1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Baleja, J.D.
Sykes, B.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
215
411
428
10.1016/S0022-2836(05)80361-4
2231713
Solution conformation of purine-pyrimidine DNA octamers using nuclear magnetic resonance, restrained molecular dynamics and NOE-based refinement.
1990
US
J.Magn.Reson.
JOMRA4
0624
0022-2364
87
375
Distance Measurement and Structure Refinement with Noe Data
1990
10.2210/pdb1d18/pdb
pdb_00001d18
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
2426.617
DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')
2
syn
polymer
DEOXYRIBONUCLEIC ACID
no
no
(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG)
CATGCATG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
8.975
1
19
A
1
B
16
-4.433
A_DC1:DG16_B
1
-7.563
0.221
0.203
-0.181
10.611
1
20
A
2
B
15
-6.807
A_DA2:DT15_B
2
-12.379
-0.442
0.286
-0.205
9.548
1
20
A
3
B
14
-7.203
A_DT3:DA14_B
3
-8.908
0.253
0.421
-0.167
3.437
1
19
A
4
B
13
-4.865
A_DG4:DC13_B
4
-17.219
-0.398
0.365
-0.253
-3.784
1
19
A
5
B
12
-4.120
A_DC5:DG12_B
5
-17.230
0.456
0.342
-0.243
-8.844
1
20
A
6
B
11
-6.738
A_DA6:DT11_B
6
-7.882
-0.255
0.471
-0.177
-10.605
1
20
A
7
B
10
-6.654
A_DT7:DA10_B
7
-12.799
0.425
0.240
-0.205
-7.449
1
19
A
8
B
9
-4.776
A_DG8:DC9_B
8
-6.345
-0.184
0.198
-0.189
3.034
30.083
A
A
1
2
15.652
B
B
16
15
3.173
8.029
-0.749
-0.177
AA_DC1DA2:DT15DG16_BB
1
-0.735
1.432
29.007
-1.930
1.298
3.382
32.998
A
A
2
3
6.564
B
B
15
14
3.412
3.721
0.018
-0.084
AA_DA2DT3:DA14DT15_BB
2
0.155
-0.273
32.793
-0.806
-0.005
3.306
34.984
A
A
3
4
5.842
B
B
14
13
3.339
3.503
0.444
-0.419
AA_DT3DG4:DC13DA14_BB
3
2.699
-4.502
34.712
-1.235
-0.324
3.492
44.416
A
A
4
5
-8.047
B
B
13
12
3.473
-6.066
0.039
-0.372
AA_DG4DC5:DG12DC13_BB
4
0.294
-0.390
44.020
0.108
-0.022
3.268
34.205
A
A
5
6
5.863
B
B
12
11
3.301
3.439
-0.454
-0.448
AA_DC5DA6:DT11DG12_BB
5
-3.010
5.133
33.908
-1.310
0.292
3.419
32.898
A
A
6
7
7.924
B
B
11
10
3.452
4.474
0.011
-0.025
AA_DA6DT7:DA10DT11_BB
6
0.047
-0.084
32.600
-0.850
-0.012
2.990
30.620
A
A
7
8
16.770
B
B
10
9
3.124
8.738
0.696
-0.093
AA_DT7DG8:DC9DA10_BB
7
0.763
-1.464
29.366
-1.825
-1.174
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1991-07-15
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
Y
BNL
1990-08-01
REL
REL
CHEMICALLY SYNTHESIZED
sample
1
THE STRUCTURE WAS REFINED AGAINST PRIMARY NOE DATA. THE R VALUE IS 0.23 OVER ALL OBSERVED, QUANTIFIED, NOE CROSSPEAK INTENSITIES. THE NOE-BASED PROCEDURE USED TO REFINE THESE STRUCTURES INCLUDED CORRELATION TIME ADJUSTMENT FACTORS, WHICH ARE APPROXIMATELY RELATED TO THE INVERSE OF THE TEMPERATURE FACTORS ASSOCIATED WITH X-RAY CRYSTALLOGRAPHY. THESE VALUES ARE INCLUDED IN THE COLUMN NORMALLY USED FOR TEMPERATURE FACTORS. VALUES OF 0.0 APPEAR FOR NON-HYDROGEN ATOMS, WHICH WERE NOT USED IN THE NMR CALCULATIONS. FURTHER DETAILS ARE GIVEN IN REFERENCE 1.
