Sodium in PDB 6xbi: Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor UAW248

Enzymatic activity of Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor UAW248

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor UAW248:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor UAW248, PDB code: 6xbi was solved by M.Sacco, C.Ma, J.Wang, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.75 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.898, 54.903, 62.261, 60.63, 79.77, 88.83
R / Rfree (%) 17.3 / 21.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor UAW248 (pdb code 6xbi). 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 Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor UAW248, PDB code: 6xbi:

Sodium binding site 1 out of 1 in 6xbi

Go back to Sodium Binding Sites List in 6xbi
Sodium binding site 1 out of 1 in the Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor UAW248


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor UAW248 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:36.5
occ:1.00
 O A:HOH744 2.8 21.2 1.0
N A:LEU227 2.9 22.9 1.0
CB A:LEU227 3.5 26.2 1.0
CA A:THR226 3.7 26.7 1.0
C A:THR226 3.8 26.5 1.0
CD1 A:LEU262 3.8 23.4 1.0
CA A:LEU227 3.8 23.3 1.0
CB A:THR226 3.9 27.4 1.0
CD2 A:LEU262 4.6 23.2 1.0
N A:ASN228 4.6 22.2 1.0
CG2 A:THR226 4.7 28.4 1.0
CG A:LEU262 4.8 20.6 1.0
C A:LEU227 4.8 24.3 1.0
O A:HOH672 4.8 27.0 1.0
CG A:LEU227 4.9 24.9 1.0
O A:THR226 5.0 25.1 1.0

Reference:

C.Ma, M.Sacco, Y.Chen, J.Wang. Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor UAW248 To Be Published.
Page generated: Tue Dec 15 15:56:40 2020

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