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/pdb1d19/pdb
pdb_00001d19
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(*GP*TP*AP*CP*GP*TP*AP*C)-3')
2
syn
polymer
DEOXYRIBONUCLEIC ACID
no
no
(DG)(DT)(DA)(DC)(DG)(DT)(DA)(DC)
GTACGTAC
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
-7.468
1
19
A
1
B
16
-3.005
A_DG1:DC16_B
1
-10.997
-0.538
0.064
-0.175
-1.169
1
20
A
2
B
15
-4.753
A_DT2:DA15_B
2
-10.841
0.055
0.165
-0.086
9.027
1
20
A
3
B
14
-6.784
A_DA3:DT14_B
3
-7.003
0.269
0.288
-0.001
10.847
1
19
A
4
B
13
-4.003
A_DC4:DG13_B
4
-16.637
0.650
0.210
-0.216
-8.705
1
19
A
5
B
12
-3.781
A_DG5:DC12_B
5
-17.765
-0.689
0.212
-0.241
-8.641
1
20
A
6
B
11
-6.979
A_DT6:DA11_B
6
-9.726
-0.292
0.264
-0.006
0.462
1
20
A
7
B
10
-4.125
A_DA7:DT10_B
7
-13.198
-0.042
0.159
-0.065
4.511
1
19
A
8
B
9
-4.152
A_DC8:DG9_B
8
-14.031
0.698
0.217
-0.229
3.167
33.421
A
A
1
2
1.170
B
B
16
15
3.168
0.673
-0.217
-0.372
AA_DG1DT2:DA15DC16_BB
1
-1.736
3.020
33.371
-0.754
0.099
3.157
34.492
A
A
2
3
8.429
B
B
15
14
3.077
4.980
-0.636
0.621
AA_DT2DA3:DT14DA15_BB
2
-1.450
2.453
34.112
0.307
0.856
3.258
33.429
A
A
3
4
-3.996
B
B
14
13
3.261
-2.296
-0.097
-0.165
AA_DA3DC4:DG13DT14_BB
3
1.307
-2.274
33.327
0.092
0.384
3.103
38.694
A
A
4
5
16.963
B
B
13
12
3.416
11.093
0.055
-0.650
AA_DC4DG5:DC12DG13_BB
4
0.221
-0.338
37.127
-2.369
-0.055
3.285
33.938
A
A
5
6
-4.246
B
B
12
11
3.276
-2.476
-0.002
-0.268
AA_DG5DT6:DA11DC12_BB
5
-1.050
1.801
33.835
-0.061
-0.166
3.147
36.975
A
A
6
7
6.953
B
B
11
10
3.053
4.399
0.471
0.863
AA_DT6DA7:DT10DA11_BB
6
1.398
-2.210
36.696
0.797
-0.564
3.169
35.101
A
A
7
8
-1.068
B
B
10
9
3.160
-0.644
0.252
-0.269
AA_DA7DC8:DG9DT10_BB
7
0.651
-1.079
35.089
-0.354
-0.324
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 THEN REFINED AGAINST PRIMARY NOE DATA. THE R VALUE IS 0.19 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
G
1
n
1
DG
1
A
T
2
n
2
DT
2
A
A
3
n
3
DA
3
A
C
4
n
4
DC
4
A
G
5
n
5
DG
5
A
T
6
n
6
DT
6
A
A
7
n
7
DA
7
A
C
8
n
8
DC
8
A
G
9
n
1
DG
9
B
T
10
n
2
DT
10
B
A
11
n
3
DA
11
B
C
12
n
4
DC
12
B
G
13
n
5
DG
13
B
T
14
n
6
DT
14
B
A
15
n
7
DA
15
B
C
16
n
8
DC
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
DG
1
0.077
SIDE CHAIN
1
A
DT
2
0.086
SIDE CHAIN
1
A
DA
3
0.050
SIDE CHAIN
1
A
DC
4
0.077
SIDE CHAIN
1
A
DG
5
0.101
SIDE CHAIN
1
A
DT
6
0.099
SIDE CHAIN
1
B
DG
9
0.092
SIDE CHAIN
1
B
DT
10
0.110
SIDE CHAIN
1
B
DC
12
0.078
SIDE CHAIN
1
B
DG
13
0.099
SIDE CHAIN
1
B
DT
14
0.092
SIDE CHAIN
1
-5.24
0.60
125.10
119.86
A
A
A
C6
N1
C2
DG
DG
DG
1
