52.4 1.0
CE2 B:TYR54 4.8 32.2 1.0
N B:GLU55 4.8 43.4 1.0
HE2 B:TYR54 4.8 38.7 1.0
HB3 B:TYR54 4.8 43.0 1.0
NH1 B:ARG40 4.8 27.3 1.0
HG3 B:GLU55 4.9 81.2 1.0
CZ B:ARG188 4.9 81.0 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 11:27:19 2024

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