Sodium in PDB 8ds2: Structure of Sars-Cov-2 Mpro in Complex with the NSP13-NSP14 (C13) Cut Site Sequence (Form 2)

Enzymatic activity of Structure of Sars-Cov-2 Mpro in Complex with the NSP13-NSP14 (C13) Cut Site Sequence (Form 2)

All present enzymatic activity of Structure of Sars-Cov-2 Mpro in Complex with the NSP13-NSP14 (C13) Cut Site Sequence (Form 2):
3.4.22.69;

Protein crystallography data

The structure of Structure of Sars-Cov-2 Mpro in Complex with the NSP13-NSP14 (C13) Cut Site Sequence (Form 2), PDB code: 8ds2 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) 47.64 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.996, 107.44, 54.388, 90, 103.5, 90
R / Rfree (%) 15.4 / 18.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Sars-Cov-2 Mpro in Complex with the NSP13-NSP14 (C13) Cut Site Sequence (Form 2) (pdb code 8ds2). 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 Structure of Sars-Cov-2 Mpro in Complex with the NSP13-NSP14 (C13) Cut Site Sequence (Form 2), PDB code: 8ds2:

Sodium binding site 1 out of 1 in 8ds2

Go back to Sodium Binding Sites List in 8ds2
Sodium binding site 1 out of 1 in the Structure of Sars-Cov-2 Mpro in Complex with the NSP13-NSP14 (C13) 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 Structure of Sars-Cov-2 Mpro in Complex with the NSP13-NSP14 (C13) Cut Site Sequence (Form 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:20.2
occ:1.00
 OD1 A:ASP263 2.3 24.3 1.0
O A:ASN221 2.4 24.9 1.0
OD1 A:ASN221 2.4 24.6 1.0
O A:PHE223 2.4 21.2 1.0
O A:ASP263 2.5 19.6 1.0
OG A:SER267 3.0 24.0 1.0
C A:ASN221 3.2 24.5 1.0
O A:HOH551 3.3 29.5 1.0
CG A:ASP263 3.4 21.4 1.0
C A:ASP263 3.4 17.9 1.0
N A:PHE223 3.5 23.2 1.0
CG A:ASN221 3.5 24.1 1.0
C A:PHE223 3.5 20.6 1.0
N A:SER267 3.8 19.4 1.0
CA A:ASP263 3.8 17.8 1.0
CB A:ALA266 3.9 20.3 1.0
C A:ARG222 4.0 24.3 1.0
CA A:PHE223 4.0 27.3 1.0
CA A:ASN221 4.0 20.6 1.0
N A:ASN221 4.0 23.2 1.0
N A:ARG222 4.1 25.7 1.0
CB A:ASP263 4.2 19.1 1.0
CB A:SER267 4.2 21.9 1.0
OD2 A:ASP263 4.2 23.6 1.0
O A:HOH655 4.3 37.0 1.0
CB A:ASN221 4.3 21.8 1.0
CA A:ARG222 4.3 25.5 1.0
C A:ALA266 4.3 18.2 1.0
CA A:SER267 4.4 18.9 1.0
ND2 A:ASN221 4.4 22.5 1.0
CB A:PHE223 4.5 24.3 1.0
N A:MET264 4.5 16.8 1.0
CA A:ALA266 4.6 18.2 1.0
N A:THR224 4.6 20.8 0.5
O A:ARG222 4.6 31.9 1.0
N A:THR224 4.6 20.9 0.5
N A:ALA266 4.8 18.8 1.0
CA A:MET264 4.9 14.2 1.0
O A:HOH581 5.0 38.4 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 18:45:07 2023

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