Caesium 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:
Caesium Binding Sites:
Caesium binding site 1 out
of 32 in 5d5l
Go back to
Caesium Binding Sites List in 5d5l
Caesium binding site 1 out
of 32 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 Caesium with other atoms in the Cs 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:Cs101
b:87.9
occ:0.50
|
O3A
|
A:GTP1
|
3.2
|
94.7
|
1.0
|
O2A
|
A:GTP1
|
3.3
|
78.0
|
1.0
|
O1G
|
A:GTP1
|
3.4
|
99.4
|
1.0
|
OP2
|
A:G2
|
3.5
|
64.2
|
1.0
|
O
|
A:HOH231
|
3.7
|
40.7
|
1.0
|
PA
|
A:GTP1
|
3.8
|
66.5
|
1.0
|
O
|
A:HOH227
|
3.9
|
55.7
|
1.0
|
O
|
A:HOH206
|
3.9
|
42.5
|
1.0
|
C5'
|
A:GTP1
|
4.2
|
60.4
|
1.0
|
PB
|
A:GTP1
|
4.3
|
72.5
|
1.0
|
H3'
|
A:GTP1
|
4.3
|
67.9
|
1.0
|
PG
|
A:GTP1
|
4.4
|
95.6
|
1.0
|
P
|
A:G2
|
4.4
|
61.4
|
1.0
|
O3B
|
A:GTP1
|
4.5
|
77.8
|
1.0
|
O5'
|
A:GTP1
|
4.5
|
60.7
|
1.0
|
O2B
|
A:GTP1
|
4.5
|
67.2
|
1.0
|
OP1
|
A:G2
|
4.5
|
59.9
|
1.0
|
O3G
|
A:GTP1
|
4.6
|
98.0
|
1.0
|
O3'
|
A:GTP1
|
4.7
|
58.9
|
1.0
|
C3'
|
A:GTP1
|
4.9
|
56.6
|
1.0
|
|
Caesium binding site 2 out
of 32 in 5d5l
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Caesium Binding Sites List in 5d5l
Caesium binding site 2 out
of 32 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 Caesium with other atoms in the Cs 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:Cs102
b:73.2
occ:1.00
|
O6
|
A:G6
|
3.1
|
52.7
|
1.0
|
O4
|
A:U15
|
3.3
|
61.9
|
1.0
|
O6
|
A:G14
|
3.4
|
48.8
|
1.0
|
O6
|
A:G5
|
3.5
|
52.7
|
1.0
|
H42
|
A:C7
|
3.6
|
66.3
|
1.0
|
H3
|
A:U15
|
3.8
|
64.6
|
1.0
|
H42
|
A:C16
|
3.8
|
63.5
|
1.0
|
N4
|
A:C7
|
4.0
|
55.3
|
1.0
|
H41
|
A:C7
|
4.0
|
66.3
|
1.0
|
O
|
A:HOH203
|
4.0
|
57.3
|
1.0
|
C6
|
A:G6
|
4.2
|
53.5
|
1.0
|
C6
|
A:G5
|
4.2
|
53.8
|
1.0
|
C4
|
A:U15
|
4.3
|
56.4
|
1.0
|
N4
|
A:C16
|
4.3
|
52.9
|
1.0
|
N3
|
A:U15
|
4.4
|
53.8
|
1.0
|
C6
|
A:G14
|
4.4
|
48.8
|
1.0
|
N7
|
A:G6
|
4.5
|
57.8
|
1.0
|
H41
|
A:C16
|
4.6
|
63.5
|
1.0
|
C5
|
A:G6
|
4.7
|
57.0
|
1.0
|
C5
|
A:G5
|
4.9
|
58.5
|
1.0
|
H1
|
A:G5
|
4.9
|
65.0
|
1.0
|
N1
|
A:G5
|
4.9
|
