1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Znosko, B.M.
Barnes III, T.W.
Krugh, T.R.
Turner, D.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C12 H16 N3 O7 P
345.245
n
5(1-PROPYNYL)-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C12 H15 N2 O8 P
346.230
5(1-PROPYNYL)-2'-DEOXYURIDINE-5-MONOPHOSPHATE
DNA linking
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
125
6090
6097
10.1021/ja021285d
12785839
NMR Studies of DNA Single Strands and DNA:RNA Hybrids With and Without 1-Propynylation at C5 of Oligopyrimidines
2003
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
123
4107
4118
10.1021/ja003208t
Long-Range Cooperativity in Molecular Recognition of RNA by Oligodeoxynucleotides with Multiple C5-(1-Propynyl) Pyrimidines
2001
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
2981.895
5'-R(*AP*AP*AP*GP*GP*AP*GP*GP*A)-3'
1
syn
polymer
2210.558
5'-D(*CP*(5PC)P*(PDU)P*(5PC)P*(5PC)P*(PDU)P*(PDU))-3'
1
syn
polymer
no
no
AAAGGAGGA
AAAGGAGGA
A
polyribonucleotide
no
yes
(DC)(5PC)(PDU)(5PC)(5PC)(PDU)(PDU)
CCXCCXX
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-9.980
1
20
A
3
B
7
1.980
A_A3:PDU7_B
1
-13.535
-0.090
-0.242
0.279
0.482
1
20
A
4
B
6
3.526
A_A4:PDU6_B
2
-16.681
-0.297
0.524
0.261
4.032
1
19
A
5
B
5
1.148
A_G5:5PC5_B
3
-17.768
-1.383
0.352
-0.061
-2.769
1
19
A
6
B
4
-6.331
A_G6:5PC4_B
4
-14.332
-0.479
-0.305
0.132
3.255
1
20
A
7
B
3
-0.149
A_A7:PDU3_B
5
-14.110
-0.594
0.094
0.222
5.741
1
19
A
8
B
2
3.110
A_G8:5PC2_B
6
-16.352
-1.355
0.252
-0.032
-4.324
1
19
A
9
B
1
-0.610
A_G9:DC1_B
7
-22.792
-0.675
-0.460
0.057
2.980
30.203
A
A
3
4
3.740
B
B
7
6
3.130
1.942
0.428
-0.948
AA_A3A4:PDU6PDU7_BB
1
-4.077
7.853
29.871
-2.189
-1.599
3.242
29.327
A
A
4
5
1.322
B
B
6
5
3.293
0.668
-0.128
-1.084
AA_A4G5:5PC5PDU6_BB
2
2.786
-5.511
29.190
-2.285
0.853
3.489
36.443
A
A
5
6
4.991
B
B
5
4
3.658
3.113
-0.580
-0.960
AA_G5G6:5PC45PC5_BB
3
3.778
-6.058
36.124
-2.008
1.502
3.157
32.579
A
A
6
7
4.491
B
B
4
3
3.279
2.516
0.695
-0.947
AA_G6A7:PDU35PC4_BB
4
-1.779
3.176
32.437
-2.120
-1.544
3.083
28.518
A
A
7
8
7.146
B
B
3
2
3.306
3.509
0.278
-1.415
AA_A7G8:5PC2PDU3_BB
5
-2.091
4.259
28.230
-3.657
-1.032
3.430
40.137
A
A
8
9
11.671
B
B
2
1
3.698
7.959
-0.496
-0.964
AA_G8G9:DC15PC2_BB
6
1.221
-1.790
39.353
-2.403
0.876
atom_site
chem_comp
entity
entity_poly
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Atomic model
Data collection
Derived calculations
Non-polymer description
Polymer sequence
Structure summary
1
0
2003-06-10
1
1
2008-04-29
1
2
2011-07-13
2
0
2021-07-28
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_atom_id
_atom_site.label_atom_id
_chem_comp.formula
_chem_comp.formula_weight
_chem_comp.mon_nstd_flag
_entity.formula_weight
_entity_poly.pdbx_seq_one_letter_code_can
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
DNA:RNA hybrid with same sequence
DNA:RNA hybrid with propynylated bases 1-7 in DNA strand
RCSB
Y
RCSB
2003-01-30
REL
REL
1
2D NOESY
80 mM NaCl
7.0
ambient
273
K
80 mM NaCl
7.0
ambient
303
K
The structure is based on a total of 160 interproton distance restraints, 18 hydrogen bond restraints, and 59 dihedral angle restraints.
