Sodium in PDB 7m1y: The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen

Protein crystallography data

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen, PDB code: 7m1y was solved by J.Osipiuk, C.Tesar, M.Endres, N.Maltseva, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.80 / 2.02
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 114.887, 114.887, 252.82, 90, 90, 120
R / Rfree (%) 18.4 / 21.3

Other elements in 7m1y:

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 2 atoms
Iodine (I) 13 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen (pdb code 7m1y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen, PDB code: 7m1y:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7m1y

Go back to Sodium Binding Sites List in 7m1y
Sodium binding site 1 out of 2 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na514

b:66.5
occ:1.00
O A:LEU120 2.5 47.4 1.0
O A:HOH628 2.6 66.1 1.0
O A:HOH700 2.6 58.7 1.0
O A:ILE123 2.6 49.2 1.0
OH A:TYR136 2.8 63.8 1.0
O A:HOH605 3.3 60.6 1.0
CZ A:TYR136 3.4 57.1 1.0
C A:LEU120 3.6 46.5 1.0
CE2 A:TYR136 3.7 61.6 1.0
O A:LEU125 3.7 54.0 1.0
C A:ILE123 3.8 50.0 1.0
N A:LEU125 3.9 49.8 1.0
CB A:LEU125 4.1 58.6 1.0
CA A:LEU120 4.4 46.1 1.0
CA A:LEU125 4.5 51.7 1.0
C A:LEU125 4.5 56.0 1.0
N A:GLN121 4.5 42.9 1.0
CE1 A:TYR136 4.6 52.3 1.0
CA A:GLN121 4.6 45.2 1.0
N A:ILE123 4.7 46.9 1.0
CA A:GLU124 4.7 53.1 1.0
N A:GLU124 4.7 51.4 1.0
C A:GLU124 4.7 52.0 1.0
CB A:LEU120 4.8 46.0 1.0
CA A:ILE123 4.8 50.2 1.0
C A:GLN121 4.8 46.0 1.0
CD2 A:TYR136 4.9 56.4 1.0
CG1 A:ILE123 4.9 48.9 1.0
CD2 A:LEU125 5.0 68.0 1.0

Sodium binding site 2 out of 2 in 7m1y

Go back to Sodium Binding Sites List in 7m1y
Sodium binding site 2 out of 2 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na413

b:56.8
occ:1.00
O B:ILE123 2.2 50.4 1.0
O B:LEU120 2.2 43.8 1.0
O B:HOH588 2.3 61.3 1.0
O B:HOH592 2.4 51.0 1.0
OH B:TYR136 2.7 51.5 1.0
CZ B:TYR136 3.4 51.8 1.0
C B:ILE123 3.4 48.7 1.0
C B:LEU120 3.5 45.3 1.0
CE1 B:TYR136 3.8 49.1 1.0
N B:ILE123 4.0 47.3 1.0
CA B:GLN121 4.0 46.2 1.0
C B:GLN121 4.1 44.3 1.0
N B:LEU125 4.2 55.0 1.0
N B:GLN121 4.2 45.6 1.0
CE2 B:TYR136 4.2 51.6 1.0
N B:GLU124 4.3 50.9 1.0
O B:HOH518 4.3 50.6 1.0
CA B:ILE123 4.4 47.9 1.0
N B:GLN122 4.4 42.6 1.0
CA B:GLU124 4.4 57.7 1.0
O B:GLN121 4.4 45.0 1.0
CA B:LEU120 4.5 44.2 1.0
O B:LEU125 4.5 61.0 1.0
O B:HOH606 4.7 67.6 1.0
CB B:LEU125 4.7 53.7 1.0
C B:GLU124 4.8 57.0 1.0
CG1 B:ILE123 4.8 47.0 1.0
C B:GLN122 4.9 46.4 1.0
CD1 B:TYR136 5.0 49.5 1.0
CA B:LEU125 5.0 55.8 1.0

Reference:

J.Osipiuk, C.Tesar, M.Endres, N.Maltseva, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen To Be Published.
Page generated: Sat Apr 3 17:56:23 2021

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