1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Gollmick, F.A.
Lorenz, M.
Dornberger, U.
von Langen, J.
Diekmann, S.
Fritzsche, H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
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
30
2669
2677
10.1093/nar/gkf375
12060684
Solution structure of dAATAA and dAAUAA DNA bulges.
2002
10.2210/pdb1jrw/pdb
pdb_00001jrw
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
5220.412
5'-D(*GP*CP*AP*TP*CP*GP*AP*AP*TP*AP*AP*GP*CP*TP*AP*CP*G)-3'
1
syn
polymer
3663.392
5'-D(*CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*C)-3'
1
syn
polymer
no
no
(DG)(DC)(DA)(DT)(DC)(DG)(DA)(DA)(DT)(DA)(DA)(DG)(DC)(DT)(DA)(DC)(DG)
GCATCGAATAAGCTACG
A
polydeoxyribonucleotide
no
no
(DC)(DG)(DT)(DA)(DG)(DC)(DC)(DG)(DA)(DT)(DG)(DC)
CGTAGCCGATGC
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-0.074
1
19
A
2
B
28
-3.576
A_DC2:DG28_B
1
8.348
-0.223
-0.077
-0.046
0.624
1
20
A
3
B
27
5.187
A_DA3:DT27_B
2
-11.465
-0.429
0.129
-0.107
-12.544
1
20
A
4
B
26
-1.988
A_DT4:DA26_B
3
-14.075
-0.033
0.656
-0.146
-13.881
1
19
A
5
B
25
-1.484
A_DC5:DG25_B
4
-12.635
-0.209
0.265
0.052
-8.485
1
19
A
6
B
24
-2.101
A_DG6:DC24_B
5
5.445
0.253
0.645
-0.100
11.670
1
19
A
12
B
23
-1.809
A_DG12:DC23_B
6
13.913
-0.166
0.286
-0.030
-6.933
1
19
A
13
B
22
-2.388
A_DC13:DG22_B
7
-3.841
-0.387
0.955
-0.123
5.182
1
20
A
14
B
21
-8.217
A_DT14:DA21_B
8
-3.342
0.234
0.536
-0.140
9.329
1
20
A
15
B
20
0.492
A_DA15:DT20_B
9
-7.136
-0.471
0.667
-0.198
-0.184
1
19
A
16
B
19
-0.530
A_DC16:DG19_B
10
-1.287
0.091
0.454
-0.064
13.891
1
19
A
17
B
18
-12.919
A_DG17:DC18_B
11
7.118
1.278
-1.630
-0.566
3.118
38.396
A
A
2
3
18.764
B
B
28
27
3.208
12.121
-0.213
0.195
AA_DC2DA3:DT27DG28_BB
1
-4.197
6.498
36.267
-1.211
-0.199
3.540
31.485
A
A
3
4
1.271
B
B
27
26
3.507
0.687
-0.588
-0.677
AA_DA3DT4:DA26DT27_BB
2
-4.733
8.755
31.129
-1.386
0.126
3.089
36.127
A
A
4
5
10.595
B
B
26
25
3.106
6.509
0.411
0.028
AA_DT4DC5:DG25DA26_BB
3
5.844
-9.512
35.087
-0.838
0.132
3.332
34.501
A
A
5
6
23.867
B
B
25
24
3.413
13.750
-0.216
0.483
AA_DC5DG6:DC24DG25_BB
4
-4.095
7.108
31.459
-1.494
-0.322
3.744
38.037
A
A
12
13
2.683
B
B
23
22
3.786
1.743
-0.250
-0.866
AA_DG12DC13:DG22DC23_BB
5
-5.159
7.941
37.659
-1.585
-0.374
2.820
30.636
A
A
13
14
2.200
B
B
22
21
2.910
1.159
-0.412
-0.459
AA_DC13DT14:DA21DG22_BB
6
3.788
-7.189
30.385
-1.069
1.437
2.761
38.373
A
A
14
15
29.231
B
B
21
20
3.189
18.468
0.115
-0.117
AA_DT14DA15:DT20DA21_BB
7
-0.933
1.477
33.771
-2.424
-0.288
3.459
33.097
A
A
15
16
1.699
B
B
20
19
3.477
0.968
0.078
-0.543
AA_DA15DC16:DG19DT20_BB
8
-0.495
0.869
33.079
-1.127
-0.225
3.410
38.541
A
A
16
17
0.805
B
B
19
18
3.555
0.524
-0.053
0.229
AA_DC16DG17:DC18DG19_BB
9
10.813
-16.589
37.045
0.276
1.536
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-08-28
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
1QSK contains a similar pentanucleotide DNA bulge with AAAAA in the bulge loop
1JRV IS the SOLUTION STRUCTURE OF DAATAA DNA BULGE (ENSEMBLE)
1JS5 IS the AVERAGED SOLUTION STRUCTURE OF DAAUAA DNA BULGE
1JS7 IS the SOLUTION STRUCTURE (ENSEMBLE) OF DAAUAA DNA BULGE
RCSB
Y
RCSB
2001-08-15
REL
THE FINAL AVERAGE STRUCTURE WAS OBTAINED BY COORDINATE AVERAGING OF THE FINAL ENSEMBLE OF STRUCTURES, FOLLOWED BY RESTRAINED ENERGY MINIMIZATION.
This structure was determined using standard 2D homonuclear and heteronuclear techniques.