54.2
|
1.0
|
H1
|
A:G14
|
4.9
|
64.2
|
1.0
|
C4
|
A:C7
|
4.9
|
55.4
|
1.0
|
|
Caesium binding site 3 out
of 32 in 5d5l
Go back to
Caesium Binding Sites List in 5d5l
Caesium binding site 3 out
of 32 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 Caesium with other atoms in the Cs 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:Cs103
b:62.5
occ:0.25
|
O
|
A:HOH255
|
2.8
|
42.9
|
1.0
|
HO2'
|
A:C16
|
3.1
|
78.2
|
1.0
|
O2'
|
A:C16
|
3.4
|
65.2
|
1.0
|
O2
|
A:C16
|
3.4
|
60.0
|
1.0
|
H22
|
A:G6
|
3.5
|
67.6
|
1.0
|
H1'
|
A:C16
|
3.7
|
78.4
|
1.0
|
H22
|
A:G5
|
3.8
|
74.2
|
1.0
|
H21
|
A:G5
|
3.8
|
74.2
|
1.0
|
N3
|
A:G6
|
3.8
|
58.0
|
1.0
|
O4'
|
A:U17
|
3.8
|
68.6
|
1.0
|
N2
|
A:G6
|
3.9
|
56.4
|
1.0
|
H1'
|
A:U17
|
3.9
|
73.8
|
1.0
|
H1'
|
A:G6
|
4.1
|
75.7
|
1.0
|
C2
|
A:G6
|
4.1
|
55.6
|
1.0
|
N2
|
A:G5
|
4.1
|
61.9
|
1.0
|
C2'
|
A:C16
|
4.2
|
62.7
|
1.0
|
H2'
|
A:C16
|
4.2
|
75.2
|
1.0
|
C1'
|
A:U17
|
4.4
|
61.5
|
1.0
|
C1'
|
A:C16
|
4.4
|
65.3
|
1.0
|
H21
|
A:G6
|
4.5
|
67.6
|
1.0
|
C2
|
A:C16
|
4.6
|
54.4
|
1.0
|
C4
|
A:G6
|
4.6
|
61.0
|
1.0
|
H4'
|
A:U17
|
4.8
|
80.2
|
1.0
|
H5'
|
A:U17
|
4.8
|
77.9
|
1.0
|
C4'
|
A:U17
|
4.9
|
66.8
|
1.0
|
C1'
|
A:G6
|
4.9
|
63.1
|
1.0
|
N1
|
A:U17
|
5.0
|
57.9
|
1.0
|
|
Caesium binding site 4 out
of 32 in 5d5l
Go back to
Caesium Binding Sites List in 5d5l
Caesium binding site 4 out
of 32 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 Caesium with other atoms in the Cs 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:Cs104
b:85.3
occ:0.50
|
O
|
A:HOH253
|
3.0
|
56.1
|
1.0
|
O2'
|
A:U44
|
3.1
|
39.5
|
1.0
|
O2
|
A:U44
|
3.3
|
44.2
|
1.0
|
H1'
|
A:U44
|
3.3
|
46.5
|
1.0
|
OP1
|
B:C8
|
3.4
|
60.6
|
1.0
|
O2
|
A:U28
|
3.5
|
55.4
|
1.0
|
O4'
|
A:C45
|
3.6
|
42.7
|
1.0
|
O
|
A:HOH205
|
3.7
|
52.9
|
1.0
|
C2'
|
A:U44
|
3.8
|
38.6
|
1.0
|
H2'
|
A:U44
|
3.8
|
46.3
|
1.0
|
H1'
|
A:C45
|
3.9
|
44.9
|
1.0
|
H1'
|
A:U28
|
4.0
|
59.6
|
1.0
|
C1'
|
A:U44
|
4.0
|
38.8
|
1.0
|
O3'
|
B:C7
|
4.2
|
45.8
|
1.0
|
C1'
|
A:C45
|
4.3
|
37.5
|
1.0
|
P
|
B:C8
|
4.3
|
51.9
|
1.0
|
H2
|
