1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Bilbille, Y.
Agris, P.F.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H13 N2 O9 P
324.181
n
PSEUDOURIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N3 O9 P
351.207
n
5-formylcytidine 5'-(dihydrogen phosphate)
RNA linking
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
R
C
N
12
N
O
N
13
R
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
R
C
N
49
N
O
N
50
R
C
N
51
N
N
N
52
N
C
N
53
N
O
N
54
N
N
N
55
N
C
N
56
N
N
N
57
N
C
N
58
N
C
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
O
N
74
N
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
C
N
79
R
C
N
80
N
O
N
81
S
C
N
82
N
O
N
83
R
C
N
84
N
O
N
85
R
C
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
N
Y
96
N
C
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
N
N
112
N
C
N
113
N
N
N
114
N
C
N
115
N
C
N
116
N
C
N
117
N
O
N
118
N
O
N
119
S
C
N
120
R
C
N
121
N
O
N
122
S
C
N
123
R
C
N
124
N
O
N
125
N
O
N
126
N
C
N
127
N
O
N
128
N
P
N
129
N
O
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
P
N
146
N
N
N
147
N
C
N
148
N
O
N
149
N
N
N
150
N
C
N
151
N
N
N
152
N
C
N
153
N
C
N
154
R
C
N
155
N
C
N
156
R
C
N
157
N
O
N
158
S
C
N
159
N
O
N
160
N
O
N
161
R
C
N
162
N
O
N
163
N
C
N
164
N
O
N
165
N
O
N
166
N
O
N
167
N
O
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
O
N
183
N
P
N
184
N
O
N
185
N
O
N
186
N
O
N
187
N
C
N
188
R
C
N
189
N
O
N
190
S
C
N
191
N
O
N
192
R
C
N
193
N
O
N
194
R
C
N
195
N
N
N
196
N
C
N
197
N
O
N
198
N
N
N
199
N
C
N
200
N
O
N
201
N
C
N
202
N
C
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
N
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
N
35
N
sing
Y
36
N
sing
Y
37
N
doub
N
38
N
sing
Y
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
doub
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
doub
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
Y
100
N
sing
Y
101
N
sing
Y
102
N
doub
N
103
N
sing
Y
104
N
sing
N
105
N
sing
Y
106
N
doub
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
doub
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
doub
N
125
N
doub
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
doub
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
doub
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
N
159
N
sing
N
160
N
doub
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
doub
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
doub
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
doub
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
doub
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
doub
N
220
N
sing
N
221
N
doub
N
222
N
sing
N
223
N
sing
To be Published
0353
The Human Mitochondrial tRNAMet ASL structure solved by Nuclear Magnetic Resonance
10.2210/pdb2kry/pdb
pdb_00002kry
5405.279
RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')
1
syn
polymer
no
yes
(PSU)CGGGCC(RSQ)AUACCCCGA
UCGGGCCXAUACCCCGA
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
10.250
1
19
A
2
A
16
-5.395
A_C2:G16_A
1
-25.518
0.392
0.004
-0.174
8.937
1
19
A
3
A
15
-4.953
A_G3:C15_A
2
-12.223
-0.708
0.295
-0.287
-7.328
1
19
A
4
A
14
2.342
A_G4:C14_A
3
-33.738
-0.609
-0.302
-0.383
-25.535
1
19
A
5
A
13
-9.921
A_G5:C13_A
4
-24.982
0.216
0.222
-0.045
-34.716
A
6
A
12
-24.932
A_C6:C12_A
5
17.540
6.088
2.346
-3.326
2.504
35.794
A
A
2
3
29.867
A
A
16
15
3.227
17.590
-0.414
-0.726
AA_C2G3:C15G16_AA
1
-2.490
4.228
