Magnesium 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:

Sodium (Na) 4 atoms
Potassium (K) 2 atoms
Cobalt (Co) 1 atom

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 9 in 7mky

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Magnesium binding site 1 out of 9 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:Mg104

b:18.1
occ:1.00
 OP1 A:A37 2.0 18.1 1.0
O A:HOH392 2.1 20.5 1.0
O A:HOH387 2.1 21.2 1.0
P A:A37 3.4 17.0 1.0
O A:HOH410 3.7 25.1 1.0
OP2 A:A37 4.0 20.1 1.0
O A:HOH428 4.2 33.0 1.0
O5' A:A37 4.3 17.8 1.0
O A:HOH390 4.3 41.5 1.0
O3' A:C36 4.3 16.2 1.0
C5' A:A37 4.6 19.0 1.0

Magnesium binding site 2 out of 9 in 7mky

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Magnesium binding site 2 out of 9 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:Mg105

b:23.6
occ:1.00
 OP1 A:G28 2.1 22.4 1.0
O A:HOH327 2.1 24.4 1.0
O A:HOH409 2.1 23.5 1.0
O A:HOH318 2.1 20.9 1.0
O A:HOH432 2.1 24.4 1.0
P A:G28 3.4 20.0 1.0
O5' A:G28 3.9 22.3 1.0
O A:HOH450 3.9 45.8 1.0
O A:HOH233 4.1 39.4 1.0
NA A:NA114 4.1 46.3 1.0
C5' A:G28 4.1 22.1 1.0
O A:HOH282 4.2 23.1 1.0
OP2 A:G28 4.2 22.1 1.0
O A:HOH254 4.2 43.1 1.0
OP1 A:G52 4.2 21.2 1.0
OP1 A:U51 4.4 23.5 1.0
O3' A:C27 4.5 17.6 1.0
OP2 A:U29 4.8 24.4 1.0
OP2 A:G52 5.0 21.5 1.0

Magnesium binding site 3 out of 9 in 7mky

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Magnesium binding site 3 out of 9 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:Mg106

b:29.6
occ:1.00
 O A:HOH289 2.1 29.5 1.0
O A:HOH463 2.1 38.6 1.0
O A:HOH235 2.1 28.3 1.0
O A:HOH340 2.1 22.9 1.0
O A:HOH465 2.1 39.6 1.0
O A:HOH250 2.1 30.3 1.0
O A:HOH370 3.8 38.9 1.0
O A:HOH323 4.1 24.2 1.0
O4 A:U56 4.2 16.3 1.0
O A:HOH460 4.2 33.7 1.0
O4 A:U29 4.2 18.3 1.0
O A:HOH457 4.2 37.7 1.0
O A:HOH369 4.3 21.1 1.0
O6 A:G28 4.3 20.3 1.0
N7 A:G28 4.3 19.4 1.0
K A:K102 4.4 18.4 1.0
O A:HOH411 4.4 29.3 1.0
O A:HOH453 4.5 32.4 1.0
O A:HOH380 4.8 27.7 1.0
O A:HOH426 4.9 35.4 1.0
O A:HOH436 4.9 27.2 1.0
C6 A:G28 5.0 19.8 1.0

Magnesium binding site 4 out of 9 in 7mky

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Magnesium binding site 4 out of 9 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:Mg107

b:24.9
occ:1.00
 O2 A:MPD117 2.0 26.1 1.0
O A:HOH213 2.0 26.0 1.0
O A:HOH364 2.1 35.2 1.0
O A:HOH425 2.1 22.6 1.0
O A:HOH451 2.1 28.1 1.0
O A:HOH207 2.1 24.8 1.0
C2 A:MPD117 3.0 30.1 1.0
O A:HOH359 4.0 23.1 1.0
O A:HOH226 4.1 27.6 1.0
O6 A:G49 4.1 16.8 1.0
O A:HOH381 4.1 18.9 1.0
N7 A:G49 4.2 19.9 1.0
O A:HOH375 4.3 28.1 1.0
O A:HOH337 4.4 20.2 1.0
N4 A:C34 4.5 15.3 1.0
O A:HOH402 4.5 31.5 1.0
O A:HOH464 4.5 34.4 1.0
O A:HOH314 4.7 27.7 1.0
C6 A:G49 4.8 17.0 1.0
C5 A:G49 4.8 17.7 1.0