ENERGY MINIMIZATION, MOLECULAR DYNAMICS
DE VLIEG ET AL
refinement
GROMOS
C
1
n
1
DC
1
A
A
2
n
2
DA
2
A
T
3
n
3
DT
3
A
G
4
n
4
DG
4
A
C
5
n
5
DC
5
A
A
6
n
6
DA
6
A
T
7
n
7
DT
7
A
G
8
n
8
DG
8
A
C
9
n
1
DC
9
B
A
10
n
2
DA
10
B
T
11
n
3
DT
11
B
G
12
n
4
DG
12
B
C
13
n
5
DC
13
B
A
14
n
6
DA
14
B
T
15
n
7
DT
15
B
G
16
n
8
DG
16
B
author_defined_assembly
2
dimeric
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
DC
1
0.068
SIDE CHAIN
1
A
DA
2
0.077
SIDE CHAIN
1
A
DC
5
0.095
SIDE CHAIN
1
A
DA
6
0.135
SIDE CHAIN
1
B
DC
9
0.090
SIDE CHAIN
1
B
DA
10
0.062
SIDE CHAIN
1
B
DG
12
0.066
SIDE CHAIN
1
B
DC
13
0.092
SIDE CHAIN
1
B
DA
14
0.121
SIDE CHAIN
1
-6.98
0.50
129.30
122.32
A
A
A
N1
C2
N3
DA
DA
DA
2
2
2
N
1
8.81
0.50
110.60
119.41
A
A
A
C2
N3
C4
DA
DA
DA
2
2
2
N
1
-6.59
0.70
126.80
120.21
A
A
A
N3
C4
C5
DA
DA
DA
2
2
2
N
1
3.24
0.50
103.90
107.14
A
A
A
C5
N7
C8
DA
DA
DA
2
2
2
N
1
-3.82
0.50
113.80
109.98
A
A
A
N7
C8
N9
DA
DA
DA
2
2
2
N
1
5.57
0.80
127.40
132.97
A
A
A
N3
C4
N9
DA
DA
DA
2
2
2
N
1
5.06
0.60
114.60
119.66
A
A
A
N1
C2
N3
DT
DT
DT
3
3
3
N
1
-5.76
0.60
127.20
121.44
A
A
A
C2
N3
C4
DT
DT
DT
3
3
3
N
1
4.12
0.60
115.20
119.32
A
A
A
N3
C4
C5
DT
DT
DT
3
3
3
N
1
-3.71
0.60
122.30
118.59
A
A
A
N3
C2
O2
DT
DT
DT
3
3
3
N
1
-4.56
0.60
122.90
118.34
A
A
A
C6
C5
C7
DT
DT
DT
3
3
3
N
1
-4.54
0.60
125.10
120.56
A
A
A
C6
N1
C2
DG
DG
DG
4
4
4
N
1
-4.02
0.60
123.90
119.88
A
A
A
N1
C2
N3
DG
DG
DG
4
4
4
N
1
8.97
0.50
111.90
120.87
A
A
A
C2
N3
C4
DG
DG
DG
4
4
4
N
1
-7.21
0.50
128.60
121.39
A
A
A
N3
C4
C5
DG
DG
DG
4
4
4
N
1
6.51
0.50
111.50
118.01
A
A
A
C5
C6
N1
DG
DG
DG
4
4
4
N
1
-2.54
0.40
110.80
108.26
A
A
A
C4
C5
N7
DG
DG
DG
4
4
4
N
1
5.66
0.60
126.00
131.66
A
A
A
N3
C4
N9
DG
DG
DG
4
4
4
N
1
-8.19
0.60
128.60
120.41
A
A
A
C5
C6
O6
DG
DG
DG
4
4
4
N
1
3.08
0.50
119.90
122.98
A
A
A
C2
N3
C4
DC
DC
DC
5
5
5
N
1
-6.65
0.50
129.30
122.65
A
A
A
N1
C2
N3
DA
DA
DA
6
6
6
N
1
9.27
0.50
110.60
119.87
A
A
A
C2
N3
C4
DA
DA
DA
6
6
6
N
1
-7.58
0.70
126.80
119.22
A
A
A
N3
C4
C5
DA
DA
DA
6
6
6
N
1
-3.04
0.50
110.70
107.66
A
A
A
C4
C5
N7
DA
DA
DA
6
6
6
N
1
3.43
0.50
103.90
107.33
A
A
A
C5
N7
C8
DA
DA
DA
6
6
6
N
1
