1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Yang, X.-L.
Sugiyama, H.
Ikeda, S.
Saito, I.
Wang, A.H.-J.
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
C10 H14 N5 O7 P
347.221
n
2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE
DNA linking
C10 H16 N3 O7 P
321.224
n
N1-[2-DEOXY-RIBOFURANOSYL]-[2-AMINO-5-METHYL-4-OXO-4H-PYRIMIDINE]-5'-MONOPHOSPHATE
DNA linking
US
Biophys.J.
BIOJAU
0030
0006-3495
75
1163
1171
9726918
Structural studies of a stable parallel-stranded DNA duplex incorporating isoguanine:cytosine and isocytosine:guanine basepairs by nuclear magnetic resonance spectroscopy.
1998
10.2210/pdb1be5/pdb
pdb_00001be5
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3087.086
DNA DUPLEX (TGCACGGACT)
1
syn
polymer
3045.004
DNA DUPLEX (TGCACGGACT)
1
syn
polymer
no
yes
(DT)(IGU)(IMC)(DA)(IMC)(IGU)(IGU)(DA)(IMC)(DT)
TGCACGGACT
A
polydeoxyribonucleotide
no
no
(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DA)
ACGTGCCTGA
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
5.695
2
A
2
B
12
162.979
A_IGU2:DC12_B
1
-10.430
0.150
-0.791
1.544
-12.489
2
A
3
B
13
-162.541
A_IMC3:DG13_B
2
-9.332
-0.206
0.141
-1.625
40.772
2
21
A
4
B
14
174.619
A_DA4:DT14_B
3
18.001
0.269
-0.500
1.880
-34.882
2
A
5
B
15
-165.019
A_IMC5:DG15_B
4
-2.744
-0.303
0.056
-1.976
18.418
A
6
B
16
172.349
A_IGU6:DC16_B
5
-24.195
-0.052
-0.923
0.714
6.604
A
7
B
17
168.266
A_IGU7:DC17_B
6
-19.865
0.092
-0.550
1.041
19.942
2
21
A
8
B
18
177.551
A_DA8:DT18_B
7
1.029
0.358
-0.307
1.205
-23.730
2
A
9
B
19
-165.257
A_IMC9:DG19_B
8
1.728
-0.214
0.194
-1.519
-39.746
2
21
A
10
B
20
-164.305
A_DT10:DA20_B
9
34.459
-0.033
1.054
-1.685
2.583
-156.607
A
A
2
3
3.478
B
B
12
13
2.561
-6.811
-2.120
-0.385
AA_IGU2IMC3:DG13DC12_BB
1
7.065
3.608
-156.520
0.213
-1.066
3.028
-136.697
A
A
3
4
-2.277
B
B
13
14
3.024
4.231
-1.031
1.161
AA_IMC3DA4:DT14DG13_BB
2
6.161
3.315
-136.600
-0.649
-0.520
3.472
-137.376
A
A
4
5
-2.005
B
B
14
15
3.464
3.736
-0.876
0.528
AA_DA4IMC5:DG15DT14_BB
3
5.513
2.959
-137.300
-0.307
-0.435
3.433
-141.637
A
A
5
6
-4.623
B
B
15
16
3.450
8.730
-0.407
1.030
AA_IMC5IGU6:DC16DG15_BB
4
10.606
5.617
-141.348
-0.594
-0.156
2.812
37.986
A
A
6
7
-2.255
B
B
16
17
2.884
-1.462
0.173
0.304
AA_IGU6IGU7:DC17DC16_BB
5
-5.919
9.130
37.511
0.631
-0.927
2.844
30.537
A
A
7
8
2.494
B
B
17
