Magnesium in PDB 5d5l: PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+
Protein crystallography data
The structure of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+, PDB code: 5d5l
was solved by
J.E.Wedekind,
J.A.Liberman,
M.Salim,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.37 /
2.50
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
86.358,
57.833,
99.493,
90.00,
107.64,
90.00
|
R / Rfree (%)
|
19.9 /
24.7
|
Other elements in 5d5l:
The structure of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
15;
Binding sites:
The binding sites of Magnesium atom in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+
(pdb code 5d5l). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the
PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+, PDB code: 5d5l:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 15 in 5d5l
Go back to
Magnesium Binding Sites List in 5d5l
Magnesium binding site 1 out
of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg118
b:0.0
occ:1.00
|
O
|
A:HOH236
|
2.1
|
43.8
|
1.0
|
O
|
A:HOH220
|
2.1
|
62.0
|
1.0
|
O
|
A:HOH202
|
2.1
|
72.5
|
1.0
|
O
|
A:HOH235
|
2.1
|
64.7
|
1.0
|
O
|
A:HOH216
|
2.1
|
42.7
|
1.0
|
OP1
|
A:U41
|
2.1
|
25.9
|
1.0
|
P
|
A:U41
|
3.5
|
28.4
|
1.0
|
H5''
|
A:U41
|
3.6
|
26.8
|
1.0
|
HO2'
|
A:U53
|
3.8
|
38.3
|
1.0
|
O2'
|
A:U53
|
4.0
|
31.9
|
1.0
|
OP2
|
A:A24
|
4.1
|
29.5
|
1.0
|
O5'
|
A:U41
|
4.1
|
22.3
|
1.0
|
OP1
|
A:A24
|
4.1
|
31.5
|
1.0
|
OP1
|
A:G23
|
4.2
|
42.8
|
1.0
|
C5'
|
A:U41
|
4.3
|
22.3
|
1.0
|
OP2
|
A:A55
|
4.3
|
37.0
|
1.0
|
OP2
|
A:U41
|
4.4
|
34.3
|
1.0
|
P
|
A:A24
|
4.6
|
27.2
|
1.0
|
O3'
|
A:U40
|
4.6
|
33.6
|
1.0
|
H5'
|
A:U41
|
4.6
|
26.8
|
1.0
|
H5'
|
A:U54
|
4.6
|
49.4
|
1.0
|
H5''
|
A:G23
|
4.7
|
44.0
|
1.0
|
H4'
|
A:U53
|
4.8
|
43.8
|
1.0
|
O
|
A:HOH245
|
4.9
|
31.4
|
1.0
|
|
Magnesium binding site 2 out
of 15 in 5d5l
Go back to
Magnesium Binding Sites List in 5d5l
Magnesium binding site 2 out
of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg119
b:62.0
occ:1.00
|
O
|
A:HOH238
|
2.1
|
90.1
|
1.0
|
OP1
|
A:U51
|
2.2
|
62.5
|
1.0
|
H5''
|
A:U51
|
3.2
|
70.3
|
1.0
|
P
|
A:U51
|
3.4
|
53.8
|
1.0
|
O
|
A:HOH215
|
3.7
|
26.9
|
1.0
|
O5'
|
A:U51
|
3.8
|
56.8
|
1.0
|
C5'
|
A:U51
|
3.9
|
58.6
|
1.0
|
OP2
|
A:U51
|
4.1
|
51.3
|
1.0
|
H5'
|
A:U51
|
4.1
|
70.3
|
1.0
|
H5''
|
A:U50
|
4.4
|
48.0
|
1.0
|
H4'
|
A:U50
|
4.5
|
48.5
|
1.0
|
H3'
|
A:U50
|
4.6
|
47.8
|
1.0
|
O3'
|
A:U50
|
4.7
|
44.0
|
1.0
|
C3'
|
A:U50
|
5.0
