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Sodium in PDB 8ds1: Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) Cut Site Sequence

Enzymatic activity of Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) Cut Site Sequence

All present enzymatic activity of Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) Cut Site Sequence:
3.4.22.69;

Protein crystallography data

The structure of Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) Cut Site Sequence, PDB code: 8ds1 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) 48.52 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.001, 105.783, 276.341, 90, 90.93, 90
R / Rfree (%) 19.8 / 24.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) Cut Site Sequence (pdb code 8ds1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) Cut Site Sequence, PDB code: 8ds1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 8ds1

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Sodium binding site 1 out of 5 in the Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) 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 Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) Cut Site Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:55.4
occ:1.00
 OD1 A:ASP263 2.5 51.8 1.0
O A:ASN221 2.7 54.1 1.0
O A:ASP263 2.8 38.2 1.0
OD1 A:ASN221 2.8 45.2 1.0
OG A:SER267 2.9 40.2 1.0
N A:ASN221 3.1 35.2 1.0
CG A:ASP263 3.3 52.2 1.0
C A:ASN221 3.6 48.2 1.0
CG A:ASN221 3.6 47.5 1.0
C A:ASP263 3.6 38.0 1.0
OD2 A:ASP263 3.8 41.4 1.0
CA A:ASN221 3.8 44.2 1.0
O A:PHE223 3.9 41.2 1.0
CB A:SER267 3.9 36.9 1.0
C A:LEU220 4.1 40.4 1.0
N A:SER267 4.1 35.3 1.0
CA A:LEU220 4.1 39.6 1.0
CB A:ASN221 4.3 42.0 1.0
CA A:ASP263 4.3 40.3 1.0
ND2 A:ASN221 4.4 48.0 1.0
CB A:ASP263 4.4 37.9 1.0
N A:MET264 4.4 32.3 1.0
CA A:SER267 4.4 29.0 1.0
CD2 A:LEU220 4.5 34.2 1.0
CB A:LEU220 4.5 35.4 1.0
CA A:MET264 4.6 33.0 1.0
CB A:ALA266 4.7 36.1 1.0
N A:ARG222 4.8 46.7 1.0
N A:PHE223 4.8 49.5 1.0
C A:ALA266 4.9 33.5 1.0

Sodium binding site 2 out of 5 in 8ds1

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Sodium binding site 2 out of 5 in the Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) Cut Site Sequence


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) Cut Site Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na401

b:54.6
occ:1.00
 OD1 F:ASP263 2.5 72.6 1.0
OD1 F:ASN221 2.7 69.0 1.0
O F:ASP263 2.8 44.6 1.0
O F:ASN221 2.8 50.4 1.0
O F:PHE223 3.3 62.4 1.0
OG F:SER267 3.3 58.9 1.0
N F:ASN221 3.4 59.0 1.0
C F:ASN221 3.5 56.9 1.0
CG F:ASN221 3.7 69.6 1.0
C F:ASP263 3.7 46.5 1.0
CG F:ASP263 3.7 64.6 1.0
CA F:ASN221 3.9 57.0 1.0
CB F:ALA266 4.3 47.3 1.0
N F:SER267 4.3 53.9 1.0
CA F:ASP263 4.3 51.2 1.0
C F:LEU220 4.3 57.2 1.0
CB F:ASN221 4.4 61.1 1.0
N F:PHE223 4.4 59.7 1.0
C F:PHE223 4.5 61.3 1.0
CA F:LEU220 4.5 57.9 1.0
CB F:SER267 4.5 52.0 1.0
CB F:ASP263 4.5 53.0 1.0
N F:ARG222 4.5 58.4 1.0
ND2 F:ASN221 4.6 69.9 1.0
OD2 F:ASP263 4.6 65.5 1.0
N F:MET264 4.7 44.2 1.0
C F:ARG222 4.8 61.4 1.0
CA F:SER267 4.8 56.0 1.0
CB F:LEU220 4.8 51.8 1.0
C F:ALA266 4.9 54.1 1.0
CA F:MET264 5.0 46.2 1.0

Sodium binding site 3 out of 5 in 8ds1

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Sodium binding site 3 out of 5 in the Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) Cut Site Sequence