18
2.764
1.310
-0.585
0.705
AA_IGU7DA8:DT18DC17_BB
6
-4.025
7.666
30.249
1.115
0.422
3.339
-146.248
A
A
8
9
-1.256
B
B
18
19
3.330
2.405
-0.708
0.560
AA_DA8IMC9:DG19DT18_BB
7
7.124
3.723
-146.173
-0.304
-0.337
3.936
52.914
A
A
9
10
-0.615
B
B
19
20
4.076
-0.547
0.815
0.056
AA_IMC9DT10:DA20DG19_BB
8
-7.347
8.268
52.435
0.106
-1.497
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1998-08-12
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
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
Y
BNL
1998-05-19
REL
REL
THE STRUCTURE WAS DETERMINED USING 1H 2D NMR SPECTROSCOPY
MINIMIZED AVERAGE
1
1
NOESY
TOCSY
20mM PHOSPHATE BUFFER
7.0
1
atm
275
K
REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NOE-RMD
WATER
BRUNGER
refinement
X-PLOR
structure solution
X-PLOR
structure solution
SPEDREF
750
Varian
UNITY 750
500
Varian
VXR 500
T
1
n
1
DT
1
A
IGU
2
n
2
IGU
2
A
IMC
3
n
3
IMC
3
A
A
4
n
4
DA
4
A
IMC
5
n
5
IMC
5
A
IGU
6
n
6
IGU
6
A
IGU
7
n
7
IGU
7
A
A
8
n
8
DA
8
A
IMC
9
n
9
IMC
9
A
T
10
n
10
DT
10
A
A
11
n
1
DA
11
B
C
12
n
2
DC
12
B
G
13
n
3
DG
13
B
T
14
n
4
DT
14
B
G
15
n
5
DG
15
B
C
16
n
6
DC
16
B
C
17
n
7
DC
17
B
T
18
n
8
DT
18
B
G
19
n
9
DG
19
B
A
20
n
10
DA
20
B
author_defined_assembly
2
dimeric
A
IGU
2
2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE
A
IGU
2
DG
A
IMC
3
A
IMC
3
DC
A
IMC
5
A
IMC
5
DC
A
IGU
6
2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE
A
IGU
6
DG
A
IGU
7
2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE
A
IGU
7
DG
A
IMC
9
A
IMC
9
DC
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
DT
10
0.098
SIDE CHAIN
1
B
DG
15
0.097
SIDE CHAIN
1
B
DA
20
0.085
SIDE CHAIN
1
4.06
0.30
108.30
112.36
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
1
2.42
0.40
105.80
108.22
A
A
A
N9
C4
C5
DA
DA
DA
4
4
4
N
1
3.08
0.30
108.30
111.38
A
A
A
O4'
C1'
N9
DA
DA
DA
8
8
8
N
1
6.67
0.30
108.30
114.97
B
B
B
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
5.34
0.60
106.00
111.34
B
B
B
O4'
C4'
C3'
DG
DG
DG
15
15
15
N
1
-5.26
0.70
102.20
96.94
B
B
B
C4'
C3'
C2'
DG
DG
DG
15
15
15
N
1
-5.94
0.70
108.00
102.06
B
B
B
O4'
C1'
N1
DC
DC
DC
17
17
17
N
1
-5.87
0.70
102.20
96.33
B
B
B
C4'
C3'
C2'
DG
DG
DG
19
19
19
N
1
6.31
0.30
108.30
114.61
B
B
B
O4'
C1'
N9
DG
DG
DG
19
19
19
N
1
2.10
0.30
108.30
110.40
B
B
B
O4'
C1'
N9
DA
DA
DA
20
20
20
N
1
A
