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Sodium in PDB 9n6n: Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Pomotrelvir

Enzymatic activity of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Pomotrelvir

All present enzymatic activity of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Pomotrelvir:
3.4.22.69;

Protein crystallography data

The structure of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Pomotrelvir, PDB code: 9n6n was solved by D.Bhandari, A.Kovalevsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.48 / 1.85
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 52.338, 82.365, 91.088, 90, 95.44, 90
R / Rfree (%) 17.4 / 21.8

Other elements in 9n6n:

The structure of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Pomotrelvir also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Pomotrelvir (pdb code 9n6n). 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 Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Pomotrelvir, PDB code: 9n6n:

Sodium binding site 1 out of 1 in 9n6n

Go back to Sodium Binding Sites List in 9n6n
Sodium binding site 1 out of 1 in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Pomotrelvir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Pomotrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:50.6
occ:1.00
 O A:HOH503 2.3 49.1 1.0
OD1 A:ASN221 2.4 48.8 1.0
O A:ASN221 2.4 42.9 1.0
OD1 A:ASP263 2.5 42.9 0.5
O A:PHE223 2.7 56.1 1.0
O A:ASP263 3.1 35.0 0.5
O A:ASP263 3.1 34.9 0.5
C A:ASN221 3.2 45.3 1.0
N A:PHE223 3.5 60.5 1.0
CG A:ASN221 3.6 48.5 1.0
C A:PHE223 3.6 57.7 1.0
CG A:ASP263 3.7 44.3 0.5
N A:ASN221 3.8 42.2 1.0
CB A:ALA266 3.8 42.5 1.0
OG A:SER267 3.8 37.8 1.0
C A:ASP263 3.9 38.3 0.5
C A:ASP263 3.9 38.3 0.5
CA A:ASN221 3.9 43.4 1.0
C A:ARG222 4.0 58.2 1.0
N A:ARG222 4.0 53.7 1.0
CA A:PHE223 4.1 55.9 1.0
CA A:ASP263 4.2 41.4 0.5
CA A:ASP263 4.2 41.4 0.5
CA A:ARG222 4.3 53.9 1.0
N A:SER267 4.3 31.7 1.0
CB A:ASN221 4.3 46.8 1.0
CB A:ASP263 4.5 41.9 0.5
CB A:ASP263 4.5 42.0 0.5
OD2 A:ASP263 4.5 47.0 0.5
ND2 A:ASN221 4.6 44.4 1.0
O A:ARG222 4.6 61.0 1.0
CB A:PHE223 4.7 55.3 1.0
C A:ALA266 4.7 32.8 1.0
CA A:ALA266 4.8 34.2 1.0
CG A:ASP263 4.8 46.0 0.5
N A:THR224 4.8 51.2 1.0
CB A:SER267 5.0 34.5 1.0
C A:LEU220 5.0 40.9 1.0
N A:MET264 5.0 38.3 1.0

Reference:

D.Bhandari, O.Gerlits, S.Keable, L.Coates, A.Aniana, R.Ghirlando, N.T.Nashed, A.Kovalevsky, J.M.Louis. Characterization of An Unusual Sars-Cov-2 Main Protease Natural Variant Exhibiting Resistance to Nirmatrelvir and Ensitrelvir. Commun Biol V. 8 1061 2025.
ISSN: ESSN 2399-3642
PubMed: 40676153
DOI: 10.1038/S42003-025-08487-W
Page generated: Mon Aug 18 17:27:38 2025

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