|
39.9
|
1.0
|
|
Magnesium binding site 3 out
of 15 in 5d5l
Go back to
Magnesium Binding Sites List in 5d5l
Magnesium binding site 3 out
of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg120
b:49.8
occ:1.00
|
OP1
|
A:U53
|
2.1
|
36.4
|
1.0
|
O
|
A:HOH208
|
2.1
|
37.1
|
1.0
|
O
|
A:HOH219
|
2.1
|
55.9
|
1.0
|
P
|
A:U53
|
3.5
|
37.2
|
1.0
|
H5''
|
A:U53
|
3.6
|
46.1
|
1.0
|
OP2
|
A:U54
|
3.8
|
48.1
|
1.0
|
OP1
|
A:U54
|
4.1
|
48.8
|
1.0
|
OP2
|
A:U53
|
4.3
|
37.7
|
1.0
|
O5'
|
A:U53
|
4.3
|
41.3
|
1.0
|
P
|
A:U54
|
4.4
|
45.6
|
1.0
|
O3'
|
A:A52
|
4.4
|
61.0
|
1.0
|
C5'
|
A:U53
|
4.4
|
38.4
|
1.0
|
O3'
|
A:U53
|
4.8
|
34.7
|
1.0
|
H3'
|
A:U53
|
4.9
|
43.3
|
1.0
|
|
Magnesium binding site 4 out
of 15 in 5d5l
Go back to
Magnesium Binding Sites List in 5d5l
Magnesium binding site 4 out
of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg121
b:63.8
occ:1.00
|
O
|
A:HOH213
|
2.1
|
49.8
|
1.0
|
O
|
A:HOH241
|
2.1
|
49.4
|
1.0
|
O
|
A:HOH223
|
2.1
|
64.3
|
1.0
|
N7
|
A:G73
|
2.3
|
25.4
|
1.0
|
C8
|
A:G73
|
3.2
|
24.9
|
1.0
|
H8
|
A:G73
|
3.3
|
29.9
|
1.0
|
C5
|
A:G73
|
3.3
|
25.9
|
1.0
|
O6
|
A:G73
|
3.6
|
38.9
|
1.0
|
C6
|
A:G73
|
3.9
|
26.8
|
1.0
|
OP2
|
A:G73
|
4.1
|
35.3
|
1.0
|
O
|
A:HOH217
|
4.3
|
55.1
|
1.0
|
N7
|
A:G74
|
4.4
|
35.6
|
1.0
|
N9
|
A:G73
|
4.4
|
25.0
|
1.0
|
C5
|
A:A72
|
4.4
|
24.9
|
1.0
|
C4
|
A:G73
|
4.5
|
25.6
|
1.0
|
C6
|
A:A72
|
4.6
|
23.7
|
1.0
|
O
|
A:HOH249
|
4.6
|
36.2
|
1.0
|
N7
|
A:A72
|
4.6
|
25.2
|
1.0
|
H2'
|
A:A72
|
4.6
|
30.6
|
1.0
|
H8
|
A:G74
|
4.7
|
40.0
|
1.0
|
C4
|
A:A72
|
4.8
|
30.1
|
1.0
|
N6
|
A:A72
|
4.8
|
24.5
|
1.0
|
C8
|
A:G74
|
4.9
|
33.4
|
1.0
|
H62
|
A:A72
|
4.9
|
29.4
|
1.0
|
H3'
|
A:A72
|
4.9
|
31.0
|
1.0
|
N1
|
A:A72
|
5.0
|
33.2
|
1.0
|
|
Magnesium binding site 5 out
of 15 in 5d5l
Go back to
Magnesium Binding Sites List in 5d5l
Magnesium binding site 5 out
of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg122
b:51.4
occ:1.00
|
OP2
|
A:U53
|
2.2
|
37.7
|
1.0
|
OP2
|
A:A52
|
2.4
|
55.8
|
1.0
|
H5''
|
A:A52
|
3.3
|
76.9
|
1.0
|
P
|
A:U53
|
3.7
|
37.2
|
1.0
|
P
|
A:A52
|
3.8
|
56.6
|
1.0
|
OP1
|
A:G65
|
4.0
|
58.8
|
1.0
|
H5
|
A:U53
|
4.0
|
38.9
|
1.0
|
C5'
|
A:A52
|
4.1
|
64.0
|
1.0
|
O5'
|
A:A52
|
4.3
|
65.2
|
1.0
|
CS
|
A:CS106
|
4.3
|
65.5
|
0.8
|
OP1
|
A:U53
|
4.4
|
36.4
|
1.0
|
O5'
|
A:U53
|
4.5
|
41.3
|
1.0
|
OP1
|
A:A52
|
4.6
|
61.8
|
1.0
|
O3'
|
A:A52
|
4.6
|
61.0
|
1.0
|
H5'
|
A:A52
|
4.6
|
76.9
|
1.0
|
H3'
|
A:A52
|
4.7
|
76.2
|
1.0
|
H6
|
