Atomistry » Sodium » PDB 8oyf-8ph7 » 8p57
Atomistry »
  Sodium »
    PDB 8oyf-8ph7 »
      8p57 »

Sodium in PDB 8p57: Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 75 Micromolar X77.

Enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 75 Micromolar X77.

All present enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 75 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 75 Micromolar X77., PDB code: 8p57 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) 49.50 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.66, 100.829, 104.647, 90, 90, 90
R / Rfree (%) 16.8 / 18.3

Other elements in 8p57:

The structure of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 75 Micromolar X77. 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 75 Micromolar X77. (pdb code 8p57). 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 75 Micromolar X77., PDB code: 8p57:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8p57

Go back to Sodium Binding Sites List in 8p57
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 75 Micromolar X77.


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 75 Micromolar X77. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na509

b:31.3
occ:1.00
 OD1 B:ASP263 2.1 42.1 1.0
O B:PHE223 2.3 24.6 1.0
O B:HOH616 2.3 26.4 1.0
OD1 B:ASN221 2.4 25.9 1.0
O B:ASN221 2.6 25.6 1.0
H B:PHE223 3.0 26.2 1.0
HB3 B:ALA266 3.0 37.5 1.0
O B:ASP263 3.1 31.9 1.0
H B:ASN221 3.2 33.0 1.0
C B:PHE223 3.3 24.5 1.0
N B:PHE223 3.3 21.8 1.0
CG B:ASP263 3.4 43.5 1.0
C B:ASN221 3.4 25.8 1.0
HA B:ASP263 3.5 43.2 1.0
CG B:ASN221 3.5 30.4 1.0
C B:ASP263 3.8 32.4 1.0
CB B:ALA266 3.9 31.3 1.0
CA B:PHE223 3.9 22.2 1.0
N B:ASN221 3.9 27.4 1.0
O B:HOH704 3.9 45.1 1.0
HB1 B:ALA266 3.9 37.5 1.0
C B:ARG222 4.0 21.7 1.0
CA B:ASP263 4.0 36.0 1.0
CA B:ASN221 4.1 26.7 1.0
HB2 B:PHE223 4.1 29.4 1.0
N B:ARG222 4.2 21.9 1.0
OD2 B:ASP263 4.2 47.5 1.0
H B:SER267 4.2 34.3 1.0
CB B:ASP263 4.3 43.4 1.0
HD21 B:ASN221 4.3 34.6 1.0
HB2 B:ALA266 4.3 37.5 1.0
HA B:THR224 4.3 32.1 1.0
OG B:SER267 4.3 29.3 1.0
ND2 B:ASN221 4.4 28.9 1.0
CB B:ASN221 4.4 27.5 1.0
CA B:ARG222 4.5 21.1 1.0
HA B:ARG222 4.5 25.2 1.0
N B:THR224 4.5 22.5 1.0
HG B:SER267 4.5 35.1 1.0
N B:SER267 4.6 28.6 1.0
CB B:PHE223 4.6 24.5 1.0
HA B:PHE223 4.7 26.7 1.0
O B:ARG222 4.7 22.4 1.0
HB3 B:ASP263 4.8 52.1 1.0
H B:ARG222 4.8 26.4 1.0
HG23 B:ILE259 4.8 49.0 1.0
HA B:LEU220 4.9 30.7 1.0
HB2 B:ASN221 4.9 33.1 1.0
CA B:ALA266 4.9 31.5 1.0
H B:ALA266 4.9 36.6 1.0
C B:ALA266 4.9 31.4 1.0
CA B:THR224 4.9 26.8 1.0
HB2 B:ASP263 4.9 52.1 1.0
HA B:ASN221 5.0 32.0 1.0
N B:MET264 5.0 30.3 1.0

Sodium binding site 2 out of 2 in 8p57

Go back to Sodium Binding Sites List in 8p57
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 75 Micromolar X77.


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 75 Micromolar X77. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na510

b:34.4
occ:1.00
 HH B:TYR101 1.7 28.1 1.0
OD2 B:ASP33 2.4 35.9 1.0
OH B:TYR101 2.5 23.4 1.0
O B:HOH662 2.6 27.9 1.0
HB2 B:ASP33 2.6 30.9 1.0
HE1 B:TYR101 3.1 28.6 1.0
CG B:ASP33 3.2 36.3 1.0
CB B:ASP33 3.3 25.7 1.0
CZ B:TYR101 3.5 21.7 1.0
CE1 B:TYR101 3.6 23.9 1.0
HB3 B:ASP33 3.8 30.9 1.0
HB3 B:LEU32 4.0 21.9 1.0
O B:HOH607 4.1 36.8 1.0
O B:LEU32 4.1 19.4 1.0
HB2 B:LEU32 4.3 21.9 1.0
C B:LEU32 4.3 19.1 1.0
OD1 B:ASP33 4.4 36.7 1.0
N B:ASP33 4.5 23.0 1.0
CA B:ASP33 4.5 23.9 1.0
CB B:LEU32 4.6 18.2 1.0
HG21 B:THR98 4.6 29.6 1.0
CE2 B:TYR101 4.8 20.3 1.0
OH B:TYR37 4.8 21.8 1.0
H B:ASP33 4.9 27.6 1.0
CD1 B:TYR101 5.0 22.2 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 12:52:33 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy