1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Stuart, J.W.
Koshlap, K.M.
Guenther, R.H.
Agris, P.F.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C11 H16 N5 O8 P
377.247
n
1N-METHYLGUANOSINE-5'-MONOPHOSPHATE
RNA linking
C10 H16 N3 O8 P
337.223
n
5-METHYLCYTIDINE-5'-MONOPHOSPHATE
RNA linking
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
C10 H16 N3 O8 P
337.223
n
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
RNA linking
C11 H16 N5 O8 P
377.247
n
O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
334
901
918
10.1016/j.jmb.2003.09.058
14643656
Naturally-occurring Modification Restricts the Anticodon Domain Conformational Space of tRNA(Phe).
2003
10.2210/pdb1luu/pdb
pdb_00001luu
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
ANTICODON (RESIDUES 27-43) OF TRNA-PHE WITH FOUR MODIFIED RESIDUES (OMC at position 32, OMG at 34, 1MG at 37, and 5MC at position 40)
5522.430
5'-R(*CP*CP*AP*GP*AP*(OMC)P*UP*(OMG)P*AP*AP*(1MG)P*AP*UP*(5MC)P*UP*GP*G)-3'
1
syn
polymer
no
yes
CCAGA(OMC)U(OMG)AA(1MG)AU(5MC)UGG
CCAGACUGAAGAUCUGG
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
8.735
1
19
A
27
A
43
-3.183
A_C27:G43_A
1
-6.496
-0.211
-0.033
-0.035
15.331
1
19
A
28
A
42
-0.803
A_C28:G42_A
2
-11.798
-0.428
-0.114
-0.008
-3.519
1
20
A
29
A
41
2.525
A_A29:U41_A
3
-11.069
-0.535
-0.594
-0.210
-16.975
1
19
A
30
A
40
-4.456
A_G30:5MC40_A
4
-6.340
0.311
-1.102
-0.177
-16.861
1
20
A
31
A
39
-0.102
A_A31:U39_A
5
3.104
0.035
-0.216
0.043
-8.413
1
A
32
A
38
7.868
A_OMC32:A38_A
6
-0.272
3.709
0.143
-0.805
-47.808
A
34
A
36
165.804
A_OMG34:A36_A
7
1.244
-1.622
-0.685
-5.162
2.383
31.631
A
A
27
28
25.382
A
A
43
42
3.090
13.417
0.289
-1.014
AA_C27C28:G42G43_AA
1
-0.651
1.231
28.704
-4.044
-0.637
1.896
47.106
A
A
28
29
46.517
A
A
42
41
4.021
33.620
0.245
-1.432
AA_C28A29:U41G42_AA
2
5.345
-7.395
33.055
-4.791
0.170
3.079
36.794
A
A
29
30
22.695
A
A
41
40
3.846
13.985
-0.686
-1.266
AA_A29G30:5MC40U41_AA
3
1.407
-2.283
34.090
-4.104
1.298
2.867
34.941
A
A
30
31
10.592
A
A
40
39
3.400
6.286
0.886
-1.378
AA_G30A31:U395MC40_AA
4
-7.026
11.839
33.684
-3.223
-2.512
2.671
43.990
A
A
31
32
17.533
A
A
39
38
3.184
12.950
-0.054
-1.339
AA_A31OMC32:A38U39_AA
5
2.599
-3.518
42.054
-2.910
0.298
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2003-09-09
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_conn.pdbx_leaving_atom_flag
NMR SOLUTION STRUCTURE OF THE ANTICODON OF YEAST TRNA-PHE WITH 3 MODIFICATIONS (OMC32 OMG34 M5C40)
RCSB
Y
RCSB
2002-05-23
REL
REL
SEQUENCE WITH NATURALLY OCCURRING MODIFICATIONS SYNTHESIZED USING PHOSPHORAMIDITE CHEMISTRY.