A
C5'
C4'
DT
DT
1
1
0.069
0.007
1.512
1.581
N
1
A
A
C5
C7
DT
DT
1
1
0.042
0.006
1.496
1.538
N
1
A
A
C5
C7
DT
DT
10
10
0.042
0.006
1.496
1.538
N
1
B
B
C3'
C2'
DG
DG
13
13
-0.048
0.008
1.516
1.468
N
1
B
B
C5'
C4'
DT
DT
14
14
0.067
0.007
1.512
1.579
N
1
B
B
C5
C7
DT
DT
14
14
0.039
0.006
1.496
1.535
N
1
B
B
C5'
C4'
DC
DC
16
16
0.055
0.007
1.512
1.567
N
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
STRUCTURAL STUDIES OF A STABLE PARALLEL-STRANDED DNA DUPLEX INCORPORATING ISOGUANINE:CYTOSINE AND ISOCYTOSINE:GUANINE BASE PAIRS BY NMR, MINIMIZED AVERAGE STRUCTURE
1
N
N
2
N
N
covale
1.614
both
A
DT
1
A
O3'
DT
1
1_555
A
IGU
2
A
P
IGU
2
1_555
covale
1.634
both
A
IGU
2
A
O3'
IGU
2
1_555
A
IMC
3
A
P
IMC
3
1_555
covale
1.613
both
A
IMC
3
A
O3'
IMC
3
1_555
A
DA
4
A
P
DA
4
1_555
covale
1.625
both
A
DA
4
A
O3'
DA
4
1_555
A
IMC
5
A
P
IMC
5
1_555
covale
1.622
both
A
IMC
5
A
O3'
IMC
5
1_555
A
IGU
6
A
P
IGU
6
1_555
covale
1.616
both
A
IGU
6
A
O3'
IGU
6
1_555
A
IGU
7
A
P
IGU
7
1_555
covale
1.621
both
A
IGU
7
A
O3'
IGU
7
1_555
A
DA
8
A
P
DA
8
1_555
covale
1.632
both
A
DA
8
A
O3'
DA
8
1_555
A
IMC
9
A
P
IMC
9
1_555
covale
1.631
both
A
IMC
9
A
O3'
IMC
9
1_555
A
DT
10
A
P
DT
10
1_555
hydrog
IGU-DC PAIR
A
IGU
2
A
N1
IGU
2
1_555
B
DC
12
B
O2
DC
2
1_555
hydrog
IMC-DG PAIR
A
IMC
3
A
N3
IMC
3
1_555
B
DG
13
B
N1
DG
3
1_555
hydrog
REVERSED WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
14
B
N3
DT
4
1_555
hydrog
REVERSED WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
14
B
O2
DT
4
1_555
hydrog
IMC-DG PAIR
A
IMC
5
A
N3
IMC
5
1_555
B
DG
15
B
N1
DG
5
1_555
hydrog
IGU-DC PAIR
A
IGU
6
A
N1
IGU
6
1_555
B
DC
16
B
N3
DC
6
1_555
hydrog
IGU-DC PAIR
A
IGU
7
A
N1
IGU
7
1_555
B
DC
17
B
N3
DC
7
1_555
hydrog
REVERSED WATSON-CRICK
A
DA
8
A
N1
DA
8
1_555
B
DT
18
B
N3
DT
8
1_555
hydrog
REVERSED WATSON-CRICK
A
DA
8
A
N6
DA
8
1_555
B
DT
18
B
O2
DT
8
1_555
hydrog
IMC-DG PAIR
A
IMC
9
A
N3
IMC
9
1_555
B
DG
19
B
N1
DG
9
1_555
hydrog
REVERSED WATSON-CRICK
A
DT
10
A
N3
DT
10
1_555
B
DA
20
B
N1
DA
10
1_555
hydrog
REVERSED WATSON-CRICK
A
DT
10
A
O2
DT
10
1_555
B
DA
20
B
N6
DA
10
1_555
DNA
DNA STRUCTURE, NOVEL DNA BASES, ANTISENSE OLIGONUCLEOTIDES, INTERCALATOR BINDING, REVERSE WATSON-CRICK BASE PAIRS, DEOXYRIBONUCLEIC ACID, DNA
1BE5
PDB
1
1
10
1BE5
1
10
1BE5
A
1
1
10
11
20
1BE5
11
20
1BE5
B
1
1
10
1
P 1