-3.38
0.50
113.80
110.42
A
A
A
N7
C8
N9
DA
DA
DA
6
6
6
N
1
6.15
0.80
127.40
133.55
A
A
A
N3
C4
N9
DA
DA
DA
6
6
6
N
1
-6.66
1.00
110.10
103.44
A
A
A
C1'
O4'
C4'
DT
DT
DT
7
7
7
N
1
4.84
0.60
114.60
119.44
A
A
A
N1
C2
N3
DT
DT
DT
7
7
7
N
1
-5.98
0.60
127.20
121.22
A
A
A
C2
N3
C4
DT
DT
DT
7
7
7
N
1
4.36
0.60
115.20
119.56
A
A
A
N3
C4
C5
DT
DT
DT
7
7
7
N
1
-4.26
0.60
122.30
118.04
A
A
A
N3
C2
O2
DT
DT
DT
7
7
7
N
1
-5.03
0.60
122.90
117.87
A
A
A
C6
C5
C7
DT
DT
DT
7
7
7
N
1
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
-5.03
0.60
125.10
120.07
A
A
A
C6
N1
C2
DG
DG
DG
8
8
8
N
1
-4.05
0.60
123.90
119.85
A
A
A
N1
C2
N3
DG
DG
DG
8
8
8
N
1
9.11
0.50
111.90
121.01
A
A
A
C2
N3
C4
DG
DG
DG
8
8
8
N
1
-6.96
0.50
128.60
121.64
A
A
A
N3
C4
C5
DG
DG
DG
8
8
8
N
1
6.71
0.50
111.50
118.21
A
A
A
C5
C6
N1
DG
DG
DG
8
8
8
N
1
-2.55
0.40
110.80
108.25
A
A
A
C4
C5
N7
DG
DG
DG
8
8
8
N
1
-3.56
0.50
113.10
109.54
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
1
5.50
0.60
126.00
131.50
A
A
A
N3
C4
N9
DG
DG
DG
8
8
8
N
1
-8.10
0.60
128.60
120.50
A
A
A
C5
C6
O6
DG
DG
DG
8
8
8
N
1
-6.90
0.50
129.30
122.40
B
B
B
N1
C2
N3
DA
DA
DA
10
10
10
N
1
9.32
0.50
110.60
119.92
B
B
B
C2
N3
C4
DA
DA
DA
10
10
10
N
1
-7.32
0.70
126.80
119.48
B
B
B
N3
C4
C5
DA
DA
DA
10
10
10
N
1
-3.70
0.50
113.80
110.10
B
B
B
N7
C8
N9
DA
DA
DA
10
10
10
N
1
6.12
0.80
127.40
133.52
B
B
B
N3
C4
N9
DA
DA
DA
10
10
10
N
1
4.70
0.60
114.60
119.30
B
B
B
N1
C2
N3
DT
DT
DT
11
11
11
N
1
-5.72
0.60
127.20
121.48
B
B
B
C2
N3
C4
DT
DT
DT
11
11
11
N
1
4.13
0.60
115.20
119.33
B
B
B
N3
C4
C5
DT
DT
DT
11
11
11
N
1
-3.76
0.60
122.30
118.54
B
B
B
N3
C2
O2
DT
DT
DT
11
11
11
N
1
3.64
0.60
119.00
122.64
B
B
B
C4
C5
C7
DT
DT
DT
11
11
11
N
1
-5.27
0.60
122.90
117.63
B
B
B
C6
C5
C7
DT
DT
DT
11
11
11
N
1
-5.30
0.60
125.10
119.80
B
B
B
C6
N1
C2
DG
DG
DG
12
12
12
N
1
-4.01
0.60
123.90
119.89
B
B
B
N1
C2
N3
DG
DG
DG
12
12
12
N
1
9.13
0.50
111.90
121.03
B
B
B
C2
N3
C4
DG
DG
DG
12
12
12
N
1
-7.25
0.50
128.60
121.35
B
B
B
N3
C4
C5
DG
DG
DG
12
12
12
N
1
7.14
0.50
111.50
118.64
B
B
B
C5
C6
N1
DG
DG
DG
12
12
12
N
1
-2.74
0.40
110.80
108.06
B
B
B
C4
C5
N7
DG
DG
DG
12
12
12
