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:
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
Go back to
Magnesium Binding Sites List in 7mky
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
Go back to
Magnesium Binding Sites List in 7mky
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
Go back to
Magnesium Binding Sites List in 7mky
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
Go back to
Magnesium Binding Sites List in 7mky
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
Go back to
Magnesium Binding Sites List in 7mky
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
Go back to
Magnesium Binding Sites List in 7mky
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
Go back to
Magnesium Binding Sites List in 7mky
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
Go back to
Magnesium Binding Sites List in 7mky
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
Go back to
Magnesium Binding Sites List in 7mky
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: Thu Oct 3 01:00:56 2024
|