sample
THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES
structures with the least restraint violations,structures with the lowest energy
50
11
2D NOESY
DQF-COSY
5.60
1
atm
298
K
269 RESTRAINTS (256 NOE-DERIVED, 13 H-BOND) 96 DIHEDRAL ANGLE.
GLOBAL FOLD BY DISTANCE GEOMETRY. REFINEMENT BY SIMULATED ANNEALING USING THE AMBER FORCEFIELD
1
minimized average structure
1.2 MM RNA, 10 MM CACODYLATE BUFFER, PH 5.6, 0.1 MM EDTA
Bruker
collection
XwinNMR
Accelrys
data analysis
Felix
98
Accelrys
refinement
Discover
98
500
Bruker
AVANCE
C
27
n
1
C
27
A
C
28
n
2
C
28
A
A
29
n
3
A
29
A
G
30
n
4
G
30
A
A
31
n
5
A
31
A
OMC
32
n
6
OMC
32
A
U
33
n
7
U
33
A
OMG
34
n
8
OMG
34
A
A
35
n
9
A
35
A
A
36
n
10
A
36
A
1MG
37
n
11
1MG
37
A
A
38
n
12
A
38
A
U
39
n
13
U
39
A
5MC
40
n
14
5MC
40
A
U
41
n
15
U
41
A
G
42
n
16
G
42
A
G
43
n
17
G
43
A
author_defined_assembly
1
monomeric
A
OMC
32
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
A
OMC
6
C
A
OMG
34
O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
A
OMG
8
G
A
1MG
37
1N-METHYLGUANOSINE-5'-MONOPHOSPHATE
A
1MG
11
G
A
5MC
40
5-METHYLCYTIDINE-5'-MONOPHOSPHATE
A
5MC
14
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
1
A
C
27
0.088
SIDE CHAIN
1
A
C
28
0.075
SIDE CHAIN
1
A
A
29
0.079
SIDE CHAIN
1
A
G
42
0.076
SIDE CHAIN
2
A
C
27
0.086
SIDE CHAIN
2
A
C
28
0.057
SIDE CHAIN
2
A
A
29
0.073
SIDE CHAIN
2
A
U
33
0.059
SIDE CHAIN
2
A
A
35
0.071
SIDE CHAIN
2
A
U
41
0.069
SIDE CHAIN
2
A
G
42
0.073
SIDE CHAIN
3
A
C
27
0.070
SIDE CHAIN
3
A
C
28
0.062
SIDE CHAIN
3
A
G
30
0.073
SIDE CHAIN
3
A
U
33
0.098
SIDE CHAIN
3
A
A
35
0.073
SIDE CHAIN
3
A
G
42
0.074
SIDE CHAIN
4
A
C
27
0.096
SIDE CHAIN
4
A
G
30
0.085
SIDE CHAIN
4
A
A
35
0.090
SIDE CHAIN
4
A
G
42
0.081
SIDE CHAIN
5
A
C
27
0.063
SIDE CHAIN
5
A
C
28
0.105
SIDE CHAIN
5
A
A
29
0.104
SIDE CHAIN
5
A
G
30
0.082
SIDE CHAIN
5
A
U
33
0.057
SIDE CHAIN
5
A
U
41
0.076
SIDE CHAIN
5
A
G
42
0.075
SIDE CHAIN
6
A
C
27
0.077
SIDE CHAIN
6
A
C
28
0.092
SIDE CHAIN
6
A
G
30
0.078
SIDE CHAIN
6
A
A
35
0.094
SIDE CHAIN
6
A
G
42
0.065
SIDE CHAIN
7
A
C
27
0.103
SIDE CHAIN
7
A
A
29
0.064
SIDE CHAIN
7
A
G
42
0.078
SIDE CHAIN
8
A
C
27
0.082
SIDE CHAIN
8
A
C
28
0.112
SIDE CHAIN
8
A
A
29
0.087
SIDE CHAIN
8
A
G
30
0.061
SIDE CHAIN
8
A
U
33
0.056
SIDE CHAIN
8
A
A
38
0.060
SIDE CHAIN
8
A
U
41
0.065
SIDE CHAIN
8
A
G
42
0.077
SIDE CHAIN
9
A
C
27
0.072
SIDE CHAIN
9
A
C
28
0.096
SIDE CHAIN
9
A
A
29
0.061
SIDE CHAIN
9
A
G
30
0.078
SIDE CHAIN
9
A
G
42
0.075
SIDE CHAIN
10
A
C
27
0.086
SIDE CHAIN
10
A
C
28
0.115
SIDE CHAIN
10
A
G
30
0.066
SIDE CHAIN
10
A
U
41
0.067
SIDE CHAIN
10
A
G
42
0.083
SIDE CHAIN
11
A
C
27
0.068
SIDE CHAIN
11
A
C
28
0.070
SIDE CHAIN
11
A
G
30
0.059
SIDE CHAIN
11
A
G
42
0.068
