Atomistry » Sodium » PDB 8djz-8e62 » 8e5c
Atomistry »
  Sodium »
    PDB 8djz-8e62 »
      8e5c »

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

Last articles

Zn in 9FS1
Zn in 9FS3
Zn in 9FS2
Zn in 9H3H
Zn in 9F29
Zn in 9F2A
Zn in 9EY2
Zn in 9F26
Zn in 9E8J
Zn in 9E8N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy