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Sodium in PDB 7tiz: Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63

Enzymatic activity of Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63

All present enzymatic activity of Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63, PDB code: 7tiz was solved by F.Forouhar, H.Liu, S.Iketani, A.Zack, N.Khanizeman, E.Bednarova, B.Fowler, S.J.Hong, H.Mohri, M.S.Nair, Y.Huang, N.E.S.Tay, S.Lee, C.Karan, S.J.Resnick, C.Quinn, W.Li, H.Shion, C.Jurtschenko, M.A.Lauber, T.Mcdonald, M.E.Stokes, B.Hurst, T.Rovis, A.Chavez, D.D.Ho, B.R.Stockwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.17 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.433, 81.64, 51.831, 90, 114.5, 90
R / Rfree (%) 17 / 19.1

Other elements in 7tiz:

The structure of Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63 also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63 (pdb code 7tiz). 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 Sars-Cov-2 3CL in Complex with Inhibitor NK01-63, PDB code: 7tiz:

Sodium binding site 1 out of 1 in 7tiz

Go back to Sodium Binding Sites List in 7tiz
Sodium binding site 1 out of 1 in the Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63


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 Sars-Cov-2 3CL in Complex with Inhibitor NK01-63 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:48.0
occ:1.00
 OD1 A:ASP263 2.2 69.8 1.0
OD1 A:ASN221 2.3 50.5 1.0
O A:HOH519 2.4 44.6 1.0
O A:PHE223 2.4 49.6 1.0
O A:ASP263 2.6 42.0 1.0
O A:ASN221 2.8 45.1 1.0
CG A:ASN221 3.4 50.9 1.0
CG A:ASP263 3.5 69.8 1.0
C A:ASN221 3.5 47.5 1.0
C A:ASP263 3.5 39.1 1.0
C A:PHE223 3.5 58.6 1.0
CB A:ALA266 3.7 48.4 1.0
N A:PHE223 3.7 52.1 1.0
OG A:SER267 3.8 43.5 1.0
N A:ASN221 3.9 40.3 1.0
CA A:ASP263 4.0 48.7 1.0
CA A:PHE223 4.1 57.5 1.0
CA A:ASN221 4.1 44.0 1.0
ND2 A:ASN221 4.2 51.2 1.0
N A:SER267 4.2 41.2 1.0
CB A:ASP263 4.3 53.6 1.0
C A:ARG222 4.3 55.9 1.0
CB A:ASN221 4.3 46.5 1.0
OD2 A:ASP263 4.4 73.7 1.0
N A:ARG222 4.4 47.8 1.0
CB A:PHE223 4.6 63.4 1.0
N A:MET264 4.6 37.2 1.0
CA A:ALA266 4.6 41.5 1.0
N A:THR224 4.7 53.4 1.0
C A:ALA266 4.7 44.4 1.0
CA A:ARG222 4.7 43.7 1.0
CB A:SER267 4.8 41.1 1.0
N A:ALA266 4.9 42.1 1.0
CA A:SER267 5.0 37.9 1.0
O A:ARG222 5.0 58.8 1.0

Reference:

H.Liu, S.Iketani, A.Zask, N.Khanizeman, E.Bednarova, F.Forouhar, B.Fowler, S.J.Hong, H.Mohri, M.S.Nair, Y.Huang, N.E.S.Tay, S.Lee, C.Karan, S.J.Resnick, C.Quinn, W.Li, H.Shion, X.Xia, J.D.Daniels, M.Bartolo-Cruz, M.Farina, P.Rajbhandari, C.Jurtschenko, M.A.Lauber, T.Mcdonald, M.E.Stokes, B.L.Hurst, T.Rovis, A.Chavez, D.D.Ho, B.R.Stockwell. Development of Optimized Drug-Like Small Molecule Inhibitors of the Sars-Cov-2 3CL Protease For Treatment of Covid-19. Nat Commun V. 13 1891 2022.
ISSN: ESSN 2041-1723
PubMed: 35393402
DOI: 10.1038/S41467-022-29413-2
Page generated: Mon Aug 18 12:04:17 2025

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