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Sodium in PDB 8okn: Crystal Structure of F2F-2020198-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

Enzymatic activity of Crystal Structure of F2F-2020198-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

All present enzymatic activity of Crystal Structure of F2F-2020198-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of F2F-2020198-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 8okn was solved by E.Costanzi, N.Demitri, P.Storici, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.36 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.848, 99.853, 104.367, 90, 90, 90
R / Rfree (%) 15.9 / 17.4

Other elements in 8okn:

The structure of Crystal Structure of F2F-2020198-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of F2F-2020198-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. (pdb code 8okn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of F2F-2020198-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 8okn:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 8okn

Go back to Sodium Binding Sites List in 8okn
Sodium binding site 1 out of 3 in the Crystal Structure of F2F-2020198-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


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 F2F-2020198-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:46.6
occ:1.00
 OE1 A:GLU178 2.2 40.2 1.0
O A:HOH516 2.3 25.2 1.0
O A:HOH779 2.5 23.3 1.0
O A:HOH807 2.7 33.9 1.0
HB2 A:GLU178 2.9 24.0 1.0
CD A:GLU178 2.9 44.9 1.0
HG3 A:GLU178 3.0 29.3 1.0
O A:HOH825 3.1 43.4 1.0
HB2 A:ARG105 3.2 17.9 1.0
CG A:GLU178 3.3 24.4 1.0
OD2 A:ASP176 3.3 17.9 1.0
CB A:GLU178 3.5 20.0 1.0
CG A:ASP176 3.7 15.9 1.0
OE2 A:GLU178 3.9 53.8 1.0
HB3 A:GLU178 4.0 24.0 1.0
OD1 A:ASP176 4.1 14.3 1.0
HD2 A:ARG105 4.1 20.0 1.0
H A:GLU178 4.1 17.1 1.0
O A:HOH770 4.1 43.2 1.0
CB A:ARG105 4.2 14.9 1.0
HB2 A:ASP176 4.2 15.3 1.0
HG2 A:GLU178 4.2 29.3 1.0
HB3 A:ARG105 4.3 17.9 1.0
H A:ARG105 4.5 15.8 1.0
CB A:ASP176 4.6 12.8 1.0
N A:GLU178 4.7 14.3 1.0
CA A:GLU178 4.7 15.6 1.0
OD1 A:ASN180 4.8 28.9 1.0
N A:ARG105 4.8 13.2 1.0
CD A:ARG105 4.8 16.7 1.0
HB3 A:ASP176 4.9 15.3 1.0
O A:HOH642 4.9 16.8 1.0
HH11 A:ARG105 5.0 18.1 1.0
HD3 A:ARG105 5.0 20.0 1.0

Sodium binding site 2 out of 3 in 8okn

Go back to Sodium Binding Sites List in 8okn
Sodium binding site 2 out of 3 in the Crystal Structure of F2F-2020198-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of F2F-2020198-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:56.5
occ:1.00
 OD1 A:ASP48 2.4 44.8 1.0
HA A:ASP48 2.6 44.0 1.0
O A:HOH688 2.7 23.6 1.0
CG A:ASP48 3.3 43.2 1.0
HD21 A:LEU57 3.3 32.4 1.0
O A:HOH508 3.4 50.7 1.0
CA A:ASP48 3.4 36.6 1.0
HB3 A:ASP48 3.5 34.7 1.0
HA A:PRO52 3.5 25.4 1.0
CB A:ASP48 3.6 28.9 1.0
HD11 A:LEU57 3.8 26.1 1.0
O A:ASP48 4.1 32.9 1.0
H A:ASN53 4.1 23.4 1.0
CD2 A:LEU57 4.3 27.0 1.0
C A:ASP48 4.3 30.6 1.0
O A:HOH583 4.3 31.5 1.0
O A:HOH513 4.4 31.4 1.0
N A:ASP48 4.4 36.7 1.0
OD2 A:ASP48 4.4 34.9 1.0
CA A:PRO52 4.5 21.2 1.0
HB2 A:ASP48 4.6 34.7 1.0
HG A:LEU57 4.6 24.9 1.0
CD1 A:LEU57 4.6 21.7 1.0
HD23 A:LEU57 4.6 32.4 1.0
HB3 A:PRO52 4.6 28.3 1.0
HG2 A:GLU47 4.7 76.6 1.0
CG A:LEU57 4.8 20.7 1.0
H A:ASP48 4.8 44.0 1.0
O A:GLU47 4.8 49.4 1.0
HD22 A:LEU57 4.8 32.4 1.0
O A:ASN51 4.9 23.4 1.0
N A:ASN53 4.9 19.5 1.0
C A:GLU47 4.9 47.3 1.0

