Magnesium in PDB 7lyj: Sars-Cov-2 Frameshifting Pseudoknot Rna

The structure of Sars-Cov-2 Frameshifting Pseudoknot Rna, PDB code: 7lyj 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)	57.09 / 2.11
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.465, 39.477, 39.398, 90, 98.53, 90
R / Rfree (%)	21 / 25.1

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

Potassium	(K)	2 atoms
Iridium	(Ir)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Sars-Cov-2 Frameshifting Pseudoknot Rna (pdb code 7lyj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Sars-Cov-2 Frameshifting Pseudoknot Rna, PDB code: 7lyj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Sars-Cov-2 Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:32.1 occ:1.00 O6 A:G30 2.5 34.8 1.0 O6 A:G55 2.7 38.0 1.0 O4 A:U29 2.9 40.3 1.0 O4 A:U56 2.9 42.7 1.0 O A:HOH221 3.0 37.5 1.0 O A:HOH223 3.1 53.3 1.0 N4 A:C31 3.7 37.0 1.0 C6 A:G30 3.7 36.6 1.0 C4 A:U56 3.7 42.6 1.0 C4 A:U29 3.7 41.2 1.0 C6 A:G55 3.8 38.1 1.0 N3 A:U56 3.9 42.3 1.0 N6 A:A57 4.1 47.4 1.0 N7 A:G30 4.5 39.6 1.0 C5 A:G30 4.5 38.3 1.0 C5 A:U29 4.5 42.5 1.0 N3 A:U29 4.6 42.3 1.0 MG A:MG113 4.6 70.2 1.0 C4 A:C31 4.7 39.1 1.0 N1 A:G55 4.7 39.2 1.0 C5 A:G55 4.7 38.0 1.0 N1 A:G30 4.8 37.5 1.0 N7 A:G55 5.0 37.5 1.0 N3 A:C31 5.0 40.1 1.0

Magnesium binding site 2 out of 12 in the Sars-Cov-2 Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:58.4 occ:0.50 O A:HOH224 2.9 70.6 1.0 OP1 A:C47 3.0 63.3 1.0 O3' A:G46 3.6 48.0 1.0 P A:C47 4.0 61.9 1.0 O A:HOH226 4.7 71.8 1.0 C5' A:C47 4.8 50.9 1.0 C3' A:G46 4.9 46.6 1.0 O5' A:C47 4.9 49.0 1.0

Magnesium binding site 3 out of 12 in the Sars-Cov-2 Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:67.1 occ:1.00 O A:HOH226 2.6 71.8 1.0 OP1 A:G33 3.8 51.8 1.0 O A:HOH224 4.8 70.6 1.0 P A:G33 4.8 49.2 1.0 OP2 A:G33 4.9 46.4 1.0 OP1 A:C47 4.9 63.3 1.0

Magnesium binding site 4 out of 12 in the Sars-Cov-2 Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:53.1 occ:1.00 OP2 A:A37 4.3 44.0 1.0 OP2 A:C36 4.9 43.2 1.0

Magnesium binding site 5 out of 12 in the Sars-Cov-2 Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:64.5 occ:1.00 O A:HOH239 2.1 60.0 1.0 O A:HOH203 2.2 34.5 1.0 O4 A:U6 4.0 38.2 1.0 O A:HOH210 4.3 43.0 1.0 O4 A:U22 4.6 46.6 1.0 N6 A:A7 4.9 34.7 1.0

Magnesium binding site 6 out of 12 in the Sars-Cov-2 Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:63.4 occ:1.00 O A:HOH206 4.0 33.8 1.0 OP2 A:G32 4.2 50.5 1.0 OP2 A:C31 4.3 58.3 1.0 O A:HOH214 4.5 48.6 1.0 OP2 A:G49 4.8 64.4 1.0

Magnesium binding site 7 out of 12 in the Sars-Cov-2 Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:50.9 occ:1.00 OP1 A:U6 2.7 38.6 1.0 C5' A:U6 3.4 42.4 1.0 P A:U6 3.8 38.6 1.0 O3' A:G5 3.9 35.5 1.0 O5' A:U6 4.0 40.8 1.0 C4' A:U6 4.7 42.7 1.0 O2' A:G5 5.0 37.5 1.0

Magnesium binding site 8 out of 12 in the Sars-Cov-2 Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg110 b:50.4 occ:1.00 OP1 A:A37 2.0 48.3 1.0 O A:HOH228 2.1 43.5 1.0 O A:HOH222 2.2 30.5 1.0 P A:A37 3.4 45.0 1.0 OP2 A:A37 4.0 44.0 1.0 O5' A:A37 4.2 42.3 1.0 O3' A:C36 4.5 42.7 1.0 C5' A:A37 4.5 45.0 1.0

Magnesium binding site 9 out of 12 in the Sars-Cov-2 Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg111 b:54.3 occ:1.00 O A:HOH238 2.4 54.1 1.0 O A:HOH214 2.8 48.6 1.0 O6 A:G49 2.9 39.7 1.0 C6 A:G49 3.8 41.4 1.0 N6 A:A35 3.8 32.2 1.0 N4 A:C34 3.9 35.8 1.0 N7 A:G49 4.2 45.0 1.0 C5 A:G49 4.3 43.6 1.0 O4 A:U48 4.4 43.8 1.0 N4 A:C36 4.5 32.7 1.0 C4 A:C34 4.7 35.8 1.0 N1 A:G49 4.9 41.2 1.0 C5 A:C34 4.9 36.2 1.0 N7 A:A35 5.0 33.8 1.0 C6 A:A35 5.0 32.9 1.0

Magnesium binding site 10 out of 12 in the Sars-Cov-2 Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg112 b:75.0 occ:1.00 O A:HOH237 2.3 53.3 1.0 OP2 A:G2 3.5 66.2 1.0 OP2 A:U22 3.9 53.2 1.0 P A:G2 5.0 68.2 1.0

C.P.Jones, A.R.Ferre-D'amare. Sars-Cov-2 Frameshifting Pseudoknot Rna To Be Published.