1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Aramini, J.M.
Mujeeb, A.
Germann, M.W.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C10 H15 N2 O8 P
322.208
n
THYMIDINE-3'-PHOSPHATE
DNA linking
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
Nucleic Acids Res.
NARHAD
0389
0305-1048
26
5644
5654
10.1093/nar/26.24.5644
9837995
NMR solution structures of [d(GCGAAT-3'-3'-alphaT-5'-5'-CGC)2] and its unmodified control.
1998
10.2210/pdb1bx5/pdb
pdb_00001bx5
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
ALPHA ANOMERIC THYMIDINES AT POSITION 7 3'-3' PHOSPHODIESTER LINKAGE BETWEEN T6 AND ALPHAT7 5'-5' PHOSPHODIESTER LINKAGE BETWEEN ALPHAT7 AND C8
3045.005
DNA (5'-D(*GP*CP*GP*AP*AP*TP*(ATD)P*CP*GP*C)-3')
ALPHA ANOMERIC T, 3'-3' AND 5'-5' PHOSPHODIESTER LINKAGES
2
syn
polymer
no
yes
(DG)(DC)(DG)(DA)(DA)(DT)(ATD)(DC)(DG)(DC)
GCGAATTCGC
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
24.446
1
19
A
1
B
20
0.487
A_DG1:DC20_B
1
7.540
-0.439
0.204
-0.104
8.425
1
19
A
2
B
19
0.727
A_DC2:DG19_B
2
-13.345
0.144
-0.655
-0.267
10.251
1
19
A
3
B
18
0.171
A_DG3:DC18_B
3
0.902
0.068
-0.052
-0.108
3.441
1
20
A
4
B
17
-2.115
A_DA4:ATD17_B
4
-7.115
0.024
-0.097
-0.107
7.079
1
20
A
5
B
16
-2.353
A_DA5:DT16_B
5
-18.641
-0.056
0.120
-0.160
-5.272
1
20
A
6
B
15
-3.980
A_DT6:DA15_B
6
-19.563
-0.021
0.073
-0.148
-0.031
1
20
A
7
B
14
-1.685
A_ATD7:DA14_B
7
-6.696
-0.013
-0.244
-0.110
-4.941
1
19
A
8
B
13
0.413
A_DC8:DG13_B
8
-3.164
-0.142
-0.101
-0.113
3.622
1
19
A
9
B
12
-1.028
A_DG9:DC12_B
9
-4.972
-0.167
-0.269
-0.242
-14.946
1
19
A
10
B
11
-0.347
A_DC10:DG11_B
10
4.533
0.436
0.037
-0.168
3.353
36.858
A
A
1
2
9.229
B
B
20
19
3.599
5.795
-0.019
-1.121
AA_DG1DC2:DG19DC20_BB
1
5.011
-7.980
36.080
-2.617
0.759
2.415
35.579
A
A
2
3
39.317
B
B
19
18
3.422
22.322
-0.424
-0.473
AA_DC2DG3:DC18DG19_BB
2
-0.660
1.162
27.875
-4.058
0.597
3.284
37.856
A
A
3
4
-10.312
B
B
18
17
3.435
-6.656
-0.907
0.433
AA_DG3DA4:ATD17DC18_BB
3
1.155
-1.790
37.270
1.553
1.552
3.229
39.458
A
A
4
5
-3.486
B
B
17
16
3.188
-2.345
-0.528
-0.076
AA_DA4DA5:DT16ATD17_BB
4
-5.408
8.038
39.033
0.160
0.153
3.592
31.817
A
A
5
6
-6.640
B
B
16
15
3.533
-3.632
-0.164
-0.726
AA_DA5DT6:DA15DT16_BB
5
-0.116
0.211
31.614
-0.598
0.276
3.205
39.877
A
A
6
7
-4.270
B
B
15
14
3.141
-2.899
0.683
-0.086
AA_DT6ATD7:DA14DA15_BB
6
6.080
-8.955
39.327
0.201
-0.316
3.205
38.110
A
A
7
8
-9.647
B
B
14
13
3.364
-6.269
0.886
0.378
AA_ATD7DC8:DG13DA14_BB
7
-2.287
3.519
37.542
1.382
-1.650
2.138
34.465
A
A
8
9
38.786
B
B
13
12
3.160
21.324
-0.224
-0.610
AA_DC8DG9:DC12DG13_BB
8
-4.329
7.873
26.891
-4.071
-0.240
3.427
37.336
A
A
9
10
9.089
B
B
12
11
3.678
5.796
0.222
-1.348
AA_DG9DC10:DG11DC12_BB
9
-1.138
1.784
36.883
-2.942
-0.511
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
pdbx_validate_polymer_linkage
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Advisory
Data collection
Database references
Derived calculations
1
0
1999-01-06
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
BNL
Y
RCSB
1998-09-28
REL
REL
MEAN STRUCTURE. THE STRUCTURE WAS DETERMINED USING DISTANCE AND TORSION ANGLE
RESTRAINTS OBTAINED FROM HOMONUCLEAR NOESY (75, 150, 300 MS MIXING TIMES) AND
DQF-COSY EXPERIMENTS.