Sodium binding site 3 out of 3 in 8okn

Go back to Sodium Binding Sites List in 8okn
Sodium binding site 3 out of 3 in the Crystal Structure of F2F-2020198-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of F2F-2020198-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:23.6
occ:1.00
 OD1 B:ASN221 2.2 20.3 1.0
OD1 B:ASP263 2.2 28.4 1.0
O B:PHE223 2.3 16.9 1.0
O B:HOH534 2.3 20.2 1.0
O B:ASN221 2.7 18.5 1.0
O B:ASP263 2.9 22.9 1.0
HB3 B:ALA266 3.0 30.7 1.0
H B:PHE223 3.1 19.8 1.0
H B:ASN221 3.2 22.2 1.0
CG B:ASN221 3.3 20.5 1.0
C B:PHE223 3.4 17.1 1.0
C B:ASN221 3.4 16.2 1.0
CG B:ASP263 3.4 28.1 1.0
N B:PHE223 3.4 16.5 1.0
HA B:ASP263 3.4 29.7 1.0
C B:ASP263 3.7 23.1 1.0
N B:ASN221 3.9 18.5 1.0
CA B:PHE223 3.9 17.0 1.0
CB B:ALA266 3.9 25.6 1.0
CA B:ASP263 3.9 24.8 1.0
HB2 B:PHE223 4.0 20.6 1.0
CA B:ASN221 4.0 17.1 1.0
H B:SER267 4.0 25.5 1.0
HB1 B:ALA266 4.0 30.7 1.0
C B:ARG222 4.1 16.5 1.0
HD21 B:ASN221 4.1 26.4 1.0
O B:HOH595 4.1 32.4 1.0
ND2 B:ASN221 4.2 22.0 1.0
N B:ARG222 4.2 15.8 1.0
HG B:SER267 4.2 26.1 1.0
CB B:ASN221 4.2 17.4 1.0
OG B:SER267 4.2 21.8 1.0
CB B:ASP263 4.2 25.6 1.0
OD2 B:ASP263 4.3 33.1 1.0
HA B:THR224 4.3 22.9 1.0
N B:SER267 4.4 21.2 1.0
HB2 B:ALA266 4.5 30.7 1.0
CB B:PHE223 4.5 17.1 1.0
N B:THR224 4.5 17.7 1.0
CA B:ARG222 4.6 16.1 1.0
HA B:ARG222 4.6 19.4 1.0
HB2 B:ASN221 4.7 20.9 1.0
HA B:PHE223 4.7 20.4 1.0
H B:ALA266 4.8 26.5 1.0
C B:ALA266 4.8 22.0 1.0
O B:ARG222 4.8 16.9 1.0
N B:MET264 4.8 22.0 1.0
HB2 B:ASP263 4.8 30.7 1.0
CA B:ALA266 4.8 22.9 1.0
HA B:MET264 4.8 24.6 1.0
H B:ARG222 4.8 18.9 1.0
HA B:LEU220 4.8 22.1 1.0
HB3 B:ASP263 4.9 30.7 1.0
HA B:ASN221 4.9 20.6 1.0
HB3 B:ASN221 4.9 20.9 1.0
CA B:THR224 4.9 19.1 1.0
HD22 B:ASN221 4.9 26.4 1.0
HA B:SER267 5.0 25.7 1.0

Reference:

I.Stefanelli, A.Corona, C.Cerchia, E.Cassese, S.Improta, E.Costanzi, S.Pelliccia, S.Morasso, F.Esposito, A.Paulis, S.Scognamiglio, F.S.Di Leva, P.Storici, M.Brindisi, E.Tramontano, R.Cannalire, V.Summa. Broad-Spectrum Coronavirus 3C-Like Protease Peptidomimetic Inhibitors Effectively Block Sars-Cov-2 Replication in Cells: Design, Synthesis, Biological Evaluation, and X-Ray Structure Determination. Eur.J.Med.Chem. V. 253 15311 2023.
ISSN: ISSN 0223-5234
PubMed: 37043904
DOI: 10.1016/J.EJMECH.2023.115311
Page generated: Wed Oct 9 12:46:02 2024

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