Sodium in PDB 8e5c: Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States

Enzymatic activity of Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States

All present enzymatic activity of Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States, PDB code: 8e5c 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) 25.41 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 45.129, 63.693, 105.323, 90, 90, 90
R / Rfree (%) 19.6 / 25.4

Other elements in 8e5c:

The structure of Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Fluorine (F) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States (pdb code 8e5c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States, PDB code: 8e5c:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 8e5c

Go back to Sodium Binding Sites List in 8e5c
Sodium binding site 1 out of 6 in the Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States


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 L50F with Nirmatrelvir Captured in Two Conformational States within 5.0Å range:

Sodium binding site 2 out of 6 in 8e5c

Go back to Sodium Binding Sites List in 8e5c
Sodium binding site 2 out of 6 in the Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States


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 L50F with Nirmatrelvir Captured in Two Conformational States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:37.8
occ:1.00
 O A:HOH770 2.5 29.8 1.0
O A:TYR101 3.5 13.7 1.0
CE1 A:TYR101 3.6 18.1 1.0
CZ A:TYR101 3.7 16.9 1.0
CD1 A:TYR101 4.0 12.9 1.0
O A:HOH855 4.0 22.5 1.0
OH A:TYR101 4.1 39.3 1.0
CE2 A:TYR101 4.2 15.2 1.0
CG A:TYR101 4.4 17.4 1.0
C A:TYR101 4.4 16.1 1.0
CD2 A:TYR101 4.5 11.3 1.0
N A:TYR101 4.7 8.0 1.0

Sodium binding site 3 out of 6 in 8e5c

Go back to Sodium Binding Sites List in 8e5c
Sodium binding site 3 out of 6 in the Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States


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 L50F with Nirmatrelvir Captured in Two Conformational States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:41.4
occ:1.00
 O A:THR257 2.7 11.2 1.0
C A:THR257 3.8 9.2 1.0
CA A:THR257 4.2 17.6 1.0
CG1 A:VAL212 4.2 10.7 1.0
CL A:CL512 4.3 45.4 0.5
CB A:THR257 4.4 10.7 1.0
CG1 A:ILE259 4.7 15.6 1.0
O A:HOH836 4.7 38.6 1.0
CD1 A:ILE259 4.9 21.8 1.0
N A:GLY258 5.0 9.7 1.0

Sodium binding site 4 out of 6 in 8e5c

Go back to Sodium Binding Sites List in 8e5c
Sodium binding site 4 out of 6 in the Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States


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 L50F with Nirmatrelvir Captured in Two Conformational States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:38.2
occ:1.00
 O A:HOH864 3.0 27.9 1.0

Sodium binding site 5 out of 6 in 8e5c

Go back to Sodium Binding Sites List in 8e5c
Sodium binding site 5 out of 6 in the Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States


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 L50F with Nirmatrelvir Captured in Two Conformational States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na507

b:59.4
occ:1.00
 O A:HOH904 3.3 34.5 1.0

Sodium binding site 6 out of 6 in 8e5c

Go back to Sodium Binding Sites List in 8e5c
Sodium binding site 6 out of 6 in the Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States


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 L50F with Nirmatrelvir Captured in Two Conformational States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na508

b:47.0
occ:1.00
 O A:HOH854 3.2 19.7 1.0
O A:HOH734 4.7 28.6 1.0
CG A:PRO168 4.8 36.2 1.0
CB A:PRO168 4.8 40.8 1.0

Reference:

A.M.Shaqra, C.A.Schiffer. Crystal Structure of Sars Cov-2 Mpro Mutant L50F with Nirmatrelvir Captured in Two Conformational States To Be Published.
Page generated: Wed Oct 9 11:38:05 2024

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