N
1
5.67
0.60
126.00
131.67
B
B
B
N3
C4
N9
DG
DG
DG
12
12
12
N
1
-7.54
0.60
128.60
121.06
B
B
B
C5
C6
O6
DG
DG
DG
12
12
12
N
1
-6.23
0.50
129.30
123.07
B
B
B
N1
C2
N3
DA
DA
DA
14
14
14
N
1
9.05
0.50
110.60
119.65
B
B
B
C2
N3
C4
DA
DA
DA
14
14
14
N
1
-7.39
0.70
126.80
119.41
B
B
B
N3
C4
C5
DA
DA
DA
14
14
14
N
1
3.06
0.50
103.90
106.96
B
B
B
C5
N7
C8
DA
DA
DA
14
14
14
N
1
-3.39
0.50
113.80
110.41
B
B
B
N7
C8
N9
DA
DA
DA
14
14
14
N
1
6.38
0.80
127.40
133.78
B
B
B
N3
C4
N9
DA
DA
DA
14
14
14
N
1
-6.28
1.00
110.10
103.82
B
B
B
C1'
O4'
C4'
DT
DT
DT
15
15
15
N
1
4.50
0.60
114.60
119.10
B
B
B
N1
C2
N3
DT
DT
DT
15
15
15
N
1
-5.71
0.60
127.20
121.49
B
B
B
C2
N3
C4
DT
DT
DT
15
15
15
N
1
4.13
0.60
115.20
119.33
B
B
B
N3
C4
C5
DT
DT
DT
15
15
15
N
1
-3.66
0.60
122.30
118.64
B
B
B
N3
C2
O2
DT
DT
DT
15
15
15
N
1
-5.56
0.60
122.90
117.34
B
B
B
C6
C5
C7
DT
DT
DT
15
15
15
N
1
2.78
0.30
108.30
111.08
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
1
-5.01
0.60
125.10
120.09
B
B
B
C6
N1
C2
DG
DG
DG
16
16
16
N
1
-4.10
0.60
123.90
119.80
B
B
B
N1
C2
N3
DG
DG
DG
16
16
16
N
1
9.64
0.50
111.90
121.54
B
B
B
C2
N3
C4
DG
DG
DG
16
16
16
N
1
-7.43
0.50
128.60
121.17
B
B
B
N3
C4
C5
DG
DG
DG
16
16
16
N
1
6.91
0.50
111.50
118.41
B
B
B
C5
C6
N1
DG
DG
DG
16
16
16
N
1
-2.78
0.40
110.80
108.02
B
B
B
C4
C5
N7
DG
DG
DG
16
16
16
N
1
5.99
0.60
126.00
131.99
B
B
B
N3
C4
N9
DG
DG
DG
16
16
16
N
1
-8.69
0.60
128.60
119.91
B
B
B
C5
C6
O6
DG
DG
DG
16
16
16
N
1
A
A
N1
C6
DC
DC
1
1
0.040
0.006
1.367
1.407
N
1
A
A
C5
N7
DA
DA
2
2
-0.069
0.006
1.388
1.319
N
1
A
A
N9
C4
DA
DA
2
2
-0.042
0.006
1.374
1.332
N
1
A
A
C5
C6
DT
DT
3
3
0.043
0.007
1.339
1.382
N
1
A
A
C5
N7
DG
DG
4
4
-0.062
0.006
1.388
1.326
N
1
A
A
N1
C6
DC
DC
5
5
0.038
0.006
1.367
1.405
N
1
A
A
C5
N7
DA
DA
6
6
-0.063
0.006
1.388
1.325
N
1
A
A
N9
C4
DA
DA
6
6
-0.048
0.006
1.374
1.326
N
1
A
A
C4
C5
DT
DT
7
7
-0.057
0.009
1.445
1.388
N
1
A
A
C5
C6
DT
DT
7
7
0.052
0.007
1.339
1.391
N
1
A
A
C5
N7
DG
DG
8
8
-0.066
0.006
1.388
1.322
N
1
A
A
N9
C4
DG
DG
8
8
-0.054
0.008
1.375
1.321
N
1
B
B
N1
C6
DC
DC
9
9
0.039
0.006
1.367
1.406
N
1
B
B
C5
N7
DA
DA
10
10
-0.062
0.006
1.388
1.326
