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
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/pdb1lux/pdb
pdb_00001lux
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
ANTICODON (RESIDUES 27-43) OF TRNA-PHE WITH THREE MODIFIED RESIDUES (OMC at position 32, OMG at 34, M5C at position 40)
5508.404
5'-R(*CP*CP*AP*GP*AP*(OMC)P*UP*(OMG)P*AP*AP*GP*AP*UP*(5MC)P*UP*GP*G)-3'
1
syn
polymer
no
yes
CCAGA(OMC)U(OMG)AAGAU(5MC)UGG
CCAGACUGAAGAUCUGG
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
8.473
1
19
A
27
A
43
-4.112
A_C27:G43_A
1
-20.951
0.675
0.385
-0.267
11.278
1
19
A
28
A
42
-2.360
A_C28:G42_A
2
-20.714
-0.460
0.059
-0.043
-2.003
1
20
A
29
A
41
-1.510
A_A29:U41_A
3
-16.862
-0.530
-0.090
-0.133
-8.360
1
19
A
30
A
40
-2.090
A_G30:5MC40_A
4
-19.144
0.175
-0.033
-0.039
-5.808
1
20
A
31
A
39
0.074
A_A31:U39_A
5
-21.995
-0.527
-0.062
-0.203
-10.151
A
32
A
38
-2.349
A_OMC32:A38_A
6
-3.011
2.502
0.077
-0.328
2.424
31.774
A
A
27
28
13.591
A
A
43
42
2.877
7.371
-0.666
-1.830
AA_C27C28:G42G43_AA
1
-2.004
3.695
30.865
-4.454
0.914
2.076
41.373
A
A
28
29
31.503
A
A
42
41
3.242
21.274
-0.262
-1.486
AA_C28A29:U41G42_AA
2
-0.592
0.877
35.687
-4.108
0.314
1.975
33.495
A
A
29
30
27.381
A
A
41
40
3.232
15.230
0.243
-2.063
AA_A29G30:5MC40U41_AA
3
-0.592
1.065
29.916
-5.696
-0.503
2.161
32.703
A
A
30
31
21.010
A
A
40
39
2.991
11.586
0.256
-1.853
AA_G30A31:U395MC40_AA
4
-0.534
0.969
30.630
-4.923
-0.530
2.973
47.730
A
A
31
32
8.832
A
A
39
38
3.183
7.122
-0.263
-1.194
AA_A31OMC32:A38U39_AA
5
1.680
-2.083
47.198
-2.013
0.451
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 4 MODIFICATIONS (OMC32 OMG34 1MG37 5MC40)
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
10
2D NOESY
DQF-COSY
5.60
1
atm
298
K
271 restraints (258 NOE-Derived, 13 h-bond), 95 dihedral angle
global fold by distance geometry. refinement by simulated annealing using the amber forcefield
1.6 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
G
37
n
11
G
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
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
A
29
0.083
SIDE CHAIN
1
A
A
31
0.063
SIDE CHAIN
1
A
A
35
0.091
SIDE CHAIN
1
A
U
41
0.070
SIDE CHAIN
2
A
U
33
0.130
SIDE CHAIN
2
A
A
35
0.120
SIDE CHAIN
2
A
U
41
0.061
SIDE CHAIN
3
A
C
27
0.082
SIDE CHAIN
3
A
A
31
0.066
SIDE CHAIN
3
A
U
33
0.094
SIDE CHAIN
