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Sodium in PDB 7z2k: Crystal Structure of Sars-Cov-2 Main Protease in Orthorhombic Space Group P212121

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Orthorhombic Space Group P212121

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Orthorhombic Space Group P212121:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Orthorhombic Space Group P212121, PDB code: 7z2k was solved by P.Y.A.Reinke, S.Falke, J.Lieske, W.Ewert, J.Loboda, A.Rahmani Mashhour, M.Hauser, K.Karnicar, A.Usenik, N.Lindic, M.Lach, H.Boehler, T.Beck, R.Cox, H.N.Chapman, W.Hinrichs, D.Turk, S.Guenther, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.48 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.764, 101.002, 103.916, 90, 90, 90
R / Rfree (%) 18.8 / 21

Other elements in 7z2k:

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Orthorhombic Space Group P212121 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 Main Protease in Orthorhombic Space Group P212121 (pdb code 7z2k). 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 Sars-Cov-2 Main Protease in Orthorhombic Space Group P212121, PDB code: 7z2k:

Sodium binding site 1 out of 1 in 7z2k

Go back to Sodium Binding Sites List in 7z2k
Sodium binding site 1 out of 1 in the Crystal Structure of Sars-Cov-2 Main Protease in Orthorhombic Space Group P212121


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 Sars-Cov-2 Main Protease in Orthorhombic Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:62.1
occ:1.00
 OD1 A:ASP263 1.8 34.7 1.0
OD1 A:ASN221 1.9 41.0 1.0
H A:ASN221 2.6 55.5 1.0
O A:ASN221 2.8 30.9 1.0
CG A:ASN221 2.9 37.7 1.0
O A:ASP263 2.9 32.0 1.0
HG A:SER267 3.0 63.2 1.0
CG A:ASP263 3.0 37.0 1.0
O A:PHE223 3.0 38.0 1.0
N A:ASN221 3.3 46.3 1.0
C A:ASN221 3.3 32.5 1.0
H A:PHE223 3.5 35.4 1.0
HB1 A:ALA266 3.6 60.3 1.0
OG A:SER267 3.6 52.7 1.0
C A:ASP263 3.6 24.5 1.0
CA A:ASN221 3.6 35.4 1.0
OD2 A:ASP263 3.7 47.8 1.0
HD22 A:ASN221 3.7 47.5 1.0
ND2 A:ASN221 3.8 39.6 1.0
HA A:ASP263 3.8 43.5 1.0
CB A:ASN221 3.8 36.2 1.0
H A:SER267 3.9 41.6 1.0
N A:PHE223 4.0 29.5 1.0
HA A:LEU220 4.0 56.5 1.0
CA A:ASP263 4.0 36.2 1.0
C A:PHE223 4.1 47.3 1.0
CB A:ASP263 4.1 50.1 1.0
N A:ARG222 4.3 34.8 1.0
C A:LEU220 4.3 53.5 1.0
HB3 A:ASN221 4.4 43.5 1.0
N A:SER267 4.4 34.7 1.0
HB2 A:PHE223 4.4 37.1 1.0
HB2 A:ASN221 4.5 43.5 1.0
HD21 A:ASN221 4.5 47.5 1.0
HA A:MET264 4.5 38.7 1.0
CB A:ALA266 4.5 50.3 1.0
CA A:PHE223 4.6 29.3 1.0
N A:MET264 4.6 38.3 1.0
HA A:ASN221 4.6 42.4 1.0
C A:ARG222 4.6 26.9 1.0
HD22 A:LEU220 4.6 51.5 1.0
CA A:LEU220 4.6 47.1 1.0
HG23 A:ILE259 4.7 46.2 1.0
HB3 A:ASP263 4.7 60.1 1.0
CB A:SER267 4.7 48.3 1.0
HB3 A:LEU220 4.7 41.3 1.0
HB2 A:ASP263 4.7 60.1 1.0
HB2 A:ALA266 4.8 60.3 1.0
HB2 A:SER267 4.8 58.0 1.0
CA A:ARG222 4.9 36.1 1.0
H A:ARG222 4.9 41.8 1.0
HA A:ARG222 4.9 43.2 1.0
HA A:SER267 4.9 37.6 1.0
CA A:SER267 5.0 31.4 1.0

Reference:

P.Y.A.Reinke, S.Falke, J.Lieske, W.Ewert, J.Loboda, A.Rahmani Mashhour, M.Hauser, K.Karnicar, A.Usenik, N.Lindic, M.Lach, H.Boehler, T.Beck, R.Cox, H.N.Chapman, W.Hinrichs, D.Turk, S.Guenther, A.Meents. Sulfonated Calpeptin Is A Promising Drug Candidate Against Sars-Cov-2 Infections To Be Published.
Page generated: Wed Oct 9 10:00:17 2024

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