1
1
N
1
-3.76
0.60
123.90
120.14
A
A
A
N1
C2
N3
DG
DG
DG
1
1
1
N
1
9.11
0.50
111.90
121.01
A
A
A
C2
N3
C4
DG
DG
DG
1
1
1
N
1
-7.15
0.50
128.60
121.45
A
A
A
N3
C4
C5
DG
DG
DG
1
1
1
N
1
6.98
0.50
111.50
118.48
A
A
A
C5
C6
N1
DG
DG
DG
1
1
1
N
1
-2.97
0.40
110.80
107.83
A
A
A
C4
C5
N7
DG
DG
DG
1
1
1
N
1
-3.29
0.50
113.10
109.81
A
A
A
N7
C8
N9
DG
DG
DG
1
1
1
N
1
5.16
0.60
126.00
131.16
A
A
A
N3
C4
N9
DG
DG
DG
1
1
1
N
1
-7.80
0.60
128.60
120.80
A
A
A
C5
C6
O6
DG
DG
DG
1
1
1
N
1
5.32
0.60
114.60
119.92
A
A
A
N1
C2
N3
DT
DT
DT
2
2
2
N
1
-5.95
0.60
127.20
121.25
A
A
A
C2
N3
C4
DT
DT
DT
2
2
2
N
1
4.16
0.60
115.20
119.36
A
A
A
N3
C4
C5
DT
DT
DT
2
2
2
N
1
-3.78
0.60
122.30
118.52
A
A
A
N3
C2
O2
DT
DT
DT
2
2
2
N
1
-4.68
0.60
122.90
118.22
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
1
-6.90
0.50
129.30
122.40
A
A
A
N1
C2
N3
DA
DA
DA
3
3
3
N
1
9.02
0.50
110.60
119.62
A
A
A
C2
N3
C4
DA
DA
DA
3
3
3
N
1
-6.91
0.70
126.80
119.89
A
A
A
N3
C4
C5
DA
DA
DA
3
3
3
N
1
3.26
0.50
103.90
107.16
A
A
A
C5
N7
C8
DA
DA
DA
3
3
3
N
1
-3.42
0.50
113.80
110.38
A
A
A
N7
C8
N9
DA
DA
DA
3
3
3
N
1
5.68
0.80
127.40
133.08
A
A
A
N3
C4
N9
DA
DA
DA
3
3
3
N
1
-5.46
0.60
125.10
119.64
A
A
A
C6
N1
C2
DG
DG
DG
5
5
5
N
1
8.41
0.50
111.90
120.31
A
A
A
C2
N3
C4
DG
DG
DG
5
5
5
N
1
-7.32
0.50
128.60
121.28
A
A
A
N3
C4
C5
DG
DG
DG
5
5
5
N
1
7.55
0.50
111.50
119.05
A
A
A
C5
C6
N1
DG
DG
DG
5
5
5
N
1
-3.38
0.40
110.80
107.42
A
A
A
C4
C5
N7
DG
DG
DG
5
5
5
N
1
3.28
0.50
104.30
107.58
A
A
A
C5
N7
C8
DG
DG
DG
5
5
5
N
1
-3.09
0.50
113.10
110.01
A
A
A
N7
C8
N9
DG
DG
DG
5
5
5
N
1
5.38
0.60
126.00
131.38
A
A
A
N3
C4
N9
DG
DG
DG
5
5
5
N
1
-8.35
0.60
128.60
120.25
A
A
A
C5
C6
O6
DG
DG
DG
5
5
5
N
1
2.39
0.30
108.30
110.69
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
4.58
0.60
114.60
119.18
A
A
A
N1
C2
N3
DT
DT
DT
6
6
6
N
1
-6.27
0.60
127.20
120.93
A
A
A
C2
N3
C4
DT
DT
DT
6
6
6
N
1
4.94
0.60
115.20
120.14
A
A
A
N3
C4
C5
DT
DT
DT
6
6
6
N
1
-3.73
0.60
122.30
118.57
A
A
A
N3
C2
O2
DT
DT
DT
6
6
6
N
1
-4.50
0.60
122.90
118.40
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
1
-6.70
0.50
129.30
122.60
A
A
A
N1
C2
N3
DA
DA
DA
7
7
7
N
1
8.73
0.50
110.60
119.33
A
A
A
C2
N3
C4
DA
DA
DA
7
7
7
N
1
-7.04
0.70
126.80
119.76
A
A
A
N3
C4
C5
DA
DA
DA
7
7
7
N
1
3.11
0.50
103.90
107.01
A
A
A
C5
N7
C8
DA
DA
DA
7
7
7
N
1
-3.48
0.50
113.80
110.32
A
A
A
N7
C8
N9
DA
DA
DA
7
7
7
N
1
5.09
0.80
127.40
132.49
A
A
A
N3
C4
N9
DA
DA
DA
7
7
7
N
1
-5.57
0.60
125.10
119.53
B
B
B
C6
N1
C2
DG
DG
DG
9
9
9
N
1
-3.69
0.60
123.90
120.21
B
B
B
N1
