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Sodium in PDB 8okk: Crystal Structure of F2F-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

Enzymatic activity of Crystal Structure of F2F-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

All present enzymatic activity of Crystal Structure of F2F-2020184-00X 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-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 8okk 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) 56.92 / 1.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.001, 99.431, 104.033, 90, 90, 90
R / Rfree (%) 15.2 / 17.8

Other elements in 8okk:

The structure of Crystal Structure of F2F-2020184-00X 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-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. (pdb code 8okk). 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-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 8okk:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 8okk

Go back to Sodium Binding Sites List in 8okk
Sodium binding site 1 out of 3 in the Crystal Structure of F2F-2020184-00X 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-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:24.5
occ:1.00
 OD1 A:ASP263 2.2 32.2 1.0
OD1 A:ASN221 2.3 18.9 1.0
O A:PHE223 2.3 21.9 1.0
O A:HOH524 2.4 22.1 1.0
O A:ASN221 2.6 23.1 1.0
O A:ASP263 2.9 17.6 1.0
HB3 A:ALA266 2.9 20.2 1.0
H A:PHE223 3.1 26.2 1.0
H A:ASN221 3.2 23.7 1.0
CG A:ASP263 3.3 29.8 1.0
C A:ASN221 3.4 21.4 1.0
HA A:ASP263 3.4 20.4 1.0
CG A:ASN221 3.4 19.5 1.0
C A:PHE223 3.4 22.1 1.0
HG A:SER267 3.5 25.1 0.8
N A:PHE223 3.5 21.9 1.0
C A:ASP263 3.7 16.4 1.0
CB A:ALA266 3.8 16.8 1.0
O A:HOH561 3.9 41.2 1.0
N A:ASN221 3.9 19.8 1.0
CA A:ASP263 3.9 17.0 1.0
HB1 A:ALA266 4.0 20.2 1.0
H A:SER267 4.0 18.1 0.8
CA A:PHE223 4.0 23.5 1.0
CA A:ASN221 4.0 19.0 1.0
HB2 A:PHE223 4.1 31.7 1.0
H A:SER267 4.1 18.3 0.2
CB A:ASP263 4.2 18.0 1.0
OD2 A:ASP263 4.2 34.4 1.0
N A:ARG222 4.2 22.0 1.0
HD21 A:ASN221 4.2 26.4 1.0
C A:ARG222 4.3 23.3 1.0
ND2 A:ASN221 4.3 22.1 1.0
HB2 A:ALA266 4.3 20.2 1.0
HB2 A:SER267 4.3 22.7 0.2
HA A:THR224 4.3 23.7 1.0
CB A:ASN221 4.3 18.7 1.0
OG A:SER267 4.3 20.9 0.8
N A:SER267 4.3 15.1 0.8
N A:SER267 4.4 15.3 0.2
N A:THR224 4.6 24.5 1.0
HA A:ARG222 4.6 31.2 1.0
CB A:PHE223 4.6 26.4 1.0
CA A:ARG222 4.6 26.0 1.0
C A:ALA266 4.7 15.2 1.0
H A:ALA266 4.7 18.8 1.0
CA A:ALA266 4.7 14.8 1.0
HB2 A:ASP263 4.8 21.6 1.0
HB2 A:ASN221 4.8 22.5 1.0
N A:MET264 4.8 14.4 1.0
HB3 A:ASP263 4.8 21.6 1.0
HA A:MET264 4.8 17.3 1.0
HA A:PHE223 4.8 28.2 1.0
H A:ARG222 4.9 26.4 1.0
CA A:THR224 4.9 19.8 1.0
HA A:SER267 4.9 20.6 0.8
HA A:ASN221 5.0 22.7 1.0
HA A:LEU220 5.0 20.6 1.0
HA A:SER267 5.0 20.6 0.2