simulated annealing, energy minimization
1
minimized average structure
~1mM hybrid, 80 mM NaCl, 10 mM phosphate buffer, 0.5 mM EDTA, 90% H2O, 10% D2O
90% H2O/10% D2O
~2.5 mM hybrid, 80 mM NaCl, 10 mM phosphate, 0.5 mM EDTA, 99.996% D2O
99.996% D2O
Varian
collection
VNMR
5.2
MSI
data analysis
Felix
2000
MSI
structure solution
Discover
95.0
MSI
refinement
Discover
95.0
500
Varian
INOVA
A
2
n
1
A
2
A
A
3
n
2
A
3
A
A
4
n
3
A
4
A
G
5
n
4
G
5
A
G
6
n
5
G
6
A
A
7
n
6
A
7
A
G
8
n
7
G
8
A
G
9
n
8
G
9
A
A
10
n
9
A
10
A
C
1
n
1
DC
1
B
5PC
2
n
2
5PC
2
B
PDU
3
n
3
PDU
3
B
5PC
4
n
4
5PC
4
B
5PC
5
n
5
5PC
5
B
PDU
6
n
6
PDU
6
B
PDU
7
n
7
PDU
7
B
author_defined_assembly
2
dimeric
B
5PC
2
B
5PC
2
DC
B
PDU
3
B
PDU
3
DU
B
5PC
4
B
5PC
4
DC
B
5PC
5
B
5PC
5
DC
B
PDU
6
B
PDU
6
DU
B
PDU
7
B
PDU
7
DU
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
1
A
A
2
0.063
SIDE CHAIN
1
5.20
0.50
110.60
115.80
A
A
A
C2
N3
C4
A
A
A
2
2
2
N
1
-9.41
0.70
126.80
117.39
A
A
A
N3
C4
C5
A
A
A
2
2
2
N
1
-6.44
0.50
103.90
97.46
A
A
A
C5
N7
C8
A
A
A
2
2
2
N
1
8.60
0.50
113.80
122.40
A
A
A
N7
C8
N9
A
A
A
2
2
2
N
1
-6.38
0.40
105.80
99.42
A
A
A
C8
N9
C4
A
A
A
2
2
2
N
1
7.03
0.80
127.40
134.43
A
A
A
N3
C4
N9
A
A
A
2
2
2
N
1
-10.07
1.50
119.60
109.53
A
A
A
OP1
P
OP2
A
A
A
3
3
3
N
1
5.06
0.50
110.60
115.66
A
A
A
C2
N3
C4
A
A
A
3
3
3
N
1
-9.16
0.70
126.80
117.64
A
A
A
N3
C4
C5
A
A
A
3
3
3
N
1
-6.57
0.50
103.90
97.33
A
A
A
C5
N7
C8
A
A
A
3
3
3
N
1
8.42
0.50
113.80
122.22
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
1
-6.09
0.40
105.80
99.71
A
A
A
C8
N9
C4
A
A
A
3
3
3
N
1
6.86
0.80
127.40
134.26
A
A
A
N3
C4
N9
A
A
A
3
3
3
N
1
-10.05
1.50
119.60
109.55
A
A
A
OP1
P
OP2
A
A
A
4
4
4
N
1
5.11
0.50
110.60
115.71
A
A
A
C2
N3
C4
A
A
A
4
4
4
N
1
-9.20
0.70
126.80
117.60
A
A
A
N3
C4
C5
A
A
A
4
4
4
N
1
-6.36
0.50
103.90
97.54
A
A
A
C5
N7
C8
A
A
A
4
4
4
N
1
8.25
