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Sodium in PDB 7q5e: Crystal Structure of F2F-2020209-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

Enzymatic activity of Crystal Structure of F2F-2020209-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

All present enzymatic activity of Crystal Structure of F2F-2020209-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of F2F-2020209-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 7q5e 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) 46.04 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.978, 101.017, 103.437, 90, 90, 90
R / Rfree (%) 17.1 / 19.4

Other elements in 7q5e:

The structure of Crystal Structure of F2F-2020209-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of F2F-2020209-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. (pdb code 7q5e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of F2F-2020209-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 7q5e:

Sodium binding site 1 out of 1 in 7q5e

Go back to Sodium Binding Sites List in 7q5e
Sodium binding site 1 out of 1 in the Crystal Structure of F2F-2020209-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


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 F2F-2020209-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:35.4
occ:1.00
 OD1 B:ASP263 2.1 51.2 1.0
O B:PHE223 2.3 32.8 1.0
O B:HOH536 2.3 33.0 1.0
O B:ASN221 2.6 33.1 1.0
OD1 B:ASN221 2.6 36.4 1.0
O B:ASP263 3.1 41.3 1.0
HB3 B:ALA266 3.2 52.5 1.0
H B:ASN221 3.2 41.2 1.0
CG B:ASP263 3.3 56.2 1.0
H B:PHE223 3.4 35.0 1.0
C B:PHE223 3.5 31.8 1.0
C B:ASN221 3.5 32.5 1.0
HA B:ASP263 3.5 55.7 1.0
N B:PHE223 3.6 29.2 1.0
CG B:ASN221 3.8 36.3 1.0
C B:ASP263 3.8 44.4 1.0
N B:ASN221 4.0 34.3 1.0
CA B:ASP263 4.0 46.4 1.0
CB B:ALA266 4.1 43.8 1.0
C B:ARG222 4.1 28.6 1.0
CA B:PHE223 4.1 29.5 1.0
HG22 B:THR224 4.2 53.8 1.0
OD2 B:ASP263 4.2 52.9 1.0
CA B:ASN221 4.2 36.0 1.0
CB B:ASP263 4.2 50.4 1.0
HA B:THR224 4.3 40.6 1.0
HB1 B:ALA266 4.3 52.5 1.0
OG B:SER267 4.3 39.0 1.0
N B:ARG222 4.3 31.9 1.0
H B:SER267 4.4 45.6 1.0
HB2 B:PHE223 4.5 39.9 1.0
N B:THR224 4.5 32.0 1.0
HA B:ARG222 4.6 34.8 1.0
HB2 B:ALA266 4.6 52.5 1.0
HG B:SER267 4.6 46.9 1.0
CB B:ASN221 4.6 34.3 1.0
CA B:ARG222 4.6 29.0 1.0
HG23 B:THR224 4.6 53.8 1.0
HB3 B:ASP263 4.7 60.5 1.0
HD22 B:ASN221 4.7 41.8 1.0
ND2 B:ASN221 4.7 34.9 1.0
N B:SER267 4.7 38.1 1.0
O B:ARG222 4.8 29.3 1.0
CG2 B:THR224 4.9 44.8 1.0
HA B:LEU220 4.9 38.4 1.0
CA B:THR224 4.9 33.8 1.0
HA B:PHE223 4.9 35.5 1.0
N B:MET264 4.9 38.8 1.0
CB B:PHE223 4.9 33.2 1.0
HA B:MET264 5.0 47.9 1.0
H B:ALA266 5.0 47.5 1.0
HB2 B:ASP263 5.0 60.5 1.0

Reference:

S.Pelliccia, C.Cerchia, F.Esposito, R.Cannalire, A.Corona, E.Costanzi, M.Kuzikov, P.Gribbon, A.Zaliani, M.Brindisi, P.Storici, E.Tramontano, V.Summa. Easy Access to Alpha-Ketoamides As Sars-Cov-2 and Mers M Pro Inhibitors Via the Padam Oxidation Route. Eur.J.Med.Chem. V. 244 14853 2022.
ISSN: ISSN 0223-5234
PubMed: 36332546
DOI: 10.1016/J.EJMECH.2022.114853
Page generated: Tue Oct 8 18:35:52 2024

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