3
A
A
35
0.086
SIDE CHAIN
3
A
A
36
0.099
SIDE CHAIN
3
A
G
37
0.069
SIDE CHAIN
3
A
U
41
0.069
SIDE CHAIN
4
A
A
31
0.074
SIDE CHAIN
4
A
U
33
0.082
SIDE CHAIN
4
A
A
35
0.210
SIDE CHAIN
4
A
G
43
0.079
SIDE CHAIN
5
A
G
30
0.061
SIDE CHAIN
5
A
A
31
0.066
SIDE CHAIN
5
A
U
33
0.062
SIDE CHAIN
5
A
A
35
0.146
SIDE CHAIN
5
A
G
37
0.063
SIDE CHAIN
5
A
A
38
0.056
SIDE CHAIN
6
A
C
27
0.066
SIDE CHAIN
6
A
A
31
0.094
SIDE CHAIN
6
A
U
33
0.091
SIDE CHAIN
6
A
A
35
0.063
SIDE CHAIN
6
A
G
37
0.074
SIDE CHAIN
6
A
G
43
0.061
SIDE CHAIN
7
A
C
27
0.086
SIDE CHAIN
7
A
A
29
0.061
SIDE CHAIN
7
A
A
31
0.066
SIDE CHAIN
7
A
U
33
0.160
SIDE CHAIN
7
A
A
36
0.087
SIDE CHAIN
8
A
C
28
0.087
SIDE CHAIN
8
A
A
31
0.086
SIDE CHAIN
8
A
G
37
0.060
SIDE CHAIN
8
A
A
38
0.091
SIDE CHAIN
9
A
A
31
0.082
SIDE CHAIN
9
A
U
33
0.079
SIDE CHAIN
9
A
A
36
0.085
SIDE CHAIN
9
A
G
42
0.056
SIDE CHAIN
10
A
A
31
0.079
SIDE CHAIN
10
A
U
33
0.218
SIDE CHAIN
10
A
G
37
0.057
SIDE CHAIN
10
A
A
38
0.067
SIDE CHAIN
1
5.97
0.70
108.50
114.47
A
A
A
O4'
C1'
N1
C
C
C
27
27
27
N
1
-7.24
1.20
109.10
101.86
A
A
A
C5'
C4'
O4'
U
U
U
33
33
33
N
1
6.30
0.80
101.50
107.80
A
A
A
C3'
C2'
C1'
U
U
U
33
33
33
N
1
7.63
0.70
108.50
116.13
A
A
A
O4'
C1'
N1
U
U
U
33
33
33
N
1
11.27
1.20
119.70
130.97
A
A
A
C3'
O3'
P
OMG
OMG
A
34
34
35
Y
1
-11.80
1.90
104.00
92.20
A
A
A
O3'
P
O5'
OMG
A
A
34
35
35
Y
1
7.97
0.90
109.80
117.77
A
A
A
C5'
C4'
O4'
A
A
A
35
35
35
N
1
7.70
0.70
108.50
116.20
A
A
A
O4'
C1'
N9
A
A
A
35
35
35
N
1
-5.19
0.50
129.30
124.11
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
1
4.11
0.50
110.60
114.71
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
1
7.48
0.70
108.50
115.98
A
A
A
O4'
C1'
N9
G
G
G
43
43
43
N
2
4.32
0.70
108.50
112.82
A
A
A
O4'
C1'
N1
C
C
C
27
27
27
N
2
9.94
1.30
114.00
123.94
A
A
A
N9
C1'
C2'
A
A
A
35
35
35
N
2
7.10
0.70
108.50
115.60
A
A
A
O4'
C1'
N9
A
A
A
36
36
36
N
2
6.09
0.90
109.80
115.89
A
A
A
C5'
C4'
O4'
A
A
A
38
38
38
N
2
-5.17
0.50
129.30
124.13
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
2
4.07
0.50
110.60
114.67
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
2
4.26
0.70
108.50
112.76
A
A
A
O4'
C1'
N1
U
U
U
41
41
41
N
2
7.43
0.70
108.50
115.93
A
A
A
O4'
C1'
N9
G
G
G
43
43
43
N
3
4.79
0.70
108.50
113.29
A
A
A
O4'
C1'
N1
C
C
C
27
27
27
N
3
5.55
0.90
109.80
115.35
A
A
A
C5'
C4'
O4'
A
A
A
35
35
35
N
3