1
2D_NOESY
E-COSY
31P-1H_correlated
100mm Na+
7
ambient
300
K
the structures are based on a total of 906 restraints, 645 are NOE-derived
distance constraints, 235 dihedral angle restraints, 26 distance restraints
from hydrogen bonds.
matrix relaxation; torsion angle dynamics; energy minimization
1
minimized average structure
1.6mm in duplex; 10mm phosphate buffer; 100mm NaCl; 0.05mm EDTA; 100% D2O
100% D2O
1.6mm in duplex; 100mm NaCl; 0.05mm EDTA; 100% D2O
100% D2O
Delaglio, F., et al.
processing
NMRPipe
3
Borgias, B.A., James, T.L.
iterative matrix relaxation
MARDIGRAS
3.2
Guentert, P., Mumenthaler, C., Wuetrich, K.
structure solution
DYANA
1.5
WEINER, S.J., KOLLMAN, P.A., NGUYEN, D.T., CASE, D.A.
refinement
Amber
5.0
WEINER, S.J., KOLLMAN, P.A., NGUYEN, D.T., CASE, D.A.
data analysis
Amber
5.0
500
Varian
INOVA
600
Varian
INOVA
750
Varian
INOVA
GUA
1
n
1
DG
1
A
CYT
2
n
2
DC
2
A
ADE
3
n
3
DA
3
A
THY
4
n
4
DT
4
A
CYT
5
n
5
DC
5
A
GUA
6
n
6
DG
6
A
ADE
7
n
7
DA
7
A
ADE
8
n
8
DA
8
A
THY
9
n
9
DT
9
A
ADE
10
n
10
DA
10
A
ADE
11
n
11
DA
11
A
GUA
12
n
12
DG
12
A
CYT
13
n
13
DC
13
A
THY
14
n
14
DT
14
A
ADE
15
n
15
DA
15
A
CYT
16
n
16
DC
16
A
GUA
17
n
17
DG
17
A
CYT
18
n
1
DC
18
B
GUA
19
n
2
DG
19
B
THY
20
n
3
DT
20
B
ADE
21
n
4
DA
21
B
GUA
22
n
5
DG
22
B
CYT
23
n
6
DC
23
B
CYT
24
n
7
DC
24
B
GUA
25
n
8
DG
25
B
ADE
26
n
9
DA
26
B
THY
27
n
10
DT
27
B
GUA
28
n
11
DG
28
B
CYT
29
n
12
DC
29
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
DA
3
0.059
SIDE CHAIN
1
B
DC
18
0.086
SIDE CHAIN
1
B
DG
19
0.086
SIDE CHAIN
1
B
DG
25
0.063
SIDE CHAIN
1
B
DT
27
0.061
SIDE CHAIN
1
2.15
0.30
108.30
110.45
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
5.75
0.60
106.00
111.75
A
A
A
O4'
C4'
C3'
DA
DA
DA
3
3
3
N
1
2.25
0.30
108.30
110.55
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
-4.89
0.60
122.90
118.01
A
A
A
C6
C5
C7
DT
DT
DT
4
4
4
N
1
2.58
0.30
108.30
110.88
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
4.63
0.30
108.30
112.93
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
1
6.37
0.30
108.30
114.67
A
A
A
O4'
C1'
N9
DA
DA
DA
10
10
10
N
1
5.20
0.30
108.30
113.50
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
1
4.78
0.60
106.00
110.78
A
A
A
O4'
C4'
C3'
DC
DC
DC
13
13
13
N
1
2.78
0.30
108.30
111.08
B
B
B
O4'
C1'
N1
DT
DT
DT
20
20
20
N
1
3.81
0.60
106.00
109.81
B
B
B
O4'
C4'
C3'
DA
DA
DA
26
26
26
N
minimized average
Solution Structure of dAATAA DNA Bulge
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
28
B
N1
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
28
B
O6
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
28
B
N2
DG
11
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
27
B
N3
DT
10
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
27
B
O4
DT
10
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
B
DA
26
B
N1
DA
9
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
B
DA
26
B
N6
DA
9
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
25
B
N1
DG
8
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
25
B
O6
DG
8
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
25
B
N2
DG
8
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
DC
24
B
N3
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
24
B
O2
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
24
B
N4
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N1
DG
12
1_555
B
DC
23
B
N3
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N2
DG
12
1_555
B
DC
23
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
12
A
O6
DG
12
1_555
B
DC
23
B
N4
DC
6
1_555
hydrog
WATSON-CRICK
A
DC
13
A
N3
DC
13
1_555
B
DG
22
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
13
A
N4
DC
13
1_555
B
DG
22
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
13
A
O2
DC
13
1_555
B
DG
22
B
N2
DG
5
1_555
hydrog
WATSON-CRICK
A
DT
14
A
N3
DT
14
1_555
B
DA
21
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
14
A
O4
DT
14
1_555
B
DA
21
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DA
15
A
N1
DA
15
1_555
B
DT
20
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
15
A
N6
DA
15
1_555
B
DT
20
B
O4
DT
3
1_555
hydrog
WATSON-CRICK
A
DC
16
A
N3
DC
16
1_555
B
DG
19
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
16
A
N4
DC
16
1_555
B
DG
19
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
16
A
O2
DC
16
1_555
B
DG
19
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
17
A
N1
DG
17
1_555
B
DC
18
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
17
A
N2
DG
17
1_555
B
DC
18
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
17
A
O6
DG
17
1_555
B
DC
18
B
N4
DC
1
1_555
DNA
DNA BULGE, five-nucleotide bulge loop, deoxyribonucleic acid, DNA
1JRW
PDB
1
1JRW
1JRW
PDB
2
1JRW
1
17
1JRW
1
17
1JRW
A
1
1
17
18
29
1JRW
18
29
1JRW
B
2
1
12