0.50
113.80
122.05
A
A
A
N7
C8
N9
A
A
A
4
4
4
N
1
-6.03
0.40
105.80
99.77
A
A
A
C8
N9
C4
A
A
A
4
4
4
N
1
6.83
0.80
127.40
134.23
A
A
A
N3
C4
N9
A
A
A
4
4
4
N
1
-10.04
1.50
119.60
109.56
A
A
A
OP1
P
OP2
G
G
G
5
5
5
N
1
11.22
0.50
111.90
123.12
A
A
A
C2
N3
C4
G
G
G
5
5
5
N
1
-10.85
0.50
128.60
117.75
A
A
A
N3
C4
C5
G
G
G
5
5
5
N
1
3.66
0.50
111.50
115.16
A
A
A
C5
C6
N1
G
G
G
5
5
5
N
1
2.53
0.40
110.80
113.33
A
A
A
C4
C5
N7
G
G
G
5
5
5
N
1
-7.30
0.50
104.30
97.00
A
A
A
C5
N7
C8
G
G
G
5
5
5
N
1
8.80
0.50
113.10
121.90
A
A
A
N7
C8
N9
G
G
G
5
5
5
N
1
-6.78
0.40
106.40
99.62
A
A
A
C8
N9
C4
G
G
G
5
5
5
N
1
2.68
0.40
105.40
108.08
A
A
A
N9
C4
C5
G
G
G
5
5
5
N
1
8.15
0.60
126.00
134.15
A
A
A
N3
C4
N9
G
G
G
5
5
5
N
1
-4.81
0.60
128.60
123.79
A
A
A
C5
C6
O6
G
G
G
5
5
5
N
1
-10.04
1.50
119.60
109.56
A
A
A
OP1
P
OP2
G
G
G
6
6
6
N
1
11.22
0.50
111.90
123.12
A
A
A
C2
N3
C4
G
G
G
6
6
6
N
1
-10.91
0.50
128.60
117.69
A
A
A
N3
C4
C5
G
G
G
6
6
6
N
1
3.82
0.50
111.50
115.32
A
A
A
C5
C6
N1
G
G
G
6
6
6
N
1
2.71
0.40
110.80
113.51
A
A
A
C4
C5
N7
G
G
G
6
6
6
N
1
-7.24
0.50
104.30
97.06
A
A
A
C5
N7
C8
G
G
G
6
6
6
N
1
8.72
0.50
113.10
121.82
A
A
A
N7
C8
N9
G
G
G
6
6
6
N
1
-6.85
0.40
106.40
99.55
A
A
A
C8
N9
C4
G
G
G
6
6
6
N
1
2.63
0.40
105.40
108.03
A
A
A
N9
C4
C5
G
G
G
6
6
6
N
1
8.27
0.60
126.00
134.27
A
A
A
N3
C4
N9
G
G
G
6
6
6
N
1
-3.61
0.60
130.40
126.79
A
A
A
C6
C5
N7
G
G
G
6
6
6
N
1
-5.22
0.60
128.60
123.38
A
A
A
C5
C6
O6
G
G
G
6
6
6
N
1
-10.06
1.50
119.60
109.54
A
A
A
OP1
P
OP2
A
A
A
7
7
7
N
1
5.14
0.50
110.60
115.74
A
A
A
C2
N3
C4
A
A
A
7
7
7
N
1
-9.26
0.70
126.80
117.54
A
A
A
N3
C4
C5
A
A
A
7
7
7
N
1
-6.37
0.50
103.90
97.53
A
A
A
C5
N7
C8
A
A
A
7
7
7
N
1
8.26
0.50
113.80
122.06
A
A
A
N7
C8
N9
A
A
A
7
7
7
N
1
-6.05
0.40
105.80
99.75
A
A
A
C8
N9
C4
A
A
A
7
7
7
N
1
6.97
0.80
127.40
134.37
A
A
A
N3
C4
N9
A
A
A
7
7
7
N
1
-10.13
1.50
119.60
