Sodium in PDB 8drx: Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP10-NSP11 (C10) Cut Site Sequence (Form 2)

Enzymatic activity of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP10-NSP11 (C10) Cut Site Sequence (Form 2)

All present enzymatic activity of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP10-NSP11 (C10) Cut Site Sequence (Form 2):
3.4.22.69;

Protein crystallography data

The structure of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP10-NSP11 (C10) Cut Site Sequence (Form 2), PDB code: 8drx was solved by J.Lee, C.Kenward, L.J.Worrall, M.Vuckovic, M.Paetzel, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.00 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.67, 107.43, 53.42, 90, 103.84, 90
R / Rfree (%) 16.3 / 19.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP10-NSP11 (C10) Cut Site Sequence (Form 2) (pdb code 8drx). 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 Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP10-NSP11 (C10) Cut Site Sequence (Form 2), PDB code: 8drx:

Sodium binding site 1 out of 1 in 8drx

Go back to Sodium Binding Sites List in 8drx
Sodium binding site 1 out of 1 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP10-NSP11 (C10) Cut Site Sequence (Form 2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP10-NSP11 (C10) Cut Site Sequence (Form 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:30.4
occ:1.00
 OD1 A:ASP263 2.3 22.7 0.6
OD1 A:ASN221 2.4 30.9 1.0
O A:PHE223 2.4 24.9 1.0
O A:ASN221 2.4 34.9 1.0
O A:ASP263 2.6 21.4 1.0
O A:HOH509 3.0 36.7 1.0
OG A:SER267 3.2 23.4 1.0
C A:ASN221 3.3 29.4 1.0
CG A:ASP263 3.3 23.3 0.6
CG A:ASN221 3.4 31.3 1.0
C A:PHE223 3.5 23.2 1.0
C A:ASP263 3.5 19.2 1.0
N A:PHE223 3.5 29.2 1.0
CB A:ALA266 3.8 22.8 1.0
N A:SER267 3.8 19.9 1.0
CA A:ASP263 3.9 21.8 0.4
CA A:ASP263 3.9 21.8 0.6
N A:ASN221 4.0 27.9 1.0
CA A:PHE223 4.0 30.4 1.0
CA A:ASN221 4.0 25.9 1.0
O A:HOH716 4.1 35.6 1.0
C A:ARG222 4.1 38.4 1.0
CB A:ASP263 4.1 23.3 0.4
OD2 A:ASP263 4.1 24.7 0.6
N A:ARG222 4.2 35.1 1.0
CB A:ASP263 4.2 23.3 0.6
CB A:SER267 4.3 21.7 1.0
CB A:ASN221 4.3 27.9 1.0
C A:ALA266 4.3 20.6 1.0
ND2 A:ASN221 4.3 30.1 1.0
CA A:ARG222 4.4 31.9 1.0
CA A:SER267 4.4 20.6 1.0
CA A:ALA266 4.5 20.5 1.0
CB A:PHE223 4.5 33.3 1.0
N A:MET264 4.6 18.6 1.0
N A:THR224 4.6 24.1 1.0
CG A:ASP263 4.9 23.7 0.4
N A:ALA266 4.9 19.7 1.0
O A:ARG222 4.9 39.4 1.0
CA A:MET264 5.0 18.6 1.0
CA A:THR224 5.0 22.9 1.0

Reference:

J.Lee, C.Kenward, L.J.Worrall, M.Vuckovic, F.Gentile, A.T.Ton, M.Ng, A.Cherkasov, N.C.J.Strynadka, M.Paetzel. X-Ray Crystallographic Characterization of the Sars-Cov-2 Main Protease Polyprotein Cleavage Sites Essential For Viral Processing and Maturation. Nat Commun V. 13 5196 2022.
ISSN: ESSN 2041-1723
PubMed: 36057636
DOI: 10.1038/S41467-022-32854-4
Page generated: Fri Apr 7 18:45:03 2023

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