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Sodium in PDB 8drr: Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP4-NSP5 (C4) Cut Site Sequence

Enzymatic activity of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP4-NSP5 (C4) Cut Site Sequence

All present enzymatic activity of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP4-NSP5 (C4) Cut Site Sequence:
3.4.22.69;

Protein crystallography data

The structure of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP4-NSP5 (C4) Cut Site Sequence, PDB code: 8drr 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) 60.46 / 2.00
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.255, 107.417, 138.072, 90, 90, 90
R / Rfree (%) 20.6 / 23.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP4-NSP5 (C4) Cut Site Sequence (pdb code 8drr). 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 NSP4-NSP5 (C4) Cut Site Sequence, PDB code: 8drr:

Sodium binding site 1 out of 1 in 8drr

Go back to Sodium Binding Sites List in 8drr
Sodium binding site 1 out of 1 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP4-NSP5 (C4) Cut Site Sequence


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 NSP4-NSP5 (C4) Cut Site Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:49.5
occ:1.00
 OD1 A:ASN221 2.3 49.1 1.0
OD1 A:ASP263 2.3 57.3 1.0
O A:PHE223 2.4 44.7 1.0
O A:HOH504 2.4 43.6 1.0
O A:ASN221 2.7 54.9 1.0
O A:ASP263 2.7 41.5 1.0
CG A:ASN221 3.3 50.7 1.0
C A:ASN221 3.4 53.1 1.0
C A:PHE223 3.5 53.6 1.0
CG A:ASP263 3.5 55.6 1.0
N A:PHE223 3.6 55.6 1.0
C A:ASP263 3.7 43.2 1.0
CB A:ALA266 3.7 46.2 1.0
N A:ASN221 3.8 48.5 1.0
CA A:ASN221 4.0 50.1 1.0
OG A:SER267 4.0 47.5 1.0
CA A:ASP263 4.0 39.5 1.0
CA A:PHE223 4.1 55.1 1.0
ND2 A:ASN221 4.1 50.3 1.0
N A:SER267 4.2 41.8 1.0
C A:ARG222 4.2 54.1 1.0
N A:ARG222 4.2 50.7 1.0
CB A:ASN221 4.2 52.2 1.0
OD2 A:ASP263 4.4 53.1 1.0
CB A:ASP263 4.4 42.6 1.0
C A:ALA266 4.5 40.8 1.0
CA A:ALA266 4.6 43.9 1.0
N A:THR224 4.6 55.0 1.0
CA A:ARG222 4.6 47.5 1.0
CB A:PHE223 4.7 58.5 1.0
N A:MET264 4.8 40.9 1.0
O A:ARG222 4.9 55.3 1.0
CA A:SER267 4.9 42.5 1.0
CB A:SER267 4.9 41.2 1.0
N A:ALA266 4.9 38.0 1.0
CA A:THR224 5.0 56.6 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: Wed Oct 9 11:32:22 2024

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