109.47
A
A
A
OP1
P
OP2
G
G
G
8
8
8
N
1
11.16
0.50
111.90
123.06
A
A
A
C2
N3
C4
G
G
G
8
8
8
N
1
-10.72
0.50
128.60
117.88
A
A
A
N3
C4
C5
G
G
G
8
8
8
N
1
3.64
0.50
111.50
115.14
A
A
A
C5
C6
N1
G
G
G
8
8
8
N
1
2.48
0.40
110.80
113.28
A
A
A
C4
C5
N7
G
G
G
8
8
8
N
1
-7.12
0.50
104.30
97.18
A
A
A
C5
N7
C8
G
G
G
8
8
8
N
1
8.66
0.50
113.10
121.76
A
A
A
N7
C8
N9
G
G
G
8
8
8
N
1
-6.90
0.40
106.40
99.50
A
A
A
C8
N9
C4
G
G
G
8
8
8
N
1
2.85
0.40
105.40
108.25
A
A
A
N9
C4
C5
G
G
G
8
8
8
N
1
7.84
0.60
126.00
133.84
A
A
A
N3
C4
N9
G
G
G
8
8
8
N
1
-4.67
0.60
128.60
123.93
A
A
A
C5
C6
O6
G
G
G
8
8
8
N
1
-10.14
1.50
119.60
109.46
A
A
A
OP1
P
OP2
G
G
G
9
9
9
N
1
11.09
0.50
111.90
122.99
A
A
A
C2
N3
C4
G
G
G
9
9
9
N
1
-10.72
0.50
128.60
117.88
A
A
A
N3
C4
C5
G
G
G
9
9
9
N
1
3.65
0.50
111.50
115.15
A
A
A
C5
C6
N1
G
G
G
9
9
9
N
1
2.53
0.40
110.80
113.33
A
A
A
C4
C5
N7
G
G
G
9
9
9
N
1
-7.38
0.50
104.30
96.92
A
A
A
C5
N7
C8
G
G
G
9
9
9
N
1
8.78
0.50
113.10
121.88
A
A
A
N7
C8
N9
G
G
G
9
9
9
N
1
-6.58
0.40
106.40
99.82
A
A
A
C8
N9
C4
G
G
G
9
9
9
N
1
2.54
0.40
105.40
107.94
A
A
A
N9
C4
C5
G
G
G
9
9
9
N
1
8.16
0.60
126.00
134.16
A
A
A
N3
C4
N9
G
G
G
9
9
9
N
1
-4.80
0.60
128.60
123.80
A
A
A
C5
C6
O6
G
G
G
9
9
9
N
1
-10.18
1.50
119.60
109.42
A
A
A
OP1
P
OP2
A
A
A
10
10
10
N
1
5.12
0.50
110.60
115.72
A
A
A
C2
N3
C4
A
A
A
10
10
10
N
1
-9.27
0.70
126.80
117.53
A
A
A
N3
C4
C5
A
A
A
10
10
10
N
1
-6.35
0.50
103.90
97.55
A
A
A
C5
N7
C8
A
A
A
10
10
10
N
1
8.26
0.50
113.80
122.06
A
A
A
N7
C8
N9
A
A
A
10
10
10
N
1
-6.08
0.40
105.80
99.72
A
A
A
C8
N9
C4
A
A
A
10
10
10
N
1
6.95
0.80
127.40
134.35
A
A
A
N3
C4
N9
A
A
A
10
10
10
N
1
3.57
0.30
108.30
111.87
B
B
B
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
-3.04
0.40
120.30
117.26
B
B
B
C6
N1
C2
DC
DC
DC
1
1
1
N
1
3.63
0.50
117.40
121.03
B
B
B
C4
C5
C6
DC
DC
DC
1
1
1
N
1
8.62
1.20
119.70
128.32
