Sodium in PDB 7mky: Sars-Cov-2 Frameshifting Pseudoknot Rna

Protein crystallography data

The structure of Sars-Cov-2 Frameshifting Pseudoknot Rna, PDB code: 7mky was solved by C.P.Jones, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.43 / 1.31
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.371, 39.206, 38.803, 90, 97.98, 90
R / Rfree (%) 15.4 / 18.8

Other elements in 7mky:

The structure of Sars-Cov-2 Frameshifting Pseudoknot Rna also contains other interesting chemical elements:

Magnesium (Mg) 9 atoms
Potassium (K) 2 atoms
Cobalt (Co) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Sars-Cov-2 Frameshifting Pseudoknot Rna (pdb code 7mky). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Sars-Cov-2 Frameshifting Pseudoknot Rna, PDB code: 7mky:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7mky

Go back to Sodium Binding Sites List in 7mky
Sodium binding site 1 out of 4 in the Sars-Cov-2 Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na113

b:20.4
occ:1.00
O6 A:G41 2.6 23.2 1.0
O6 A:G40 2.7 17.2 1.0
O A:HOH378 2.8 23.7 1.0
O A:HOH419 2.9 26.3 1.0
O A:HOH261 3.6 21.8 1.0
C6 A:G41 3.6 18.2 1.0
C6 A:G40 3.7 16.9 1.0
N4 A:C39 3.7 18.8 1.0
N7 A:G40 4.0 18.2 1.0
N4 A:C45 4.2 18.9 1.0
C5 A:G40 4.2 16.7 1.0
C5 A:G41 4.3 16.4 1.0
O A:HOH247 4.3 19.1 1.0
N7 A:G41 4.4 15.9 1.0
C4 A:C39 4.5 17.8 1.0
N1 A:G41 4.6 17.5 1.0
O A:HOH458 4.6 34.7 1.0
C5 A:C39 4.8 18.2 1.0
O A:HOH441 4.9 34.9 1.0
N1 A:G40 4.9 16.5 1.0

Sodium binding site 2 out of 4 in 7mky

Go back to Sodium Binding Sites List in 7mky
Sodium binding site 2 out of 4 in the Sars-Cov-2 Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na114

b:46.3
occ:1.00
OP1 A:G28 3.0 22.4 1.0
O3' A:C27 3.0 17.6 1.0
O A:HOH450 3.2 45.8 1.0
P A:G28 3.6 20.0 1.0
MG A:MG105 4.1 23.6 1.0
C3' A:C27 4.2 16.7 1.0
C4' A:C27 4.4 17.2 1.0
O A:HOH327 4.5 24.4 1.0
C5' A:C27 4.6 18.0 1.0
OP2 A:G28 4.7 22.1 1.0
O A:HOH253 4.7 44.6 1.0
O A:HOH432 4.7 24.4 1.0
O2' A:C27 4.7 17.0 1.0
O5' A:G28 4.8 22.3 1.0
C5' A:G28 4.8 22.1 1.0

Sodium binding site 3 out of 4 in 7mky

Go back to Sodium Binding Sites List in 7mky
Sodium binding site 3 out of 4 in the Sars-Cov-2 Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na115

b:44.4
occ:1.00
O A:HOH245 2.6 27.9 1.0
N6 A:A37 3.0 17.6 1.0
O A:HOH222 3.1 33.8 1.0
N7 A:A37 3.4 17.8 1.0
O A:HOH376 3.5 25.4 1.0
N4 A:C36 3.5 14.9 1.0
C5 A:C36 3.6 15.7 1.0
C4 A:C36 3.7 14.3 1.0
O A:HOH372 3.7 19.7 1.0
O A:HOH452 3.7 39.5 1.0
O A:HOH290 3.8 32.0 1.0
C6 A:A37 3.9 17.2 1.0
C5 A:A37 4.0 17.3 1.0
O6 A:G38 4.2 18.1 1.0
N4 A:C47 4.3 16.5 0.5
O A:HOH455 4.5 33.5 1.0
C6 A:C36 4.5 14.9 1.0
N3 A:C36 4.5 14.4 1.0
N4 A:C47 4.6 23.7 0.5
C8 A:A37 4.6 16.8 1.0
MG A:MG108 4.8 29.8 1.0

Sodium binding site 4 out of 4 in 7mky

Go back to Sodium Binding Sites List in 7mky
Sodium binding site 4 out of 4 in the Sars-Cov-2 Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na116

b:27.8
occ:0.50
OP1 A:C47 3.1 26.0 0.5
O3' A:G46 3.4 21.9 0.5
O3' A:G46 3.6 21.6 0.5
OP1 A:C47 3.8 24.1 0.5
O A:HOH219 3.9 37.8 1.0
P A:C47 4.0 25.4 0.5
O A:HOH386 4.3 37.1 1.0
P A:C47 4.4 22.9 0.5
O2' A:G46 4.6 25.6 0.5
C3' A:G46 4.6 19.5 0.5
C3' A:G46 4.7 21.8 0.5
C5' A:C47 4.7 25.1 0.5
C4' A:G46 4.7 22.3 0.5
C4' A:G46 4.8 18.9 0.5
OP2 A:C47 5.0 24.3 0.5

Reference:

C.P.Jones, A.R.Ferre-D'amare. Sars-Cov-2 Frameshifting Pseudoknot Rna To Be Published.
Page generated: Mon Jul 12 16:03:13 2021

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