4.81
0.70
108.50
113.31
A
A
A
O4'
C1'
N9
A
A
A
35
35
35
N
3
4.72
0.70
108.50
113.22
A
A
A
O4'
C1'
N9
G
G
G
37
37
37
N
3
6.44
0.90
109.80
116.24
A
A
A
C5'
C4'
O4'
A
A
A
38
38
38
N
3
-5.35
0.50
129.30
123.95
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
3
4.13
0.50
110.60
114.73
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
3
4.24
0.70
108.50
112.74
A
A
A
O4'
C1'
N1
U
U
U
41
41
41
N
3
7.18
0.70
108.50
115.68
A
A
A
O4'
C1'
N9
G
G
G
43
43
43
N
4
6.17
0.70
108.50
114.67
A
A
A
O4'
C1'
N1
C
C
C
27
27
27
N
4
9.26
1.20
119.70
128.96
A
A
A
C3'
O3'
P
OMG
OMG
A
34
34
35
Y
4
7.58
0.90
109.80
117.38
A
A
A
C5'
C4'
O4'
A
A
A
35
35
35
N
4
7.49
0.70
108.50
115.99
A
A
A
O4'
C1'
N9
A
A
A
35
35
35
N
4
6.15
0.70
108.50
114.65
A
A
A
O4'
C1'
N9
A
A
A
36
36
36
N
4
5.48
0.90
109.80
115.28
A
A
A
C5'
C4'
O4'
A
A
A
38
38
38
N
4
-5.29
0.50
129.30
124.01
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
4
4.16
0.50
110.60
114.76
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
4
4.36
0.70
108.50
112.86
A
A
A
O4'
C1'
N1
U
U
U
39
39
39
N
5
4.34
0.70
108.50
112.84
A
A
A
O4'
C1'
N1
C
C
C
27
27
27
N
5
8.81
0.70
108.50
117.31
A
A
A
O4'
C1'
N9
A
A
A
35
35
35
N
5
4.49
0.70
108.50
112.99
A
A
A
O4'
C1'
N9
A
A
A
36
36
36
N
5
5.45
0.70
108.50
113.95
A
A
A
O4'
C1'
N9
G
G
G
37
37
37
N
5
5.54
0.90
109.80
115.34
A
A
A
C5'
C4'
O4'
A
A
A
38
38
38
N
5
-5.33
0.50
129.30
123.97
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
5
4.35
0.50
110.60
114.95
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
5
7.51
0.70
108.50
116.01
A
A
A
O4'
C1'
N9
G
G
G
43
43
43
N
6
4.28
0.70
108.50
112.78
A
A
A
O4'
C1'
N1
C
C
C
27
27
27
N
6
4.38
0.70
108.50
112.88
A
A
A
O4'
C1'
N1
U
U
U
33
33
33
N
6
6.54
0.90
109.80
116.34
A
A
A
C5'
C4'
O4'
A
A
A
35
35
35
N
6
12.23
0.70
108.50
120.73
A
A
A
O4'
C1'
N9
A
A
A
35
35
35
N
6
5.50
0.90
109.80
115.30
A
A
A
C5'
C4'
O4'
A
A
A
38
38
38
N
6
-5.28
0.50
129.30
124.02
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
6
4.21
0.50
110.60
114.81
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
6
4.65
0.70
108.50
113.15
A
A
A
O4'
C1'
N1
U
U
U
39
39
39
N
7
4.70
0.70
108.50
113.20
A
A
A
O4'
C1'
N1
C
C
C
27
27
27
N
7
-4.55
0.70
101.30
96.75
A
A
A
C3'
C2'
C1'
A
A
A
35
35
35
N
7
-5.33
0.50
129.30
123.97
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
7
4.23
0.50
110.60
114.83