Magnesium binding site 5 out of 9 in 7mky

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Magnesium binding site 5 out of 9 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:Mg108

b:29.8
occ:1.00
 OP2 A:A37 2.1 20.1 1.0
O A:HOH390 2.1 41.5 1.0
O A:HOH222 3.1 33.8 1.0
P A:A37 3.5 17.0 1.0
O5' A:C36 4.3 15.0 1.0
O3' A:C36 4.3 16.2 1.0
O A:HOH258 4.3 36.6 1.0
C3' A:C36 4.4 15.4 1.0
O5' A:A37 4.4 17.8 1.0
OP1 A:A37 4.4 18.1 1.0
OP2 A:C36 4.6 16.8 1.0
NA A:NA115 4.8 44.4 1.0
O A:HOH245 4.8 27.9 1.0
P A:C36 4.9 15.9 1.0
N7 A:A37 4.9 17.8 1.0
C5' A:C36 5.0 15.7 1.0

Magnesium binding site 6 out of 9 in 7mky

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Magnesium binding site 6 out of 9 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:Mg109

b:34.3
occ:1.00
 OP1 A:G40 1.9 25.5 1.0
O A:HOH262 2.1 34.9 1.0
O A:HOH280 2.1 31.9 1.0
O A:HOH274 2.1 42.6 1.0
P A:G40 3.4 21.1 1.0
O3' A:C39 3.9 21.7 1.0
O A:HOH354 4.2 40.5 1.0
O5' A:G40 4.3 19.5 1.0
OP2 A:G40 4.3 22.2 1.0
C5' A:G40 4.4 20.4 1.0
O A:HOH295 4.5 40.6 1.0

Magnesium binding site 7 out of 9 in 7mky

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Magnesium binding site 7 out of 9 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:Mg110

b:33.8
occ:1.00
 O A:HOH367 2.1 21.8 1.0
O A:HOH355 2.1 27.3 1.0
O2' A:A42 4.2 16.6 1.0
N3 A:A42 4.4 17.3 1.0
C1' A:A42 4.9 15.8 1.0
C2' A:A42 4.9 15.5 1.0

Magnesium binding site 8 out of 9 in 7mky

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Magnesium binding site 8 out of 9 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:Mg111

b:31.1
occ:1.00
 O A:HOH243 2.1 23.7 1.0
O A:HOH391 2.1 25.8 1.0
O A:HOH341 2.1 36.0 1.0
O A:HOH321 2.1 28.8 1.0
O4 A:U6 3.9 20.3 1.0
O A:HOH238 4.0 29.7 1.0
O A:HOH287 4.0 24.1 1.0
O A:HOH237 4.1 25.7 1.0
O A:HOH429 4.1 32.5 1.0
O A:HOH416 4.2 29.4 1.0
O A:HOH414 4.2 34.9 1.0
O6 A:G5 4.5 17.5 1.0
N7 A:G5 4.5 18.2 1.0
O A:HOH310 4.6 25.1 1.0
O4 A:U22 4.7 21.3 1.0
N6 A:A23 4.7 17.9 1.0
O4 A:U4 4.8 19.7 1.0
C4 A:U6 5.0 18.9 1.0

Magnesium binding site 9 out of 9 in 7mky

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Magnesium binding site 9 out of 9 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:Mg112

b:46.5
occ:1.00
 O A:HOH396 2.1 37.7 1.0
O A:HOH209 3.0 44.6 1.0
O A:HOH216 3.2 37.0 1.0
O A:HOH421 3.5 48.2 1.0
OP1 A:G46 3.7 21.3 0.5
OP1 A:G46 3.9 22.6 0.5
OP1 A:C34 4.2 18.7 1.0
OP1 A:G33 4.3 20.9 1.0
OP2 A:C34 4.4 17.5 1.0
P A:C34 4.7 16.7 1.0
O A:HOH386 4.7 37.1 1.0

Reference:

C.P.Jones, A.R.Ferre-D'amare. Sars-Cov-2 Frameshifting Pseudoknot Rna To Be Published.
Page generated: Mon Jul 12 14:29:24 2021

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