N
1
B
B
N9
C4
DA
DA
10
10
-0.051
0.006
1.374
1.323
N
1
B
B
C5
C6
DT
DT
11
11
0.047
0.007
1.339
1.386
N
1
B
B
C5
C7
DT
DT
11
11
0.036
0.006
1.496
1.532
N
1
B
B
C5
N7
DG
DG
12
12
-0.063
0.006
1.388
1.325
N
1
B
B
C8
N9
DG
DG
12
12
-0.045
0.007
1.374
1.329
N
1
B
B
C5
N7
DA
DA
14
14
-0.059
0.006
1.388
1.329
N
1
B
B
N9
C4
DA
DA
14
14
-0.044
0.006
1.374
1.330
N
1
B
B
C4
C5
DT
DT
15
15
-0.060
0.009
1.445
1.385
N
1
B
B
C5
C6
DT
DT
15
15
0.053
0.007
1.339
1.392
N
1
B
B
C5
N7
DG
DG
16
16
-0.056
0.006
1.388
1.332
N
1
B
B
N9
C4
DG
DG
16
16
-0.053
0.008
1.375
1.322
N
SOLUTION CONFORMATION OF PURINE-PYRIMIDINE DNA OCTAMERS USING NUCLEAR MAGNETIC RESONANCE, RESTRAINED MOLECULAR DYNAMICS AND NOE-BASED REFINEMENT
1
N
N
1
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
16
B
N1
DG
8
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
16
B
O6
DG
8
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
16
B
N2
DG
8
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N1
DA
2
1_555
B
DT
15
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N6
DA
2
1_555
B
DT
15
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
B
DA
14
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
B
DA
14
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
13
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
13
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
13
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
12
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
12
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
12
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
11
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
11
B
O4
DT
3
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
10
B
N1
DA
2
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
10
B
N6
DA
2
1_555
hydrog
WATSON-CRICK
A
DG
8
A
N1
DG
8
1_555
B
DC
9
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
8
A
N2
DG
8
1_555
B
DC
9
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
8
A
O6
DG
8
1_555
B
DC
9
B
N4
DC
1
1_555
DNA
DNA, DOUBLE HELIX
1D18
PDB
1
1D18
1
8
1D18
1
8
1D18
A
1
1
8
9
16
1D18
9
16
1D18
B
1
1
8
1
P 1