A:U53
|
4.7
|
38.8
|
1.0
|
C5
|
A:U53
|
4.7
|
32.5
|
1.0
|
O
|
A:HOH208
|
4.9
|
37.1
|
1.0
|
O3'
|
A:U51
|
4.9
|
49.7
|
1.0
|
C3'
|
A:A52
|
5.0
|
63.5
|
1.0
|
|
Magnesium binding site 6 out
of 15 in 5d5l
Go back to
Magnesium Binding Sites List in 5d5l
Magnesium binding site 6 out
of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg123
b:60.5
occ:1.00
|
O1A
|
A:GTP1
|
2.3
|
71.8
|
1.0
|
H2'
|
A:U50
|
3.0
|
44.5
|
1.0
|
OP2
|
A:U50
|
3.1
|
47.5
|
1.0
|
H6
|
A:U50
|
3.3
|
51.3
|
1.0
|
C6
|
A:U50
|
3.7
|
42.7
|
1.0
|
PA
|
A:GTP1
|
3.7
|
66.5
|
1.0
|
O1B
|
A:GTP1
|
3.8
|
68.8
|
1.0
|
O5'
|
A:U50
|
3.8
|
44.0
|
1.0
|
H8
|
A:GTP1
|
3.9
|
63.4
|
1.0
|
C2'
|
A:U50
|
3.9
|
37.1
|
1.0
|
H5
|
A:U50
|
3.9
|
47.5
|
1.0
|
C5
|
A:U50
|
4.0
|
39.5
|
1.0
|
P
|
A:U50
|
4.0
|
45.0
|
1.0
|
HO2'
|
A:U50
|
4.1
|
52.5
|
1.0
|
O
|
A:HOH251
|
4.2
|
92.6
|
1.0
|
O2'
|
A:U50
|
4.2
|
43.7
|
1.0
|
O5'
|
A:GTP1
|
4.3
|
60.7
|
1.0
|
N1
|
A:U50
|
4.4
|
44.6
|
1.0
|
O2A
|
A:GTP1
|
4.6
|
78.0
|
1.0
|
C8
|
A:GTP1
|
4.7
|
52.9
|
1.0
|
PB
|
A:GTP1
|
4.7
|
72.5
|
1.0
|
H3'
|
A:U50
|
4.7
|
47.8
|
1.0
|
O3A
|
A:GTP1
|
4.7
|
94.7
|
1.0
|
C1'
|
A:U50
|
4.7
|
36.4
|
1.0
|
N7
|
A:GTP1
|
4.8
|
58.0
|
1.0
|
O3B
|
A:GTP1
|
4.8
|
77.8
|
1.0
|
OP1
|
A:U50
|
4.8
|
46.5
|
1.0
|
H3'
|
A:G49
|
4.9
|
46.7
|
1.0
|
C3'
|
A:U50
|
4.9
|
39.9
|
1.0
|
|
Magnesium binding site 7 out
of 15 in 5d5l
Go back to
Magnesium Binding Sites List in 5d5l
Magnesium binding site 7 out
of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg110
b:75.9
occ:1.00
|
OP1
|
B:A10
|
2.0
|
56.8
|
1.0
|
O
|
B:HOH219
|
2.1
|
71.8
|
1.0
|
O
|
B:HOH209
|
2.1
|
80.7
|
1.0
|
O
|
B:HOH216
|
2.1
|
94.8
|
1.0
|
O
|
B:HOH250
|
2.1
|
76.8
|
1.0
|
O
|
B:HOH220
|
2.1
|
0.2
|
1.0
|
P
|
B:A10
|
3.3
|
56.3
|
1.0
|
H8
|
B:A10
|
3.4
|
55.9
|
1.0
|
H5'
|
B:A10
|
3.8
|
65.4
|
1.0
|
OP2
|
B:A10
|
3.8
|
58.9
|
1.0
|
O4'
|
B:A10
|
4.1
|
50.6
|
1.0
|
O
|
B:HOH252
|
4.1
|
54.3
|
1.0
|
C8
|
B:A10
|
4.1
|
46.6
|
1.0
|
O5'
|
B:A10
|
4.2
|
44.8
|
1.0
|
O3'
|
B:G9
|
4.4
|
44.5
|
1.0
|
CS
|
B:CS102
|
4.4
|
66.0
|
0.8
|
C5'
|
B:A10
|
4.4
|
54.5
|
1.0
|
N7
|
B:A10
|
4.9
|
47.8
|
1.0
|
C4'
|
B:A10
|
4.9
|
48.1
|
1.0
|
N9
|
B:A10
|
5.0
|
46.0
|
1.0
|
|
Magnesium binding site 8 out
of 15 in 5d5l
Go back to
Magnesium Binding Sites List in 5d5l
Magnesium binding site 8 out
of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg111
b:55.7
occ:1.00
|
O
|
B:HOH208
|
2.1
|
50.6
|
1.0
|
O
|
B:HOH214
|
2.1
|
0.6
|
1.0
|
O
|
B:HOH234