31.200
-3.564
0.336
3.481
40.010
A
A
3
4
21.718
A
A
15
14
3.857
14.520
0.663
-0.508
AA_G3G4:C14C15_AA
2
4.146
-6.201
37.159
-2.687
-0.414
3.682
43.700
A
A
4
5
17.920
A
A
14
13
3.895
13.121
-0.589
-0.315
AA_G4G5:C13C14_AA
3
-5.221
7.130
41.461
-1.921
0.195
3.522
65.583
A
A
5
6
10.126
A
A
13
12
3.677
10.896
-0.904
-1.348
AA_G5C6:C12C13_AA
4
-9.484
8.813
64.147
-1.743
0.401
chem_comp_atom
chem_comp_bond
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
struct_conn
repository
Initial release
Version format compliance
Non-polymer description
Data collection
Database references
Derived calculations
1
0
2010-08-18
1
1
2011-07-13
1
2
2016-02-17
1
3
2024-05-01
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_conn.pdbx_leaving_atom_flag
BMRB
Y
RCSB
2009-12-23
REL
REL
structures with the lowest energy
100
10
2D 1H-1H NOESY
2D 1H-1H NOESY
2D DQF-COSY
2D 1H-1H COSY
2D 1H-1H TOCSY
2D 1H-13C HSQC
2D 1H-31P HETCOR
1.0
mM
1
mM
20
6.8
ambient
298
K
simulated annealing
1
lowest energy
1.0 mM RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-1, 90% H2O/10% D2O
90% H2O/10% D2O
1 mM RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-2, 100% D2O
100% D2O
Bruker Biospin
collection
XwinNMR
Bruker Biospin
collection
TopSpin
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
data analysis
NMRDraw
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
processing
NMRPipe
Goddard
peak picking
Sparky
Goddard
chemical shift assignment
Sparky
Goddard
data analysis
Sparky
Brunger, Adams, Clore, Gros, Nilges and Read
structure solution
CNS
1.21
Koradi, Billeter and Wuthrich
data analysis
MOLMOL
Brunger, Adams, Clore, Gros, Nilges and Read
refinement
CNS
1.21
600
Varian
INOVA
Varian INOVA
500
Bruker
AVANCE
Bruker Avance
PSU
1
n
1
PSU
1
A
C
2
n
2
C
2
A
G
3
n
3
G
3
A
G
4
n
4
G
4
A
G
5
n
5
G
5
A
C
6
n
6
C
6
A
C
7
n
7
C
7
A
RSQ
8
n
8
RSQ
8
A
A
9
n
9
A
9
A
U
10
n
10
U
10
A
A
11
n
11
A
11
A
C
12
n
12
C
12
A
C
13
n
13
C
13
A
C
14
n
14
C
14
A
C
15
n
15
C
15
A
G
16
n
16
G
16
A
A
17
n
17
A
17
A
author_defined_assembly
1
monomeric
A
PSU
1
PSEUDOURIDINE-5'-MONOPHOSPHATE
A
PSU
1
U
A
RSQ
8
A
RSQ
8
C
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
Solution structure of the human mitochondrial tRNAMet ASL containing the 5-formylcytidine modification in position 34
1
N
N
covale
1.609
both
A
PSU
1
A
O3'
PSU
1
1_555
A
C
2
A
P
C
2
1_555
covale
1.611
both
A
C
7
A
O3'
C
7
1_555
A
RSQ
8
A
P
RSQ
8
1_555
hydrog
WATSON-CRICK
A
C
2
A
N3
C
2
1_555
A
G
16
A
N1
G
16
1_555
hydrog
WATSON-CRICK
A
C
2
A
N4
C
2
1_555
A
G
16
A
O6
G
16
1_555
hydrog
WATSON-CRICK
A
C
2
A
O2
C
2
1_555
A
G
16
A
N2
G
16
1_555
hydrog
WATSON-CRICK
A
G
3
A
N1
G
3
1_555
A
C
15
A
N3
C
15
1_555
hydrog
WATSON-CRICK
A
G
3
A
N2
G
3
1_555
A
C
15
A
O2
C
15
1_555
hydrog
WATSON-CRICK
A
G
3
A
O6
G
3
1_555
A
C
15
A
N4
C
15
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
A
C
14
A
N3
C
14
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
A
C
14
A
O2
C
14
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
A
C
14
A
N4
C
14
1_555
hydrog
WATSON-CRICK
A
G
5
A
N1
G
5
1_555
A
C
13
A
N3
C
13
1_555
hydrog
WATSON-CRICK
A
G
5
A
N2
G
5
1_555
A
C
13
A
O2
C
13
1_555
hydrog
WATSON-CRICK
A
G
5
A
O6
G
5
1_555
A
C
13
A
N4
C
13
1_555
hydrog
C-C MISPAIR
A
C
6
A
O2
C
6
1_555
A
C
12
A
N4
C
12
1_555
RNA
RNA, tRNA, 5-formylcytidine, ASL, modification
2KRY
PDB
1
2KRY
UCGGGCCXAUACCCCGA
1
17
2KRY
1
17
2KRY
A
1
1
17