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
7
4.49
0.70
108.50
112.99
A
A
A
O4'
C1'
N1
U
U
U
39
39
39
N
7
4.50
0.70
108.50
113.00
A
A
A
O4'
C1'
N1
U
U
U
41
41
41
N
7
7.27
0.70
108.50
115.77
A
A
A
O4'
C1'
N9
G
G
G
43
43
43
N
8
8.25
0.90
109.80
118.05
A
A
A
C5'
C4'
O4'
A
A
A
29
29
29
N
8
-4.77
0.70
101.30
96.53
A
A
A
C3'
C2'
C1'
A
A
A
35
35
35
N
8
4.73
0.70
108.50
113.23
A
A
A
O4'
C1'
N9
A
A
A
35
35
35
N
8
5.42
0.70
108.50
113.92
A
A
A
O4'
C1'
N9
G
G
G
37
37
37
N
8
-5.30
0.50
129.30
124.00
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
8
4.28
0.50
110.60
114.88
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
9
6.25
0.70
108.50
114.75
A
A
A
O4'
C1'
N1
C
C
C
27
27
27
N
9
4.90
0.70
108.50
113.40
A
A
A
O4'
C1'
N9
G
G
G
37
37
37
N
9
6.43
0.90
109.80
116.23
A
A
A
C5'
C4'
O4'
A
A
A
38
38
38
N
9
-5.11
0.50
129.30
124.19
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
9
4.17
0.50
110.60
114.77
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
9
4.47
0.70
108.50
112.97
A
A
A
O4'
C1'
N1
U
U
U
41
41
41
N
10
5.92
0.70
108.50
114.42
A
A
A
O4'
C1'
N1
C
C
C
27
27
27
N
10
6.41
0.70
108.50
114.91
A
A
A
O4'
C1'
N1
U
U
U
33
33
33
N
10
6.44
0.90
109.80
116.24
A
A
A
C5'
C4'
O4'
A
A
A
35
35
35
N
10
-4.59
0.70
109.70
105.11
A
A
A
C1'
O4'
C4'
A
A
A
35
35
35
N
10
7.57
0.70
108.50
116.07
A
A
A
O4'
C1'
N9
A
A
A
35
35
35
N
10
-5.04
0.50
129.30
124.26
A
A
A
N1
C2
N3
A
A
A
38
38
38
N
10
4.28
0.50
110.60
114.88
A
A
A
C2
N3
C4
A
A
A
38
38
38
N
9
A
A
N1
C2
A
A
38
38
0.055
0.009
1.339
1.394
N
10
A
A
N1
C2
A
A
38
38
0.055
0.009
1.339
1.394
N
NMR SOLUTION STRUCTURE OF THE ANTICODON OF YEAST TRNA-PHE WITH 3 MODIFICATIONS (OMC32 OMG34 M5C40)
1
N
N
covale
1.618
both
A
A
31
A
O3'
A
5
1_555
A
OMC
32
A
P
OMC
6
1_555
covale
1.620
both
A
OMC
32
A
O3'
OMC
6
1_555
A
U
33
A
P
U
7
1_555
covale
1.633
both
A
U
33
A
O3'
U
7
1_555
A
OMG
34
A
P
OMG
8
1_555
covale
1.586
both
A
OMG
34
A
O3'
OMG
8
1_555
A
A
35
A
P
A
9
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
1.612
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
N3
OMC
6
1_555
A
A
38
A
N6
A
12
1_555
hydrog
WATSON-CRICK
A
U
33
A
N3
U
7
1_555
A
A
38
A
N1
A
12
1_555
hydrog
WATSON-CRICK
A
U
33
A
O4
U
7
1_555
A
A
38
A
N6
A
12
1_555
RNA
TRNA, ANTICODON STEM LOOP, TRNA DOMAIN, RNA HAIRPIN, 2'-O-METHYL, M5C, RNA
1LUX
PDB
1
1LUX
27
43
1LUX
27
43
1LUX
A
1
1
17