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) Cut Site Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na401

b:42.9
occ:1.00
 OD1 G:ASP263 2.2 35.6 1.0
OD1 G:ASN221 2.3 28.5 1.0
O G:PHE223 2.4 29.7 1.0
O G:ASN221 2.4 36.2 1.0
O G:HOH507 2.5 26.5 1.0
O G:ASP263 2.9 27.0 1.0
C G:ASN221 3.2 30.0 1.0
CG G:ASN221 3.2 32.5 1.0
C G:PHE223 3.5 33.9 1.0
CG G:ASP263 3.5 37.3 1.0
N G:PHE223 3.6 34.7 1.0
CB G:ALA266 3.7 25.6 1.0
N G:ASN221 3.7 21.7 1.0
C G:ASP263 3.8 22.1 1.0
CA G:ASN221 3.8 27.5 1.0
CA G:PHE223 4.0 35.7 1.0
C G:ARG222 4.0 30.3 1.0
ND2 G:ASN221 4.0 29.8 1.0
CA G:ASP263 4.1 19.4 1.0
CB G:ASN221 4.1 34.0 1.0
N G:ARG222 4.2 32.1 1.0
OG G:SER267 4.2 26.6 1.0
OD2 G:ASP263 4.3 41.3 1.0
N G:SER267 4.3 24.2 1.0
CB G:ASP263 4.4 17.8 1.0
CB G:PHE223 4.5 36.7 1.0
CA G:ARG222 4.5 31.0 1.0
O G:ARG222 4.6 35.4 1.0
N G:THR224 4.6 40.2 1.0
CA G:ALA266 4.7 24.9 1.0
C G:ALA266 4.7 25.2 1.0
C G:LEU220 4.9 34.6 1.0
N G:MET264 5.0 24.1 1.0

Sodium binding site 4 out of 5 in 8ds1

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Sodium binding site 4 out of 5 in the Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) Cut Site Sequence


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) Cut Site Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na401

b:56.4
occ:1.00
 OD1 K:ASP263 2.3 55.4 0.5
O K:ASN221 2.8 54.2 1.0
O K:ASP263 2.8 52.3 1.0
CG K:ASP263 2.9 48.3 0.5
OG K:SER267 3.0 52.1 1.0
OD2 K:ASP263 3.3 44.3 0.5
N K:ASN221 3.3 50.3 1.0
C K:ASP263 3.5 46.5 1.0
C K:ASN221 3.8 54.2 1.0
CB K:SER267 4.0 46.6 1.0
OD1 K:ASN221 4.0 55.9 1.0
CB K:ASP263 4.0 49.4 0.5
CB K:ASP263 4.0 49.8 0.5
CA K:LEU220 4.1 39.7 1.0
CA K:ASN221 4.1 48.5 1.0
CA K:ASP263 4.2 44.2 0.5
CA K:ASP263 4.2 48.1 0.5
CD2 K:LEU220 4.2 39.5 1.0
C K:LEU220 4.3 45.2 1.0
N K:MET264 4.3 43.9 1.0
CB K:LEU220 4.3 41.8 1.0
O K:PHE223 4.3 55.9 1.0
CG K:ASN221 4.3 59.8 1.0
N K:SER267 4.4 38.8 1.0
CA K:MET264 4.5 39.4 1.0
CG2 K:ILE259 4.5 34.0 1.0
CA K:SER267 4.6 44.7 1.0
ND2 K:ASN221 4.8 62.2 1.0
CB K:ASN221 4.9 50.2 1.0
CG K:LEU220 4.9 48.3 1.0
N K:ARG222 5.0 53.5 1.0

Sodium binding site 5 out of 5 in 8ds1

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Sodium binding site 5 out of 5 in the Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) Cut Site Sequence


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Sars-Cov-2 Mpro in Complex with NSP12-NSP13 (C12) Cut Site Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na401

b:83.8
occ:1.00
 O L:ASN221 2.3 111.8 1.0
O L:ASP263 2.7 61.5 1.0
O L:PHE223 3.0 124.3 1.0
CB L:ALA266 3.0 55.4 1.0
C L:ASN221 3.1 115.7 1.0
OG L:SER267 3.2 64.1 1.0
N L:SER267 3.3 55.8 1.0
CB L:ASN221 3.6 95.4 1.0
CA L:ASN221 3.6 112.6 1.0
C L:ASP263 3.7 55.3 1.0
N L:ASN221 3.7 96.3 1.0
C L:ALA266 3.7 51.9 1.0
N L:PHE223 3.8 152.9 1.0
CA L:ALA266 3.8 48.8 1.0
OD1 L:ASP263 3.9 97.9 1.0
C L:PHE223 3.9 136.3 1.0
CA L:ASP263 4.0 57.8 1.0
CA L:SER267 4.1 55.5 1.0
N L:ARG222 4.1 116.2 1.0
C L:ARG222 4.2 132.9 1.0
CB L:SER267 4.2 58.0 1.0
CA L:PHE223 4.3 136.3 1.0
N L:ALA266 4.4 45.8 1.0
CB L:ASP263 4.5 61.9 1.0
CB L:PHE223 4.5 120.3 1.0
O L:ALA266 4.5 58.9 1.0
CA L:ARG222 4.6 119.7 1.0
CG L:ASP263 4.6 77.0 1.0
O L:ARG222 4.6 125.7 1.0
CG L:ASN221 4.8 105.2 1.0
N L:MET264 4.8 50.8 1.0
C L:LEU220 5.0 81.3 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 11:33:21 2024

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