B
B
B
C3'
O3'
P
5PC
5PC
PDU
2
2
3
Y
1
A
A
N3
C4
A
A
2
2
0.122
0.006
1.344
1.466
N
1
A
A
C4
C5
A
A
2
2
0.077
0.007
1.383
1.460
N
1
A
A
N7
C8
A
A
2
2
0.067
0.007
1.311
1.378
N
1
A
A
N3
C4
A
A
3
3
0.121
0.006
1.344
1.465
N
1
A
A
C4
C5
A
A
3
3
0.076
0.007
1.383
1.459
N
1
A
A
N7
C8
A
A
3
3
0.067
0.007
1.311
1.378
N
1
A
A
N3
C4
A
A
4
4
0.122
0.006
1.344
1.466
N
1
A
A
C4
C5
A
A
4
4
0.076
0.007
1.383
1.459
N
1
A
A
N7
C8
A
A
4
4
0.069
0.007
1.311
1.380
N
1
A
A
N1
C2
G
G
5
5
0.094
0.008
1.373
1.467
N
1
A
A
N3
C4
G
G
5
5
0.095
0.007
1.350
1.445
N
1
A
A
C4
C5
G
G
5
5
0.058
0.007
1.379
1.437
N
1
A
A
C5
C6
G
G
5
5
0.132
0.010
1.419
1.551
N
1
A
A
N7
C8
G
G
5
5
0.072
0.006
1.305
1.377
N
1
A
A
N1
C2
G
G
6
6
0.093
0.008
1.373
1.466
N
1
A
A
N3
C4
G
G
6
6
0.098
0.007
1.350
1.448
N
1
A
A
C4
C5
G
G
6
6
0.056
0.007
1.379
1.435
N
1
A
A
C5
C6
G
G
6
6
0.130
0.010
1.419
1.549
N
1
A
A
N7
C8
G
G
6
6
0.070
0.006
1.305
1.375
N
1
A
A
N3
C4
A
A
7
7
0.122
0.006
1.344
1.466
N
1
A
A
C4
C5
A
A
7
7
0.076
0.007
1.383
1.459
N
1
A
A
N7
C8
A
A
7
7
0.067
0.007
1.311
1.378
N
1
A
A
N1
C2
G
G
8
8
0.094
0.008
1.373
1.467
N
1
A
A
N3
C4
G
G
8
8
0.094
0.007
1.350
1.444
N
1
A
A
C4
C5
G
G
8
8
0.058
0.007
1.379
1.437
N
1
A
A
C5
C6
G
G
8
8
0.133
0.010
1.419
1.552
N
1
A
A
N7
C8
G
G
8
8
0.073
0.006
1.305
1.378
N
1
A
A
N1
C2
G
G
9
9
0.093
0.008
1.373
1.466
N
1
A
A
N3
C4
G
G
9
9
0.096
0.007
1.350
1.446
N
1
A
A
C4
C5
G
G
9
9
0.058
0.007
1.379
1.437
N
1
A
A
C5
C6
G
G
9
9
0.131
0.010
1.419
1.550
N
1
A
A
N7
C8
G
G
9
9
0.072
0.006
1.305
1.377
N
1
A
A
N3
C4
A
A
10
10
0.122
0.006
1.344
1.466
N
1
A
A
C4
C5
A
A
10
10
0.075
0.007
1.383
1.458
N
1
A
A
N7
C8
A
A
10
10
0.067
0.007
1.311
1.378
N
1
B
B
C4
N4
DC
DC
1
1
0.072
0.009
1.335
1.407
N
1
B
B
N1
C6
DC
DC
1
1
0.131
0.006
1.367
1.498
N
1
B
B
C2
N3
DC
DC
1
1
0.117
0.008
1.353
1.470
N
1
B
B
C4
C5
DC
DC
1
1
-0.056
0.008
1.425
1.369