C2
N3
DG
DG
DG
9
9
9
N
1
9.57
0.50
111.90
121.47
B
B
B
C2
N3
C4
DG
DG
DG
9
9
9
N
1
-8.18
0.50
128.60
120.42
B
B
B
N3
C4
C5
DG
DG
DG
9
9
9
N
1
7.13
0.50
111.50
118.63
B
B
B
C5
C6
N1
DG
DG
DG
9
9
9
N
1
-3.51
0.40
110.80
107.29
B
B
B
C4
C5
N7
DG
DG
DG
9
9
9
N
1
3.37
0.50
104.30
107.67
B
B
B
C5
N7
C8
DG
DG
DG
9
9
9
N
1
6.12
0.60
126.00
132.12
B
B
B
N3
C4
N9
DG
DG
DG
9
9
9
N
1
-7.90
0.60
128.60
120.70
B
B
B
C5
C6
O6
DG
DG
DG
9
9
9
N
1
-3.08
0.50
121.30
118.22
B
B
B
C6
N1
C2
DT
DT
DT
10
10
10
N
1
5.19
0.60
114.60
119.79
B
B
B
N1
C2
N3
DT
DT
DT
10
10
10
N
1
-5.81
0.60
127.20
121.39
B
B
B
C2
N3
C4
DT
DT
DT
10
10
10
N
1
3.92
0.60
115.20
119.12
B
B
B
N3
C4
C5
DT
DT
DT
10
10
10
N
1
-3.85
0.60
122.30
118.45
B
B
B
N3
C2
O2
DT
DT
DT
10
10
10
N
1
-4.57
0.60
122.90
118.33
B
B
B
C6
C5
C7
DT
DT
DT
10
10
10
N
1
-6.53
0.50
129.30
122.77
B
B
B
N1
C2
N3
DA
DA
DA
11
11
11
N
1
9.00
0.50
110.60
119.60
B
B
B
C2
N3
C4
DA
DA
DA
11
11
11
N
1
-7.15
0.70
126.80
119.65
B
B
B
N3
C4
C5
DA
DA
DA
11
11
11
N
1
6.06
0.80
127.40
133.46
B
B
B
N3
C4
N9
DA
DA
DA
11
11
11
N
1
-5.73
0.60
125.10
119.37
B
B
B
C6
N1
C2
DG
DG
DG
13
13
13
N
1
9.20
0.50
111.90
121.10
B
B
B
C2
N3
C4
DG
DG
DG
13
13
13
N
1
-7.48
0.50
128.60
121.12
B
B
B
N3
C4
C5
DG
DG
DG
13
13
13
N
1
7.53
0.50
111.50
119.03
B
B
B
C5
C6
N1
DG
DG
DG
13
13
13
N
1
-3.02
0.40
110.80
107.78
B
B
B
C4
C5
N7
DG
DG
DG
13
13
13
N
1
3.07
0.50
104.30
107.37
B
B
B
C5
N7
C8
DG
DG
DG
13
13
13
N
1
-3.15
0.50
113.10
109.95
B
B
B
N7
C8
N9
DG
DG
DG
13
13
13
N
1
5.67
0.60
126.00
131.67
B
B
B
N3
C4
N9
DG
DG
DG
13
13
13
N
1
-8.43
0.60
128.60
120.17
B
B
B
C5
C6
O6
DG
DG
DG
13
13
13
N
1
5.08
0.60
114.60
119.68
B
B
B
N1
C2
N3
DT
DT
DT
14
14
14
N
1
-6.18
0.60
127.20
121.02
B
B
B
C2
N3
C4
DT
DT
DT
14
14
14
N
1
4.17
0.60
115.20
119.37
B
B
B
N3
C4
C5
DT
DT
DT
14
14
14
N
1
-4.36
0.60
122.30
117.94
B
B
B
N3
C2
O2
DT
DT
DT
14
14
14
N
1
-4.68
0.60
122.90
118.22
B
B
B
C6
C5
C7
DT
DT
DT
14
14
14
N
1
-6.15
0.50
129.30
123.15
B
B
B
N1
C2
N3
DA
DA
DA
15
15
15
N
1
8.52
0.50
110.60
119.12
B
B
B
C2
N3
C4
DA
DA
DA
15
15
15
N
1
-6.67
0.70
126.80
120.13
B
B
B
N3
C4
C5
DA
DA
DA
15
15
15
N
1
3.49
0.50
103.90
107.39
B
B
B
C5
N7
C8
DA
DA
DA
15
15
15
N
1
-3.49
0.50
113.80
110.31
B
B
B
N7
C8
N9
DA
DA
DA
15
15
15
N
1
5.28
0.80
127.40
132.68
B
B
B
N3
C4
N9
DA
DA
DA
15
15
15
N
1
A
A
C5
N7
DG
DG
1
1
-0.062
0.006
1.388
1.326
N
1
A
A
N9
C4
DG
DG
1
1
-0.050
0.008
1.375
1.325
N
1
A
A
C4
C5
DT
DT
2
2
-0.057
0.009
1.445
1.388
N
1
A
A
C5
C6
DT
DT
2
2
0.054
0.007
1.339
1.393
N
1
A
A
C5
C7
DT
DT
2
2
0.037
0.006
