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Sodium in PDB 9dw6: Crystal Structure of Sars-Cov-2 Main Protease (Mpro) C145A Mutant in Complex with Peptide From Human Trna Methyltransferase TRMT1

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) C145A Mutant in Complex with Peptide From Human Trna Methyltransferase TRMT1

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) C145A Mutant in Complex with Peptide From Human Trna Methyltransferase TRMT1:
2.1.1.216; 3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) C145A Mutant in Complex with Peptide From Human Trna Methyltransferase TRMT1, PDB code: 9dw6 was solved by A.D'oliviera, J.S.Mugridge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.34 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.787, 100.029, 103.252, 90, 90, 90
R / Rfree (%) 18.1 / 21.8

Other elements in 9dw6:

The structure of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) C145A Mutant in Complex with Peptide From Human Trna Methyltransferase TRMT1 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) C145A Mutant in Complex with Peptide From Human Trna Methyltransferase TRMT1 (pdb code 9dw6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) C145A Mutant in Complex with Peptide From Human Trna Methyltransferase TRMT1, PDB code: 9dw6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 9dw6

Go back to Sodium Binding Sites List in 9dw6
Sodium binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) C145A Mutant in Complex with Peptide From Human Trna Methyltransferase TRMT1


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 (Mpro) C145A Mutant in Complex with Peptide From Human Trna Methyltransferase TRMT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:44.2
occ:1.00
 O A:HOH610 2.6 42.9 1.0
O A:HOH684 2.7 38.7 1.0
O A:CYS22 2.8 30.4 1.0
O A:CYS44 3.0 32.8 1.0
O A:VAL42 3.2 25.2 1.0
OG1 A:THR25 3.3 26.0 1.0
C A:CYS44 3.5 29.6 1.0
C A:ILE43 3.6 23.9 1.0
CB A:THR25 3.6 19.1 1.0
C A:CYS22 3.7 30.7 1.0
O A:ILE43 3.7 29.5 1.0
N A:CYS44 3.9 19.8 1.0
CA A:ILE43 3.9 20.6 1.0
N A:THR45 4.2 34.1 1.0
C A:VAL42 4.2 22.7 1.0
CB A:CYS22 4.3 25.2 1.0
CA A:CYS44 4.3 24.2 1.0
N A:THR25 4.3 28.6 1.0
CG2 A:THR45 4.3 39.3 1.0
O A:HOH516 4.4 30.5 1.0
SG A:CYS22 4.4 39.5 1.0
CA A:GLY23 4.4 33.5 1.0
N A:GLY23 4.4 32.2 1.0
N A:ILE43 4.5 20.5 1.0
CA A:CYS22 4.6 23.8 1.0
CA A:THR45 4.6 37.6 1.0
CA A:THR25 4.6 24.4 1.0
N A:THR24 4.6 27.1 1.0
CG2 A:THR25 4.7 19.6 1.0
C A:GLY23 5.0 31.9 1.0

Sodium binding site 2 out of 2 in 9dw6

Go back to Sodium Binding Sites List in 9dw6
Sodium binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) C145A Mutant in Complex with Peptide From Human Trna Methyltransferase TRMT1


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 Sars-Cov-2 Main Protease (Mpro) C145A Mutant in Complex with Peptide From Human Trna Methyltransferase TRMT1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:31.1
occ:1.00
 OD1 B:ASN221 2.3 29.3 1.0
O B:PHE223 2.3 22.9 1.0
O B:HOH548 2.3 26.8 1.0
OD1 B:ASP263 2.3 52.6 1.0
O B:ASN221 2.7 24.8 1.0
O B:ASP263 3.0 25.3 1.0
C B:PHE223 3.3 30.0 1.0
CG B:ASN221 3.3 30.2 1.0
N B:PHE223 3.4 22.3 1.0
C B:ASN221 3.4 24.2 1.0
CG B:ASP263 3.5 49.5 1.0
CB B:ALA266 3.7 29.1 1.0
C B:ASP263 3.8 31.9 1.0
N B:ASN221 3.9 28.1 1.0
CA B:PHE223 3.9 31.7 1.0
CA B:ASN221 4.0 27.8 1.0
C B:ARG222 4.0 32.5 1.0
CA B:ASP263 4.1 32.3 1.0
ND2 B:ASN221 4.2 24.9 1.0
N B:ARG222 4.2 25.3 1.0
CB B:ASN221 4.3 25.7 1.0
OG B:SER267 4.3 28.0 1.0
OD2 B:ASP263 4.4 55.9 1.0
CB B:ASP263 4.4 37.3 1.0
N B:SER267 4.5 24.6 1.0
N B:THR224 4.5 27.1 1.0
CB B:PHE223 4.5 25.2 1.0
CA B:ARG222 4.6 31.3 1.0
O B:ARG222 4.7 23.2 1.0
CA B:ALA266 4.7 30.9 1.0
C B:ALA266 4.8 30.3 1.0
CA B:THR224 4.9 26.8 1.0
N B:MET264 4.9 28.7 1.0

Reference:

A.D'oliviera, X.Dai, S.Mottaghinia, E.P.Geissler, L.Etienne, Y.Zhang, J.S.Mugridge. Recognition and Cleavage of Human Trna Methyltransferase TRMT1 By the Sars-Cov-2 Main Protease. Elife 2023.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.91168.1
Page generated: Mon Aug 18 16:46:50 2025

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