N
minimized average
5'(dCPCPUPCPCPUPUP)3':(rAGGAGGAAA)5', where P=propynyl
1
N
N
2
N
N
covale
1.616
both
B
DC
1
B
O3'
DC
1
1_555
B
5PC
2
B
P
5PC
2
1_555
covale
1.636
both
B
5PC
2
B
O3'
5PC
2
1_555
B
PDU
3
B
P
PDU
3
1_555
covale
1.631
one
B
PDU
3
B
O3'
PDU
3
1_555
B
5PC
4
B
P
5PC
4
1_555
covale
1.623
both
B
5PC
4
B
O3'
5PC
4
1_555
B
5PC
5
B
P
5PC
5
1_555
covale
1.627
both
B
5PC
5
B
O3'
5PC
5
1_555
B
PDU
6
B
P
PDU
6
1_555
covale
1.625
one
B
PDU
6
B
O3'
PDU
6
1_555
B
PDU
7
B
P
PDU
7
1_555
hydrog
WATSON-CRICK
A
A
3
A
N1
A
2
1_555
B
PDU
7
B
N3
PDU
7
1_555
hydrog
WATSON-CRICK
A
A
3
A
N6
A
2
1_555
B
PDU
7
B
O4
PDU
7
1_555
hydrog
WATSON-CRICK
A
A
4
A
N1
A
3
1_555
B
PDU
6
B
N3
PDU
6
1_555
hydrog
WATSON-CRICK
A
A
4
A
N6
A
3
1_555
B
PDU
6
B
O4
PDU
6
1_555
hydrog
WATSON-CRICK
A
G
5
A
N1
G
4
1_555
B
5PC
5
B
N3
5PC
5
1_555
hydrog
WATSON-CRICK
A
G
5
A
N2
G
4
1_555
B
5PC
5
B
O2
5PC
5
1_555
hydrog
WATSON-CRICK
A
G
5
A
O6
G
4
1_555
B
5PC
5
B
N4
5PC
5
1_555
hydrog
WATSON-CRICK
A
G
6
A
N1
G
5
1_555
B
5PC
4
B
N3
5PC
4
1_555
hydrog
WATSON-CRICK
A
G
6
A
N2
G
5
1_555
B
5PC
4
B
O2
5PC
4
1_555
hydrog
WATSON-CRICK
A
G
6
A
O6
G
5
1_555
B
5PC
4
B
N4
5PC
4
1_555
hydrog
WATSON-CRICK
A
A
7
A
N1
A
6
1_555
B
PDU
3
B
N3
PDU
3
1_555
hydrog
WATSON-CRICK
A
A
7
A
N6
A
6
1_555
B
PDU
3
B
O4
PDU
3
1_555
hydrog
WATSON-CRICK
A
G
8
A
N1
G
7
1_555
B
5PC
2
B
N3
5PC
2
1_555
hydrog
WATSON-CRICK
A
G
8
A
N2
G
7
1_555
B
5PC
2
B
O2
5PC
2
1_555
hydrog
WATSON-CRICK
A
G
8
A
O6
G
7
1_555
B
5PC
2
B
N4
5PC
2
1_555
hydrog
WATSON-CRICK
A
G
9
A
N1
G
8
1_555
B
DC
1
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
G
9
A
N2
G
8
1_555
B
DC
1
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
G
9
A
O6
G
8
1_555
B
DC
1
B
N4
DC
1
1_555
RNA/DNA
DNA, RNA, hybrid, propynyl, RNA-DNA COMPLEX
1NTT
PDB
1
1NTT
1NTT
PDB
2
1NTT
2
10
1NTT
2
10
1NTT
A
1
1
9
1
7
1NTT
1
7
1NTT
B
2
1
7