A:A27
|
4.3
|
41.2
|
1.0
|
C2
|
A:U44
|
4.3
|
41.6
|
1.0
|
HO2'
|
A:U28
|
4.4
|
65.0
|
1.0
|
H5''
|
B:C7
|
4.5
|
53.7
|
1.0
|
C2
|
A:U28
|
4.5
|
50.1
|
1.0
|
H5'
|
A:C45
|
4.6
|
53.9
|
1.0
|
N1
|
A:U44
|
4.7
|
36.5
|
1.0
|
H4'
|
A:C45
|
4.7
|
47.9
|
1.0
|
C4'
|
A:C45
|
4.7
|
39.9
|
1.0
|
H2
|
A:A43
|
4.7
|
43.8
|
1.0
|
N1
|
A:C45
|
4.8
|
35.5
|
1.0
|
OP2
|
B:C8
|
4.8
|
60.0
|
1.0
|
C1'
|
A:U28
|
4.9
|
49.7
|
1.0
|
H6
|
A:C45
|
5.0
|
42.8
|
1.0
|
|
Caesium binding site 5 out
of 32 in 5d5l
Go back to
Caesium Binding Sites List in 5d5l
Caesium binding site 5 out
of 32 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 Caesium with other atoms in the Cs 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:Cs105
b:83.9
occ:1.00
|
N7
|
A:A10
|
3.3
|
56.9
|
1.0
|
O3'
|
A:G9
|
3.3
|
52.6
|
1.0
|
H8
|
A:A10
|
3.5
|
65.3
|
1.0
|
OP1
|
A:A10
|
3.6
|
64.9
|
1.0
|
C8
|
A:A10
|
3.8
|
54.5
|
1.0
|
H4'
|
A:G9
|
3.9
|
63.5
|
1.0
|
O2'
|
A:G9
|
3.9
|
50.3
|
1.0
|
P
|
A:A10
|
4.1
|
62.2
|
1.0
|
H62
|
A:A10
|
4.3
|
66.2
|
1.0
|
C3'
|
A:G9
|
4.3
|
52.8
|
1.0
|
HO2'
|
A:G9
|
4.4
|
60.4
|
1.0
|
C4'
|
A:G9
|
4.6
|
52.9
|
1.0
|
C5
|
A:A10
|
4.6
|
50.4
|
1.0
|
C2'
|
A:G9
|
4.8
|
51.7
|
1.0
|
H5''
|
A:G9
|
4.8
|
65.7
|
1.0
|
|
Caesium binding site 6 out
of 32 in 5d5l
Go back to
Caesium Binding Sites List in 5d5l
Caesium binding site 6 out
of 32 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 Caesium with other atoms in the Cs 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:Cs106
b:65.5
occ:0.75
|
OP2
|
A:A52
|
3.2
|
55.8
|
1.0
|
O2'
|
A:G64
|
3.2
|
73.5
|
1.0
|
O5'
|
A:G65
|
3.4
|
55.1
|
1.0
|
H5
|
A:U53
|
3.4
|
38.9
|
1.0
|
O4
|
A:U53
|
3.4
|
34.7
|
1.0
|
O3'
|
A:U51
|
3.5
|
49.7
|
1.0
|
P
|
A:A52
|
3.8
|
56.6
|
1.0
|
O3'
|
A:G64
|
3.9
|
61.5
|
1.0
|
HO2'
|
A:U51
|
3.9
|
65.2
|
1.0
|
O2'
|
A:U51
|
3.9
|
54.4
|
1.0
|
C5
|
A:U53
|
4.0
|
32.5
|
1.0
|
C4
|
A:U53
|
4.1
|
33.2
|
1.0
|
P
|
A:G65
|
4.2
|
54.9
|
1.0
|
C2'
|
A:G64
|
4.2
|
68.3
|
1.0
|
OP1
|
A:A52
|
4.3
|
61.8
|
1.0
|
H4'
|
A:G65
|
4.3
|
62.4
|
1.0
|
MG
|
A:MG122
|
4.3
|
51.4
|
