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Sodium in PDB 8dt9: Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231

Enzymatic activity of Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231

All present enzymatic activity of Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231, PDB code: 8dt9 was solved by A.M.Shaqra, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.58 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.524, 98.467, 58.529, 90, 107.45, 90
R / Rfree (%) 18.5 / 24.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231 (pdb code 8dt9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231, PDB code: 8dt9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 8dt9

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Sodium binding site 1 out of 9 in the Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231


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 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:54.0
occ:1.00
 O A:HOH732 4.5 42.9 1.0
NA A:NA504 4.6 63.9 1.0

Sodium binding site 2 out of 9 in 8dt9

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Sodium binding site 2 out of 9 in the Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231


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 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:63.9
occ:1.00
 O A:HOH748 4.3 49.9 1.0
NA A:NA503 4.6 54.0 1.0

Sodium binding site 3 out of 9 in 8dt9

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Sodium binding site 3 out of 9 in the Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231


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 Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231 within 5.0Å range:

Sodium binding site 4 out of 9 in 8dt9

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Sodium binding site 4 out of 9 in the Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:62.5
occ:1.00
 O B:HOH828 4.4 25.3 1.0
NZ B:LYS236 4.9 44.9 1.0

Sodium binding site 5 out of 9 in 8dt9

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Sodium binding site 5 out of 9 in the Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na505

b:54.7
occ:1.00
 O B:HOH816 2.9 43.8 1.0
O B:LYS236 3.6 23.6 1.0
CE2 B:TYR237 4.0 29.3 1.0
CD2 B:TYR237 4.0 31.6 1.0
CZ B:TYR237 4.5 34.0 1.0
C B:LYS236 4.6 27.0 1.0
CG B:TYR237 4.6 27.3 1.0
CA B:TYR237 4.8 19.7 1.0

Sodium binding site 6 out of 9 in 8dt9

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Sodium binding site 6 out of 9 in the Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na506

b:47.0
occ:1.00
 O B:GLN256 3.4 20.8 1.0
O B:ALA255 3.5 26.8 1.0
N B:GLY258 3.9 22.4 1.0
C B:GLN256 4.0 23.9 1.0
C B:THR257 4.0 20.2 1.0
CA B:GLY258 4.3 25.8 1.0
O B:HOH684 4.3 29.5 1.0
O B:THR257 4.4 20.7 1.0
N B:THR257 4.5 14.3 1.0
CA B:THR257 4.5 15.0 1.0
C B:ALA255 4.7 23.6 1.0
CA B:GLN256 4.7 18.9 1.0

Sodium binding site 7 out of 9 in 8dt9

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Sodium binding site 7 out of 9 in the Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231 within 5.0Å range:

Sodium binding site 8 out of 9 in 8dt9

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Sodium binding site 8 out of 9 in the Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231 within 5.0Å range:

Sodium binding site 9 out of 9 in 8dt9

Go back to Sodium Binding Sites List in 8dt9
Sodium binding site 9 out of 9 in the Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na509

b:56.5
occ:1.00
 O B:HOH853 4.1 31.4 1.0
O B:HOH662 4.4 27.3 1.0
OE1 B:GLU240 4.6 31.9 1.0
O B:HOH620 4.7 27.9 1.0

Reference:

A.M.Shaqra, C.A.Schiffer. Crystal Structure of Sars Cov-2 Mpro Mutant L141R with Pfizer Intravenous Inhibitor Pf-00835231 To Be Published.
Page generated: Mon Aug 18 13:57:04 2025

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