SIDE CHAIN
11
A
G
43
0.064
SIDE CHAIN
1
4.35
0.70
108.50
112.85
A
A
A
O4'
C1'
N1
U
U
U
33
33
33
N
1
6.42
0.70
108.50
114.92
A
A
A
O4'
C1'
N9
A
A
A
36
36
36
N
1
-5.59
0.50
129.30
123.71
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
1
4.25
0.50
110.60
114.85
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
2
9.93
1.30
114.00
123.93
A
A
A
N9
C1'
C2'
A
A
A
35
35
35
N
2
4.34
0.70
108.50
112.84
A
A
A
O4'
C1'
N9
A
A
A
35
35
35
N
2
5.24
0.70
108.50
113.74
A
A
A
O4'
C1'
N9
A
A
A
36
36
36
N
2
-5.36
0.50
129.30
123.94
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
2
3.81
0.50
110.60
114.41
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
3
9.87
1.30
114.00
123.87
A
A
A
N9
C1'
C2'
A
A
A
35
35
35
N
3
-5.50
0.50
129.30
123.80
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
3
3.80
0.50
110.60
114.40
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
4
6.39
0.70
108.50
114.89
A
A
A
O4'
C1'
N1
U
U
U
33
33
33
N
4
10.62
1.30
114.00
124.62
A
A
A
N9
C1'
C2'
A
A
A
35
35
35
N
4
6.77
0.70
108.50
115.27
A
A
A
O4'
C1'
N9
A
A
A
35
35
35
N
4
-2.99
0.40
105.80
102.81
A
A
A
C8
N9
C4
A
A
A
35
35
35
N
4
-6.13
0.70
109.70
103.57
A
A
A
C1'
O4'
C4'
A
A
A
38
38
38
N
4
5.73
0.70
108.50
114.23
A
A
A
O4'
C1'
N9
A
A
A
38
38
38
N
4
-5.44
0.50
129.30
123.86
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
4
3.72
0.50
110.60
114.32
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
5
4.28
0.70
108.50
112.78
A
A
A
O4'
C1'
N9
A
A
A
36
36
36
N
5
-5.41
0.50
129.30
123.89
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
5
3.94
0.50
110.60
114.54
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
6
6.88
0.70
108.50
115.38
A
A
A
O4'
C1'
N1
U
U
U
33
33
33
N
6
11.00
1.30
114.00
125.00
A
A
A
N9
C1'
C2'
A
A
A
35
35
35
N
6
6.80
0.70
108.50
115.30
A
A
A
O4'
C1'
N9
A
A
A
35
35
35
N
6
-2.96
0.40
105.80
102.84
A
A
A
C8
N9
C4
A
A
A
35
35
35
N
6
-4.42
0.70
109.70
105.28
A
A
A
C1'
O4'
C4'
A
A
A
38
38
38
N
6
-5.66
0.50
129.30
123.64
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
6
3.67
0.50
110.60
114.27
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
6
4.21
0.70
108.50
112.71
A
A
A
O4'
C1'
N1
U
U
U
41
41
41
N
7
6.48
0.70
108.50
114.98
A
A
A
O4'
C1'
N9
A
A
A
36
36
36
N
7
-5.51
0.50
129.30
123.79
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
7
3.86
0.50
110.60
114.46
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
8
4.32
0.70
108.50
112.82
A
A
A
O4'
C1'
N1
U
U
U
33
33
33
N
8
4.27
0.70
108.50
112.77
A
A
A
O4'
C1'
N9
A
A
A
36
36
36
N
8
-5.27
0.50
129.30
124.03
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
8
3.83
0.50
110.60
114.43
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
8
4.23
0.70
108.50
112.73
A
A
A
O4'
C1'