1.0
|
OP1
|
A:G65
|
4.4
|
58.8
|
1.0
|
H2'
|
A:G64
|
4.4
|
82.0
|
1.0
|
H5'
|
A:G65
|
4.4
|
61.9
|
1.0
|
C5'
|
A:G65
|
4.4
|
51.6
|
1.0
|
C3'
|
A:U51
|
4.6
|
52.6
|
1.0
|
C3'
|
A:G64
|
4.6
|
65.4
|
1.0
|
C2'
|
A:U51
|
4.8
|
49.6
|
1.0
|
H3'
|
A:U51
|
4.8
|
63.1
|
1.0
|
C4'
|
A:G65
|
4.9
|
52.0
|
1.0
|
H1'
|
A:U51
|
4.9
|
61.2
|
1.0
|
|
Caesium binding site 7 out
of 32 in 5d5l
Go back to
Caesium Binding Sites List in 5d5l
Caesium binding site 7 out
of 32 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 Caesium with other atoms in the Cs 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
|
A:Cs107
b:84.5
occ:0.50
|
O4
|
A:U53
|
3.3
|
34.7
|
1.0
|
HO2'
|
A:G65
|
3.5
|
83.8
|
1.0
|
HO2'
|
A:U51
|
3.6
|
65.2
|
1.0
|
O3'
|
A:G65
|
3.8
|
54.6
|
1.0
|
H4'
|
A:G65
|
3.9
|
62.4
|
1.0
|
O2
|
A:U51
|
3.9
|
55.5
|
1.0
|
H3
|
A:U53
|
4.1
|
45.5
|
1.0
|
O2'
|
A:U51
|
4.2
|
54.4
|
1.0
|
OP1
|
A:C66
|
4.3
|
74.0
|
1.0
|
O2'
|
A:G65
|
4.3
|
69.8
|
1.0
|
C4
|
A:U53
|
4.3
|
33.2
|
1.0
|
C2
|
A:U51
|
4.4
|
56.6
|
1.0
|
H5'
|
A:C66
|
4.4
|
57.3
|
1.0
|
N3
|
A:U53
|
4.6
|
37.9
|
1.0
|
C4'
|
A:G65
|
4.7
|
52.0
|
1.0
|
C3'
|
A:G65
|
4.7
|
55.2
|
1.0
|
H3
|
A:U51
|
4.7
|
67.9
|
1.0
|
P
|
A:C66
|
4.7
|
61.8
|
1.0
|
N3
|
A:U51
|
4.8
|
56.6
|
1.0
|
H1'
|
A:U51
|
4.9
|
61.2
|
1.0
|
|
Caesium binding site 8 out
of 32 in 5d5l
Go back to
Caesium Binding Sites List in 5d5l
Caesium binding site 8 out
of 32 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 Caesium with other atoms in the Cs 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
|
A:Cs108
b:77.8
occ:0.50
|
O2
|
A:C48
|
3.3
|
31.4
|
1.0
|
O2'
|
A:C48
|
3.3
|
46.2
|
1.0
|
H1'
|
A:G49
|
3.4
|
50.0
|
1.0
|
H1'
|
A:C48
|
3.5
|
35.3
|
1.0
|
H4'
|
A:G49
|
3.6
|
50.8
|
1.0
|
HO2'
|
A:G49
|
3.7
|
59.1
|
1.0
|
O2'
|
A:G49
|
3.8
|
49.3
|
1.0
|
H22
|
A:G23
|
3.8
|
41.8
|
1.0
|
O4'
|
A:G49
|
3.8
|
48.6
|
1.0
|
H21
|
A:G23
|
3.8
|
41.8
|
1.0
|
H2'
|
A:C48
|
3.9
|
38.8
|
1.0
|
C1'
|
A:G49
|
4.0
|
41.6
|
1.0
|
C2'
|
A:C48
|
4.0
|
32.3
|
1.0
|
N2
|
A:G23
|
4.1
|
34.8
|
1.0
|
C4'
|
A:G49
|
4.2
|
42.4