1.496
1.533
N
1
A
A
C5
N7
DA
DA
3
3
-0.067
0.006
1.388
1.321
N
1
A
A
N9
C4
DA
DA
3
3
-0.041
0.006
1.374
1.333
N
1
A
A
N1
C6
DC
DC
4
4
0.038
0.006
1.367
1.405
N
1
A
A
C5
C6
DC
DC
4
4
0.049
0.008
1.339
1.388
N
1
A
A
C5
N7
DG
DG
5
5
-0.057
0.006
1.388
1.331
N
1
A
A
C5
C6
DT
DT
6
6
0.048
0.007
1.339
1.387
N
1
A
A
C5
N7
DA
DA
7
7
-0.059
0.006
1.388
1.329
N
1
A
A
N9
C4
DA
DA
7
7
-0.051
0.006
1.374
1.323
N
1
B
B
C5
N7
DG
DG
9
9
-0.063
0.006
1.388
1.325
N
1
B
B
N9
C4
DG
DG
9
9
-0.050
0.008
1.375
1.325
N
1
B
B
C5
C6
DT
DT
10
10
0.042
0.007
1.339
1.381
N
1
B
B
C5
N7
DA
DA
11
11
-0.059
0.006
1.388
1.329
N
1
B
B
N9
C4
DA
DA
11
11
-0.041
0.006
1.374
1.333
N
1
B
B
C5
C6
DC
DC
12
12
0.051
0.008
1.339
1.390
N
1
B
B
C5
N7
DG
DG
13
13
-0.062
0.006
1.388
1.326
N
1
B
B
N9
C4
DG
DG
13
13
-0.049
0.008
1.375
1.326
N
1
B
B
C5
C6
DT
DT
14
14
0.044
0.007
1.339
1.383
N
1
B
B
C5
N7
DA
DA
15
15
-0.062
0.006
1.388
1.326
N
1
B
B
N9
C4
DA
DA
15
15
-0.047
0.006
1.374
1.327
N
1
B
B
N1
C6
DC
DC
16
16
0.037
0.006
1.367
1.404
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
DG
1
A
N1
DG
1
1_555
B
DC
16
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
B
DC
16
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
B
DC
16
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
DT
2
A
N3
DT
2
1_555
B
DA
15
B
N1
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
2
A
O4
DT
2
1_555
B
DA
15
B
N6
DA
7
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
14
B
N3
DT
6
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
14
B
O4
DT
6
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N3
DC
4
1_555
B
DG
13
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N4
DC
4
1_555
B
DG
13
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
4
A
O2
DC
4
1_555
B
DG
13
B
N2
DG
5
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
5
1_555
B
DC
12
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
B
DC
12
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
B
DC
12
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
B
DA
11
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
B
DA
11
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
B
DT
10
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
B
DT
10
B
O4
DT
2
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
DG
9
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
DG
9
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
DG
9
B
N2
DG
1
1_555
DNA
DNA, DOUBLE HELIX
1D19
PDB
1
1D19
1
8
1D19
1
8
1D19
A
1
1
8
9
16
1D19
9
16
1D19
B
1
1
8
1
P 1