N1
U
U
U
41
41
41
N
9
6.37
0.70
108.50
114.87
A
A
A
O4'
C1'
N9
A
A
A
36
36
36
N
9
-5.44
0.50
129.30
123.86
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
9
3.78
0.50
110.60
114.38
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
10
4.59
0.70
108.50
113.09
A
A
A
O4'
C1'
N9
A
A
A
36
36
36
N
10
-5.37
0.50
129.30
123.93
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
10
3.86
0.50
110.60
114.46
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
11
4.82
0.70
108.50
113.32
A
A
A
O4'
C1'
N1
U
U
U
33
33
33
N
11
7.38
0.70
108.50
115.88
A
A
A
O4'
C1'
N9
A
A
A
36
36
36
N
11
-5.57
0.50
129.30
123.73
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
11
3.67
0.50
110.60
114.27
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
5
A
A
C6
N1
A
A
38
38
0.042
0.007
1.351
1.393
N
8
A
A
N1
C2
A
A
38
38
0.055
0.009
1.339
1.394
N
8
A
A
C6
N1
A
A
38
38
0.043
0.007
1.351
1.394
N
minimized average
NMR SOLUTION STRUCTURE OF THE ANTICODON OF YEAST TRNA-PHE WITH 4 MODIFICATIONS (OMC32 OMG34 1MG37 5MC40)
1
N
N
covale
1.614
both
A
A
31
A
O3'
A
5
1_555
A
OMC
32
A
P
OMC
6
1_555
covale
1.610
both
A
OMC
32
A
O3'
OMC
6
1_555
A
U
33
A
P
U
7
1_555
covale
1.616
both
A
U
33
A
O3'
U
7
1_555
A
OMG
34
A
P
OMG
8
1_555
covale
1.612
both
A
OMG
34
A
O3'
OMG
8
1_555
A
A
35
A
P
A
9
1_555
covale
1.609
both
A
A
36
A
O3'
A
10
1_555
A
1MG
37
A
P
1MG
11
1_555
covale
1.616
both
A
1MG
37
A
O3'
1MG
11
1_555
A
A
38
A
P
A
12
1_555
covale
1.618
both
A
U
39
A
O3'
U
13
1_555
A
5MC
40
A
P
5MC
14
1_555
covale
1.619
both
A
5MC
40
A
O3'
5MC
14
1_555
A
U
41
A
P
U
15
1_555
hydrog
WATSON-CRICK
A
C
27
A
N3
C
1
1_555
A
G
43
A
N1
G
17
1_555
hydrog
WATSON-CRICK
A
C
27
A
N4
C
1
1_555
A
G
43
A
O6
G
17
1_555
hydrog
WATSON-CRICK
A
C
27
A
O2
C
1
1_555
A
G
43
A
N2
G
17
1_555
hydrog
WATSON-CRICK
A
C
28
A
N3
C
2
1_555
A
G
42
A
N1
G
16
1_555
hydrog
WATSON-CRICK
A
C
28
A
N4
C
2
1_555
A
G
42
A
O6
G
16
1_555
hydrog
WATSON-CRICK
A
C
28
A
O2
C
2
1_555
A
G
42
A
N2
G
16
1_555
hydrog
WATSON-CRICK
A
A
29
A
N1
A
3
1_555
A
U
41
A
N3
U
15
1_555
hydrog
WATSON-CRICK
A
A
29
A
N6
A
3
1_555
A
U
41
A
O4
U
15
1_555
hydrog
WATSON-CRICK
A
G
30
A
N1
G
4
1_555
A
5MC
40
A
N3
5MC
14
1_555
hydrog
WATSON-CRICK
A
G
30
A
N2
G
4
1_555
A
5MC
40
A
O2
5MC
14
1_555
hydrog
WATSON-CRICK
A
G
30
A
O6
G
4
1_555
A
5MC
40
A
N4
5MC
14
1_555
hydrog
WATSON-CRICK
A
A
31
A
N1
A
5
1_555
A
U
39
A
N3
U
13
1_555
hydrog
WATSON-CRICK
A
A
31
A
N6
A
5
1_555
A
U
39
A
O4
U
13
1_555
hydrog
OMC-A MISPAIR
A
OMC
32
A
O2
OMC
6
1_555
A
A
38
A
N6
A
12
1_555
hydrog
OMG-A MISPAIR
A
OMG
34
A
O6
OMG
8
1_555
A
A
36
A
N6
A
10
1_555
RNA
TRNA, ANTICODON STEM LOOP, TRNA DOMAIN, RNA HAIRPIN, 1MG, 2'-O-METHYL, 5MC, RNA
1LUU
PDB
1
1LUU
27
43
1LUU
27
43
1LUU
A
1
1
17