|
1.0
|
C1'
|
A:C48
|
4.2
|
29.4
|
1.0
|
C2
|
A:C48
|
4.4
|
35.6
|
1.0
|
C2'
|
A:G49
|
4.5
|
46.8
|
1.0
|
N1
|
A:C48
|
4.8
|
40.8
|
1.0
|
O5'
|
A:G49
|
5.0
|
38.2
|
1.0
|
|
Caesium binding site 9 out
of 32 in 5d5l
Go back to
Caesium Binding Sites List in 5d5l
Caesium binding site 9 out
of 32 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 Caesium with other atoms in the Cs 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
|
A:Cs109
b:0.2
occ:0.75
|
O2
|
A:C69
|
3.3
|
32.7
|
1.0
|
O2'
|
A:C69
|
3.6
|
39.9
|
1.0
|
HO2'
|
A:C69
|
3.8
|
47.9
|
1.0
|
H1'
|
A:C69
|
3.9
|
32.0
|
1.0
|
H2'
|
A:C69
|
4.3
|
34.5
|
1.0
|
C2'
|
A:C69
|
4.3
|
28.8
|
1.0
|
H61
|
A:A55
|
4.4
|
43.4
|
1.0
|
C2
|
A:C69
|
4.5
|
32.8
|
1.0
|
C1'
|
A:C69
|
4.5
|
26.7
|
1.0
|
H42
|
A:C56
|
4.6
|
46.8
|
1.0
|
HO2'
|
A:A71
|
4.7
|
42.2
|
1.0
|
N3
|
A:C56
|
4.9
|
32.1
|
1.0
|
H5'
|
A:A70
|
4.9
|
31.2
|
1.0
|
|
Caesium binding site 10 out
of 32 in 5d5l
Go back to
Caesium Binding Sites List in 5d5l
Caesium binding site 10 out
of 32 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 Caesium with other atoms in the Cs 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
|
A:Cs110
b:94.0
occ:0.50
|
H5
|
A:U35
|
2.5
|
0.6
|
1.0
|
H3'
|
A:U34
|
3.2
|
0.7
|
1.0
|
C5
|
A:U35
|
3.3
|
99.7
|
1.0
|
O4
|
A:U35
|
3.4
|
87.9
|
1.0
|
O3'
|
A:U34
|
3.5
|
98.5
|
1.0
|
O4
|
A:U36
|
3.7
|
64.0
|
1.0
|
C4
|
A:U35
|
3.7
|
92.3
|
1.0
|
C3'
|
A:U34
|
3.9
|
0.7
|
1.0
|
C4
|
A:U36
|
3.9
|
64.2
|
1.0
|
H5
|
A:U36
|
4.0
|
79.5
|
1.0
|
C5
|
A:U36
|
4.1
|
66.3
|
1.0
|
OP2
|
A:U35
|
4.3
|
0.1
|
1.0
|
C6
|
A:U35
|
4.3
|
0.7
|
1.0
|
H6
|
A:U35
|
4.5
|
0.2
|
1.0
|
P
|
A:U35
|
4.5
|
0.4
|
1.0
|
N3
|
A:U36
|
4.7
|
63.0
|
1.0
|
H61
|
A:A75
|
4.7
|
58.3
|
1.0
|
H5'
|
A:U34
|
4.7
|
0.1
|
1.0
|
C6
|
A:U36
|
4.9
|
66.6
|
1.0
|
H3
|
A:U36
|
4.9
|
75.6
|
1.0
|
C2'
|
A:U34
|
4.9
|
0.5
|
1.0
|
C4'
|
A:U34
|
4.9
|
0.3
|
1.0
|
H4'
|
A:U34
|
4.9
|
0.6
|
1.0
|
OP1
|
A:U35
|
5.0
|
0.2
|
1.0
|
O2'
|
A:U34
|
5.0
|
0.2
|
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: Tue Jul 30 20:42:50 2024
|