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
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
O
N
146
N
P
N
147
N
O
N
148
N
O
N
149
N
O
N
150
N
C
N
151
R
C
N
152
N
O
N
153
S
C
N
154
N
O
N
155
R
C
N
156
N
O
N
157
R
C
N
158
N
N
N
159
N
C
N
160
N
O
N
161
N
N
N
162
N
C
N
163
N
O
N
164
N
C
N
165
N
C
N
166
N
H
N
167
N
H
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
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
sing
N
152
N
sing
N
153
N
doub
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
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
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
doub
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
doub
N
182
N
sing
N
183
N
doub
N
184
N
sing
N
185
N
sing
To be Published
0353
The Human Mitochondrial tRNAMet ASL structure solved by Nuclear Magnetic Resonance
10.2210/pdb2krz/pdb
pdb_00002krz
10.13018/BMR16655
5377.269
RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*CP*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')
1
syn
polymer
no
yes
(PSU)CGGGCCCAUACCCCGA
UCGGGCCCAUACCCCGA
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
15.958
1
21
A
1
A
17
-10.163
A_PSU1:A17_A
1
-31.727
-0.674
-1.397
-0.027
-21.902
1
19
A
2
A
16
-3.238
A_C2:G16_A
2
-2.886
0.425
0.783
-0.237
5.133
1
19
A
3
A
15
-4.004
A_G3:C15_A
3
-11.144
-0.448
0.422
-0.216
12.889
1
19
A
4
A
14
-5.225
A_G4:C14_A
4
-17.302
-0.696
0.321
-0.326
-2.941
1
19
A
5
A
13
-4.775
A_G5:C13_A
5
-5.146
0.412
0.210
0.029
-27.079
A
6
A
12
-13.798
A_C6:C12_A
6
27.400
4.502
1.262
-1.479
-21.653
A
9
A
11
-24.954
A_A9:A11_A
7
-25.324
-0.029
-2.325
2.983
3.762
49.174
A
A
1
2
18.172
A
A
17
16
4.471
14.615
-0.647
-1.678
AA_PSU1C2:G16A17_AA
1
-17.326
21.543
43.930
-3.488
-0.967
2.280
29.303
A
A
2
3
11.275
A
A
16
15
2.547
5.660
-0.620
-0.788
AA_C2G3:C15G16_AA
2
2.881
-5.738
28.621
-2.471
1.690
2.676
32.135
A
A
3
4
21.718
A
A
15
14
3.127
11.755
0.416
-0.711
AA_G3G4:C14C15_AA
3
0.862
-1.592
29.949
-3.223
-0.609
2.931
45.986
A
A
4
5
33.219
A
A
14
13
3.954
24.713
0.586
-0.879
AA_G4G5:C13C14_AA
4
-0.128
0.173
39.088
-3.576
-0.762
3.596
49.344
A
A
5
6
20.281
A
A
13
12
4.428
16.627
-0.414
-1.945
AA_G5C6:C12C13_AA
5
-3.273
3.992
46.515
-3.901
0.187
-4.354
169.246
A
A
6
9
58.886
A
A
12
11
-2.744
114.864
-4.952
0.114
AA_C6A9:A11C12_AA
6
117.127
-60.046
95.027
1.020
1.505
pdbx_database_status
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
database_2
pdbx_database_status
chem_comp_atom
chem_comp_bond
database_2
repository
Initial release
Version format compliance
Data collection
Derived calculations
Other
Database references
Other
Data collection
Database references
1
0
2010-08-18
1
1
2011-07-13
1
2
2020-02-26
1
3
2023-06-14
1
4
2024-05-08
_pdbx_database_status.status_code_cs
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_conn.pdbx_leaving_atom_flag
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_database_2.pdbx_DOI
BMRB
Y
RCSB
2009-12-23
REL
REL
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
1.2
mM
1.2
mM
20
6.8
ambient
298
K
simulated annealing
1
lowest energy
1.2 mM RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*CP*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-1, 90% H2O/10% D2O
90% H2O/10% D2O
1.2 mM RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*CP*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-2, 100% D2O
100% D2O
Bruker Biospin
collection
XwinNMR
Bruker Biospin
collection
TopSpin
Varian
collection
VnmrJ
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
processing
NMRPipe
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
data analysis
NMRDraw
Goddard
chemical shift assignment
Sparky
Goddard
data analysis
Sparky
Goddard
peak picking
Sparky
Brunger, Adams, Clore, Gros, Nilges and Read
structure solution
CNS
Koradi, Billeter and Wuthrich
data analysis
MOLMOL
Brunger, Adams, Clore, Gros, Nilges and Read
refinement
CNS
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
C
8
n
8
C
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
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
Solution structure of the Human Mitochondrial tRNAMet
1
N
N
covale
1.610
both
A
PSU
1
A
O3'
PSU
1
1_555
A
C
2
A
P
C
2
1_555
hydrog
REVERSED WATSON-CRICK
A
PSU
1
A
N3
PSU
1
1_555
A
A
17
A
N1
A
17
1_555
hydrog
REVERSED WATSON-CRICK
A
PSU
1
A
O2
PSU
1
1_555
A
A
17
A
N6
A
17
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
hydrog
A-A MISPAIR
A
A
9
A
N6
A
9
1_555
A
A
11
A
N7
A
11
1_555
RNA
RNA, tRNA, Methionine, ASL, modification
2KRZ
PDB
1
2KRZ
UCGGGCCCAUACCCCGA
1
17
2KRZ
1
17
2KRZ
A
1
1
17