Sodium binding site 2 out of 3 in 8okk

Go back to Sodium Binding Sites List in 8okk
Sodium binding site 2 out of 3 in the Crystal Structure of F2F-2020184-00X 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-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:51.5
occ:1.00
 OE1 A:GLU178 2.2 47.8 1.0
O A:HOH513 2.3 32.9 1.0
O A:HOH734 2.5 27.3 1.0
CD A:GLU178 3.0 42.7 1.0
HB2 A:ARG105 3.2 23.4 1.0
HG3 A:GLU178 3.3 34.0 1.0
HB2 A:GLU178 3.3 23.9 1.0
OD2 A:ASP176 3.5 19.2 1.0
CG A:GLU178 3.6 28.3 1.0
OE2 A:GLU178 3.8 53.7 1.0
CB A:GLU178 3.9 20.0 1.0
HD2 A:ARG105 4.0 21.5 1.0
CB A:ARG105 4.1 19.5 1.0
CG A:ASP176 4.1 17.8 1.0
HB3 A:ARG105 4.1 23.4 1.0
HB3 A:GLU178 4.4 23.9 1.0
HG2 A:GLU178 4.5 34.0 1.0
H A:ARG105 4.5 19.5 1.0
HB2 A:ASP176 4.5 18.4 1.0
OD1 A:ASP176 4.5 15.8 1.0
O A:HOH685 4.5 26.2 1.0
H A:GLU178 4.5 18.6 1.0
O A:HOH667 4.7 47.7 1.0
CD A:ARG105 4.8 18.0 1.0
N A:ARG105 4.8 16.3 1.0
HD3 A:ARG105 4.9 21.5 1.0
CB A:ASP176 4.9 15.4 1.0
CG A:ARG105 4.9 17.8 1.0
OD1 A:ASN180 4.9 32.8 1.0

Sodium binding site 3 out of 3 in 8okk

Go back to Sodium Binding Sites List in 8okk
Sodium binding site 3 out of 3 in the Crystal Structure of F2F-2020184-00X 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-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na410

b:20.9
occ:1.00
 OD1 B:ASP263 2.1 30.9 1.0
OD1 B:ASN221 2.2 18.5 1.0
O B:PHE223 2.3 17.2 1.0
O B:HOH522 2.4 19.3 1.0
O B:ASN221 2.6 18.0 1.0
O B:ASP263 2.8 19.6 1.0
HB3 B:ALA266 3.0 26.6 1.0
H B:PHE223 3.1 21.0 1.0
H B:ASN221 3.2 21.6 1.0
CG B:ASP263 3.3 30.5 1.0
CG B:ASN221 3.3 22.0 1.0
C B:ASN221 3.4 16.1 1.0
C B:PHE223 3.4 18.0 1.0
HA B:ASP263 3.4 23.7 1.0
N B:PHE223 3.4 17.5 1.0
C B:ASP263 3.6 18.4 1.0
CB B:ALA266 3.8 22.2 1.0
CA B:ASP263 3.9 19.8 1.0
N B:ASN221 3.9 18.0 1.0
CA B:PHE223 3.9 18.2 1.0
HB1 B:ALA266 4.0 26.6 1.0
H B:SER267 4.0 27.7 1.0
HB2 B:PHE223 4.0 23.4 1.0
CA B:ASN221 4.0 15.7 1.0
C B:ARG222 4.1 17.7 1.0
HG B:SER267 4.1 29.1 1.0
O B:HOH560 4.1 35.0 1.0
HD21 B:ASN221 4.1 26.4 1.0
OD2 B:ASP263 4.2 31.9 1.0
CB B:ASP263 4.2 22.5 1.0
ND2 B:ASN221 4.2 22.0 1.0
N B:ARG222 4.2 16.9 1.0
OG B:SER267 4.2 24.3 1.0
CB B:ASN221 4.3 18.2 1.0
HB2 B:ALA266 4.4 26.6 1.0
HA B:THR224 4.4 24.3 1.0
N B:SER267 4.4 23.1 1.0
CB B:PHE223 4.5 19.5 1.0
CA B:ARG222 4.6 17.3 1.0
N B:THR224 4.6 18.9 1.0
HA B:ARG222 4.6 20.7 1.0
H B:ALA266 4.7 22.9 1.0
N B:MET264 4.7 17.2 1.0
HB2 B:ASP263 4.7 27.0 1.0
HA B:PHE223 4.8 21.9 1.0
HB2 B:ASN221 4.8 21.8 1.0
C B:ALA266 4.8 21.1 1.0
HA B:MET264 4.8 19.4 1.0
CA B:ALA266 4.8 21.6 1.0
HB3 B:ASP263 4.8 27.0 1.0
O B:ARG222 4.8 18.3 1.0
H B:ARG222 4.8 20.2 1.0
HA B:LEU220 4.9 23.1 1.0
HA B:ASN221 4.9 18.8 1.0
CA B:THR224 5.0 20.2 1.0
HB3 B:ASN221 5.0 21.8 1.0
HD22 B:ASN221 5.0 26.4 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 12:45:41 2024

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