|
2.1
|
94.1
|
1.0
|
O
|
B:HOH235
|
2.1
|
44.1
|
1.0
|
N7
|
B:G73
|
2.3
|
44.9
|
1.0
|
C8
|
B:G73
|
3.2
|
47.5
|
1.0
|
H8
|
B:G73
|
3.3
|
57.0
|
1.0
|
C5
|
B:G73
|
3.3
|
41.3
|
1.0
|
O6
|
B:G73
|
3.7
|
55.4
|
1.0
|
C6
|
B:G73
|
3.9
|
43.6
|
1.0
|
O
|
B:HOH213
|
4.1
|
0.9
|
1.0
|
OP2
|
B:G73
|
4.3
|
40.0
|
1.0
|
N9
|
B:G73
|
4.4
|
41.9
|
1.0
|
N7
|
B:G74
|
4.4
|
43.8
|
1.0
|
C4
|
B:G73
|
4.5
|
41.7
|
1.0
|
C5
|
B:A72
|
4.5
|
46.7
|
1.0
|
C6
|
B:A72
|
4.6
|
45.8
|
1.0
|
H8
|
B:G74
|
4.7
|
51.5
|
1.0
|
N7
|
B:A72
|
4.7
|
49.0
|
1.0
|
H2'
|
B:A72
|
4.8
|
43.2
|
1.0
|
C4
|
B:A72
|
4.8
|
44.2
|
1.0
|
N6
|
B:A72
|
4.9
|
51.1
|
1.0
|
C8
|
B:G74
|
4.9
|
42.9
|
1.0
|
H62
|
B:A72
|
4.9
|
61.3
|
1.0
|
H3'
|
B:A72
|
4.9
|
47.1
|
1.0
|
N1
|
B:A72
|
5.0
|
49.6
|
1.0
|
|
Magnesium binding site 9 out
of 15 in 5d5l
Go back to
Magnesium Binding Sites List in 5d5l
Magnesium binding site 9 out
of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg112
b:61.0
occ:1.00
|
OP1
|
B:G42
|
2.2
|
53.9
|
1.0
|
O
|
B:HOH204
|
3.2
|
49.4
|
1.0
|
H5''
|
B:G42
|
3.5
|
65.9
|
1.0
|
P
|
B:G42
|
3.6
|
54.3
|
1.0
|
OP1
|
B:C22
|
3.7
|
74.1
|
1.0
|
OP2
|
B:A43
|
4.1
|
54.0
|
1.0
|
H5''
|
B:C22
|
4.2
|
80.7
|
1.0
|
O5'
|
B:G42
|
4.3
|
54.2
|
1.0
|
C5'
|
B:G42
|
4.3
|
54.9
|
1.0
|
OP2
|
B:G42
|
4.5
|
53.1
|
1.0
|
O3'
|
B:U41
|
4.6
|
50.9
|
1.0
|
H5'
|
B:G42
|
4.8
|
65.9
|
1.0
|
OP1
|
B:G23
|
4.8
|
59.2
|
1.0
|
OP2
|
B:G23
|
4.9
|
59.0
|
1.0
|
P
|
B:C22
|
4.9
|
79.8
|
1.0
|
O5'
|
B:C22
|
5.0
|
67.1
|
1.0
|
C5'
|
B:C22
|
5.0
|
67.2
|
1.0
|
|
Magnesium binding site 10 out
of 15 in 5d5l
Go back to
Magnesium Binding Sites List in 5d5l
Magnesium binding site 10 out
of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg105
b:36.5
occ:1.00
|
O
|
C:HOH222
|
2.1
|
26.0
|
1.0
|
O
|
C:HOH223
|
2.1
|
49.5
|
1.0
|
O
|
C:HOH221
|
2.1
|
36.7
|
1.0
|
OP1
|
C:A10
|
2.1
|
30.6
|
1.0
|
P
|
C:A10
|
3.5
|
32.9
|
1.0
|
H8
|
C:A10
|
3.6
|
28.5
|
1.0
|
H5'
|
C:A10
|
4.0
|
34.7
|
1.0
|
OP2
|
C:A10
|
4.2
|
41.9
|
1.0
|
C8
|
C:A10
|
4.3
|
23.7
|
1.0
|
CS
|
C:CS102
|
4.3
|
56.4
|
1.0
|
O4'
|
C:A10
|
4.3
|
31.1
|
1.0
|
O5'
|
C:A10
|
4.4
|
30.6
|
1.0
|
O3'
|
C:G9
|
4.5
|
23.9
|
1.0
|
C5'
|
C:A10
|
4.7
|
28.9
|
1.0
|
N7
|
C:A10
|
5.0
|
20.8
|
1.0
|
|
Reference:
I.A.Belashov,
J.A.Liberman,
M.Salim,
J.E.Wedekind.
Cesium(I) Binding to G-U-Wobble Base Pairs in PREQ1 Riboswitches with Implications For Crystallographic Phasing To Be Published.
Page generated: Sun Sep 29 02:31:22 2024
|