9
1
NOESY
DQF-COSY
50 mM NACL, 10 mM NAPHOSPHATE, 0.1 mM EDTA
6.5
1
atm
303
K
REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
simulated annealing
PEARLMAN ET AL., 1995
refinement
Amber
4.1
structure solution
RAMDMARDI
structure solution
Amber
4.1
600
Bruker
AMX600
G
1
n
1
DG
1
A
C
2
n
2
DC
2
A
G
3
n
3
DG
3
A
A
4
n
4
DA
4
A
A
5
n
5
DA
5
A
T
6
n
6
DT
6
A
X
7
n
7
ATD
7
A
C
8
n
8
DC
8
A
G
9
n
9
DG
9
A
C
10
n
10
DC
10
A
G
11
n
1
DG
11
B
C
12
n
2
DC
12
B
G
13
n
3
DG
13
B
A
14
n
4
DA
14
B
A
15
n
5
DA
15
B
T
16
n
6
DT
16
B
X
17
n
7
ATD
17
B
C
18
n
8
DC
18
B
G
19
n
9
DG
19
B
C
20
n
10
DC
20
B
author_defined_assembly
2
dimeric
A
ATD
7
THYMIDINE-3'-PHOSPHATE
A
ATD
7
DT
B
ATD
17
THYMIDINE-3'-PHOSPHATE
B
ATD
7
DT
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
8
0.067
SIDE CHAIN
1
4.72
0.60
106.00
110.72
A
A
A
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
1
5.23
0.30
108.30
113.53
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
-3.68
0.60
119.90
116.22
A
A
A
N1
C6
O6
DG
DG
DG
3
3
3
N
1
3.67
0.60
106.00
109.67
A
A
A
O4'
C4'
C3'
DA
DA
DA
4
4
4
N
1
3.92
0.60
106.00
109.92
A
A
A
O4'
C4'
C3'
DA
DA
DA
5
5
5
N
1
4.97
0.30
108.30
113.27
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
4.45
0.60
119.00
123.45
A
A
A
C4
C5
C7
DT
DT
DT
6
6
6
N
1
-6.80
0.60
122.90
116.10
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
1
46.68
1.90
104.00
150.68
A
A
A
O3'
P
O5'
DT
ATD
ATD
6
7
7
Y
1
5.65
0.60
106.00
111.65
A
A
A
O4'
C4'
C3'
DC
DC
DC
8
8
8
N
1
10.55
1.20
102.50
113.05
A
A
A
C3'
C2'
C1'
DC
DC
DC
8
8
8
N
1
10.75
0.30
108.30
119.05
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
4.08
0.30
108.30
112.38
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
4.72
0.60
106.00
110.72
B
B
B
O4'
C4'
C3'
DC
DC
DC
12
12
12
N
1
3.91
0.30
108.30
112.21
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
-3.63
0.60
119.90
116.27
B
B
B
N1
C6
O6
DG
DG
DG
13
13
13
N
1
3.68
0.60
106.00
109.68
B
B
B
O4'
C4'
C3'
DA
DA
DA
15
15
15
N
1
5.97
0.30
108.30
114.27
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
1
4.73
0.60
119.00
123.73
B
B
B
C4
C5
C7
DT
DT
DT
16
16
16
N
1
-6.78
0.60
122.90
116.12
B
B
B
C6
C5
C7
DT
DT
DT
16
16
16
N
1
46.65
1.90
104.00
150.65
B
B
B
O3'
P
O5'
DT
ATD
ATD
16
17
17
Y
1
5.59
0.60
106.00
111.59
B
B
B
O4'
C4'
C3'
DC
DC
DC
18
18
18
N
1
9.41
1.20
102.50
111.91
B
B
B
C3'
C2'
C1'
DC
DC
DC
18
18
18
N
1
9.90
0.30
108.30
118.20
B
B
B
O4'
C1'
N1
DC
DC
DC
18
18
18
N
1
4.17
0.30
108.30
112.47
B
B
B
O4'
C1'
N1
DC
DC
DC
20
20
20
N
NMR SOLUTION STRUCTURE OF [D(GCGAAT-3'-3'-ALPHAT-5'-5'-CGC)2]
1
N
N
1
N
N
covale
1.608
both
A
DT
6
A
O3'
DT
6
1_555
A
ATD
7
A
P
ATD
7
1_555
covale
1.610
one
A
ATD
7
A
O5'
ATD
7
1_555
A
DC
8
A
P
DC
8
1_555
covale
1.601
both
B
DT
16
B
O3'
DT
6
1_555
B
ATD
17
B
P
ATD
7
1_555
covale
1.609
one
B
ATD
17
B
O5'
ATD
7
1_555
B
DC
18
B
P
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
B
DC
20
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
B
DC
20
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
B
DC
20
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
19
B
N1
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
19
B
O6
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
19
B
N2
DG
9
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
B
DC
18
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
DC
18
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
DC
18
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
ATD
17
B
N3
ATD
7
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
ATD
17
B
O4
ATD
7
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
16
B
N3
DT
6
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
16
B
O4
DT
6
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
B
DA
15
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
B
DA
15
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
ATD
7
A
N3
ATD
7
1_555
B
DA
14
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
ATD
7
A
O4
ATD
7
1_555
B
DA
14
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
DG
13
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
DG
13
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
DG
13
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
B
DC
12
B
N3
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
B
DC
12
B
O2
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
B
DC
12
B
N4
DC
2
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N3
DC
10
1_555
B
DG
11
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N4
DC
10
1_555
B
DG
11
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
O2
DC
10
1_555
B
DG
11
B
N2
DG
1
1_555
DNA
ALPHA ANOMERIC, POLARITY REVERSALS, DNA
1BX5
PDB
1
1BX5
1
10
1BX5
1
10
1BX5
A
1
1
10
11
20
1BX5
11
20
1BX5
B
1
1
10
1
P 1