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Sodium in PDB 8p54: Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar Mg-132.

Enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar Mg-132.

All present enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar Mg-132.:
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 Mg-132., PDB code: 8p54 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) 44.93 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.742, 99.719, 103.601, 90, 90, 90
R / Rfree (%) 16.6 / 18.6

Other elements in 8p54:

The structure of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar Mg-132. also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar Mg-132. (pdb code 8p54). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar Mg-132., PDB code: 8p54:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8p54

Go back to Sodium Binding Sites List in 8p54
Sodium 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 Mg-132.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar Mg-132. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:47.6
occ:1.00
 O A:HOH512 2.2 32.5 1.0
OE1 A:GLU178 2.2 45.8 1.0
O A:HOH767 2.5 27.3 1.0
HB2 A:ARG105 3.0 23.9 1.0
OD2 A:ASP176 3.0 21.7 1.0
HB2 A:GLU178 3.1 25.8 1.0
CD A:GLU178 3.2 45.8 1.0
HG3 A:GLU178 3.4 35.8 1.0
CG A:GLU178 3.6 29.8 1.0
CG A:ASP176 3.6 20.5 1.0
HD2 A:ARG105 3.7 27.6 1.0
CB A:GLU178 3.8 21.5 1.0
CB A:ARG105 3.9 19.9 1.0
OD1 A:ASP176 4.1 17.4 1.0
HB3 A:ARG105 4.1 23.9 1.0
HB2 A:ASP176 4.1 19.1 1.0
OE2 A:GLU178 4.2 48.5 1.0
H A:GLU178 4.3 20.3 1.0
HB3 A:GLU178 4.3 25.8 1.0
H A:ARG105 4.4 22.4 1.0
CD A:ARG105 4.5 23.0 1.0
CB A:ASP176 4.5 15.9 1.0
O A:HOH691 4.5 29.1 1.0
HG2 A:GLU178 4.6 35.8 1.0
HD3 A:ARG105 4.6 27.6 1.0
CG A:ARG105 4.7 18.8 1.0
N A:ARG105 4.7 18.6 1.0
OD1 A:ASN180 4.7 34.1 1.0
HH11 A:ARG105 4.7 25.8 1.0
HB3 A:ASP176 4.8 19.1 1.0
HG3 A:ARG105 4.8 22.6 1.0
CA A:ARG105 4.8 18.2 1.0
N A:GLU178 4.9 16.9 1.0
HB2 A:ASN180 4.9 22.5 1.0
HA A:ARG105 5.0 21.9 1.0
O A:HOH674 5.0 22.4 1.0

Sodium binding site 2 out of 2 in 8p54

Go back to Sodium Binding Sites List in 8p54
Sodium 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 Mg-132.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar Mg-132. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:36.0
occ:1.00
 OD1 B:ASP263 2.1 39.4 1.0
OD1 B:ASN221 2.2 32.2 1.0
O B:PHE223 2.3 29.1 1.0
O B:HOH538 2.4 27.0 1.0
O B:ASN221 2.6 28.3 1.0
O B:ASP263 2.9 30.7 1.0
HB3 B:ALA266 2.9 38.1 1.0
H B:PHE223 3.1 34.5 1.0
H B:ASN221 3.2 36.9 1.0
CG B:ASP263 3.3 43.4 1.0
CG B:ASN221 3.3 32.9 1.0
C B:ASN221 3.4 28.0 1.0
C B:PHE223 3.4 30.4 1.0
N B:PHE223 3.4 28.9 1.0
HA B:ASP263 3.5 39.1 1.0
C B:ASP263 3.7 32.6 1.0
CB B:ALA266 3.8 31.7 1.0
N B:ASN221 3.9 30.7 1.0
CA B:PHE223 3.9 29.3 1.0
CA B:ASP263 3.9 32.6 1.0
HB1 B:ALA266 4.0 38.1 1.0
CA B:ASN221 4.0 27.7 1.0
HB2 B:PHE223 4.0 34.8 1.0
C B:ARG222 4.1 30.0 1.0
H B:SER267 4.1 34.1 1.0
OD2 B:ASP263 4.1 50.9 1.0
OG B:SER267 4.1 29.9 1.0
HD21 B:ASN221 4.2 38.4 1.0
CB B:ASP263 4.2 37.8 1.0
ND2 B:ASN221 4.2 32.0 1.0
N B:ARG222 4.2 28.6 1.0
CB B:ASN221 4.3 29.6 1.0
HB2 B:ALA266 4.3 38.1 1.0
HA B:THR224 4.3 37.8 1.0
HG B:SER267 4.3 36.0 1.0
N B:SER267 4.4 28.4 1.0
N B:THR224 4.5 30.6 1.0
CA B:ARG222 4.6 30.1 1.0
CB B:PHE223 4.6 29.1 1.0
HA B:ARG222 4.6 35.9 1.0
HB3 B:ASP263 4.7 45.4 1.0
HB2 B:ASN221 4.8 35.6 1.0
HA B:PHE223 4.8 35.0 1.0
O B:ARG222 4.8 31.2 1.0
C B:ALA266 4.8 31.2 1.0
H B:ALA266 4.8 38.5 1.0
N B:MET264 4.8 30.0 1.0
CA B:ALA266 4.8 30.8 1.0
HA B:MET264 4.8 33.1 1.0
H B:ARG222 4.9 34.2 1.0
HA B:LEU220 4.9 33.4 1.0
HB2 B:ASP263 4.9 45.4 1.0
HG23 B:ILE259 4.9 41.6 1.0
CA B:THR224 4.9 31.5 1.0
HA B:ASN221 4.9 33.2 1.0
HB3 B:ASN221 5.0 35.6 1.0
HD22 B:ASN221 5.0 38.4 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: Wed Oct 9 12:52:15 2024

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