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Sodium in PDB 8drz: Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP13-NSP14 (C13) Cut Site Sequence

Enzymatic activity of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP13-NSP14 (C13) Cut Site Sequence

All present enzymatic activity of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP13-NSP14 (C13) 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 NSP13-NSP14 (C13) Cut Site Sequence, PDB code: 8drz 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) 47.50 / 1.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.944, 216.821, 121.255, 90, 94.01, 90
R / Rfree (%) 17.7 / 22.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP13-NSP14 (C13) Cut Site Sequence (pdb code 8drz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP13-NSP14 (C13) Cut Site Sequence, PDB code: 8drz:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8drz

Go back to Sodium Binding Sites List in 8drz
Sodium binding site 1 out of 4 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP13-NSP14 (C13) 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 NSP13-NSP14 (C13) Cut Site Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:31.6
occ:0.50
 O B:HOH646 2.3 28.6 1.0
O B:HOH668 2.4 31.2 1.0
OG B:SER46 2.5 34.5 1.0
CB B:SER46 3.6 36.4 1.0
N B:SER46 3.8 32.7 1.0
O B:HOH576 4.2 34.3 1.0
CA B:SER46 4.3 34.5 1.0
O B:HOH527 4.3 42.1 1.0
O B:THR24 4.4 36.6 1.0
O B:HOH722 4.5 36.8 1.0
OG1 B:THR25 4.8 30.5 1.0
C B:THR45 4.9 32.2 1.0

Sodium binding site 2 out of 4 in 8drz

Go back to Sodium Binding Sites List in 8drz
Sodium binding site 2 out of 4 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP13-NSP14 (C13) 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 Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP13-NSP14 (C13) Cut Site Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:37.4
occ:1.00
 O E:HOH552 2.2 31.8 1.0
O C:HOH575 2.3 34.9 1.0
O C:HOH574 2.5 39.0 1.0
O E:HOH603 2.5 39.2 1.0
OG C:SER46 2.5 37.8 1.0
OG E:SER46 2.6 39.5 1.0
CB C:SER46 3.4 35.6 1.0
CB E:SER46 3.6 40.5 1.0
N C:SER46 3.7 34.0 1.0
O C:HOH553 4.0 37.6 1.0
N E:SER46 4.0 38.2 1.0
CA C:SER46 4.0 40.2 1.0
O E:HOH510 4.2 46.3 1.0
O C:HOH526 4.3 46.6 1.0
O E:HOH520 4.4 33.8 1.0
CA E:SER46 4.4 39.7 1.0
O E:THR24 4.4 35.0 1.0
O E:HOH640 4.5 40.6 1.0
O C:THR24 4.5 34.7 1.0
OG1 C:THR25 4.6 30.5 1.0
O C:HOH708 4.7 41.0 1.0
C C:THR45 4.7 36.8 1.0
OG1 E:THR25 4.8 34.2 1.0

Sodium binding site 3 out of 4 in 8drz

Go back to Sodium Binding Sites List in 8drz
Sodium binding site 3 out of 4 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP13-NSP14 (C13) 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 Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP13-NSP14 (C13) Cut Site Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na401

b:46.5
occ:1.00
 O A:HOH510 2.3 41.6 1.0
O A:HOH538 2.3 42.0 1.0
OG F:SER46 2.3 40.3 1.0
O A:HOH592 2.4 38.7 1.0
O F:HOH572 2.4 41.1 1.0
OG A:SER46 2.5 45.0 1.0
CB F:SER46 3.4 46.6 1.0
CB A:SER46 3.7 50.0 1.0
N F:SER46 3.8 49.2 1.0
N A:SER46 4.0 45.3 1.0
CA F:SER46 4.1 50.7 1.0
O A:HOH517 4.3 36.7 1.0
OG1 A:THR25 4.3 39.9 1.0
O A:HOH553 4.3 50.2 1.0
OG1 A:THR24 4.3 61.5 1.0
CA A:SER46 4.3 50.0 1.0
O F:HOH639 4.3 44.9 1.0
O F:HOH534 4.4 33.8 1.0
O A:THR24 4.5 40.7 1.0
OG1 F:THR25 4.6 39.5 1.0
O A:HOH679 4.7 45.0 1.0
O F:THR24 4.8 42.5 1.0
C F:THR45 4.9 51.7 1.0
C A:THR45 5.0 48.2 1.0

Sodium binding site 4 out of 4 in 8drz

Go back to Sodium Binding Sites List in 8drz
Sodium binding site 4 out of 4 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP13-NSP14 (C13) 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 Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP13-NSP14 (C13) Cut Site Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na401

b:47.0
occ:1.00
 OG G:SER46 2.3 42.2 1.0
O D:HOH549 2.3 36.3 1.0
O G:HOH559 2.4 37.4 1.0
O G:HOH596 2.4 43.3 1.0
O D:HOH614 2.6 43.0 1.0
OG D:SER46 2.6 43.8 1.0
CB G:SER46 3.4 46.8 1.0
CB D:SER46 3.7 45.8 1.0
N G:SER46 3.8 52.2 1.0
N D:SER46 4.0 41.3 1.0
CA G:SER46 4.1 52.6 1.0
O G:HOH518 4.2 43.4 1.0
O G:HOH603 4.2 41.2 1.0
O D:HOH523 4.2 45.2 1.0
CA D:SER46 4.3 49.3 1.0
O D:THR24 4.4 39.6 1.0
O G:THR24 4.6 45.7 1.0
OG1 G:THR25 4.8 51.2 1.0
OG1 D:THR25 4.8 35.5 1.0
O D:HOH671 4.9 51.9 1.0
C G:THR45 4.9 51.6 1.0
O D:HOH554 5.0 46.2 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 11:33:07 2024

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