1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Lin, Z.
de los Santos, C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C5 H11 O6 P
198.111
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
ABASIC DIDEOXYRIBOSE
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
J.Mol.Biol.
JMOBAK
0070
0022-2836
308
341
352
10.1006/jmbi.2001.4587
11327771
NMR characterization of clustered bistrand abasic site lesions: effect of orientation on their solution structure.
2001
10.2210/pdb1ht7/pdb
pdb_00001ht7
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
MODIFIED DNA DUPLEX CONTAINING CLUSTERED ABASIC SITES
3843.488
5'-D(*CP*GP*CP*AP*TP*GP*(3DR)P*GP*TP*AP*CP*GP*C)-3'
1
syn
polymer
3867.513
5'-D(*GP*CP*GP*TP*AP*(3DR)P*AP*CP*AP*TP*GP*CP*G)-3'
1
syn
polymer
no
yes
(DC)(DG)(DC)(DA)(DT)(DG)(3DR)(DG)(DT)(DA)(DC)(DG)(DC)
CGCATGNGTACGC
A
polydeoxyribonucleotide
no
yes
(DG)(DC)(DG)(DT)(DA)(3DR)(DA)(DC)(DA)(DT)(DG)(DC)(DG)
GCGTANACATGCG
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
-2.539
1
19
A
1
B
26
-2.082
A_DC1:DG26_B
1
-8.521
0.583
0.312
-0.250
-7.797
1
19
A
2
B
25
-2.030
A_DG2:DC25_B
2
-9.655
-0.693
-0.015
-0.283
-12.268
1
19
A
3
B
24
-3.418
A_DC3:DG24_B
3
-4.493
0.663
0.652
-0.284
-3.121
1
20
A
4
B
23
-3.500
A_DA4:DT23_B
4
-10.431
0.128
0.375
-0.199
-1.530
1
20
A
5
B
22
-3.098
A_DT5:DA22_B
5
-7.203
-0.021
0.063
-0.147
3.379
1
19
A
6
B
21
-1.193
A_DG6:DC21_B
6
2.243
-0.615
0.275
-0.211
-10.681
1
20
A
9
B
18
0.557
A_DT9:DA18_B
7
-6.885
0.129
0.253
-0.220
10.687
1
20
A
10
B
17
-4.169
A_DA10:DT17_B
8
-10.454
0.166
-0.062
-0.169
12.336
1
19
A
11
B
16
0.376
A_DC11:DG16_B
9
-16.470
0.799
0.100
-0.210
2.241
1
19
A
12
B
15
-1.264
A_DG12:DC15_B
10
-11.218
-0.783
-0.033
-0.319
6.779
1
19
A
13
B
14
-1.573
A_DC13:DG14_B
11
-6.426
0.787
-0.069
-0.301
2.579
31.298
A
A
1
2
13.831
B
B
26
25
2.922
7.351
0.581
-1.397
AA_DC1DG2:DC25DG26_BB
1
5.931
-11.159
29.873
-3.785
-0.112
3.343
42.182
A
A
2
3
-6.354
B
B
25
24
3.218
-4.541
-0.760
-0.570
AA_DG2DC3:DG24DC25_BB
2
-7.755
10.851
41.257
-0.318
0.246
2.659
37.859
A
A
3
4
-1.008
B
B
24
23
2.634
-0.653
0.187
-1.177
AA_DC3DA4:DT23DG24_BB
3
3.806
-5.876
37.669
-1.746
0.108
3.108
31.620
A
A
4
5
-4.297
B
B
23
22
3.065
-2.336
0.021
-0.902
AA_DA4DT5:DA22DT23_BB
4
3.297
-6.066
31.367
-1.245
0.539
2.245
37.464
A
A
5
6
20.214
B
B
22
21
2.773
12.716
0.245
-1.006
AA_DT5DG6:DC21DA22_BB
5
-4.160
6.613
35.074
-2.891
-0.815
2.594
38.686
A
A
9
10
14.640
B
B
18
17
2.731
9.590
-0.470
-0.015
AA_DT9DA10:DT17DA18_BB
6
3.663
-5.591
37.349
-0.999
1.083
3.072
29.649
A
A
10
11
0.480
B
B
17
16
3.211
0.245
1.068
-0.385
AA_DA10DC11:DG16DT17_BB
7
-3.308
6.477
29.467
-0.801
-2.758
1.506
36.701
A
A
11
12
37.745
B
B
16
15
2.930
22.197
-0.156
-1.410
AA_DC11DG12:DC15DG16_BB
8
2.915
-4.956
29.270
-4.551
0.551
3.071
40.550
A
A
12
13
-1.444
B
B
15
14
3.036
-1.001
0.578
-0.890
AA_DG12DC13:DG14DC15_BB
9
1.163
-1.679
40.522
-1.180
-0.713
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-05-02
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
_struct_conn.pdbx_leaving_atom_flag
Structure of a DNA duplex containing a bistrand abasic site lesion staggered in a 3'-orientation
RCSB
Y
RCSB
2000-12-29
REL
REL
Randomly designed sequence containing stable abasic sites (3DR).
sample
Randomly designed sequence containing stable abasic sites (3DR).
sample
structures with the least restraint violations
30
6
2D NOESY
COSY, COSY45, TOCSY, DQFCOSY, HETCOR
2D NOESY
not determined
7.6
ambient
298
K
not determined
7.6
ambient
276
K
1) Heating stage: from 100 to 500 K in 4ps. Introduction of experimental restraints at the end of this stage. 2) High temperature stage: 80 ps dynamics at 500K 3) Cooling stage: From 500 to 300K in 40ps. 4) Equilibration stage: 140ps dynamics at 300K.
Restrained molecular dynamics
2mM duplex in 20 mM phosphate buffer, pH 7.6; 50 mM NaCl; 1 mM EDTA.
99.96% D2O
2mM duplex in 20 mM phosphate buffer, pH 7.6; 50 mM NaCl; 1 mM EDTA.
90% H2O/10% D2O (v/v)
MSI
processing
Felix
98
Borgia & James
data analysis
MARDIGRAS
5
A. Brunger
refinement
X-PLOR
3.1
MSI
data analysis
Insight
95
UCSF
data analysis
Midas
Plus
Sklenar & Lavery
data analysis
Curves
5
500
Varian
INOVA
600
Varian
INOVA
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
A
4
n
4
DA
4
A
T
5
n
5
DT
5
A
G
6
n
6
DG
6
A
FUR
7
n
7
3DR
7
A
G
8
n
8
DG
8
A
T
9
n
9
DT
9
A
A
10
n
10
DA
10
A
C
11
n
11
DC
11
A
G
12
n
12
DG
12
A
C
13
n
13
DC
13
A
G
14
n
1
DG
14
B
C
15
n
2
DC
15
B
G
16
n
3
DG
16
B
T
17
n
4
DT
17
B
B
18
n
5
DA
18
B
FUR
19
n
6
3DR
19
B
B
20
n
7
DA
20
B
C
21
n
8
DC
21
B
B
22
n
9
DA
22
B
T
23
n
10
DT
23
B
G
24
n
11
DG
24
B
C
25
n
12
DC
25
B
G
26
n
13
DG
26
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
C3'
DG
6
WRONG HAND
1
B
C3'
3DR
19
WRONG HAND
2
A
C3'
DG
6
WRONG HAND
2
B
C3'
3DR
19
WRONG HAND
3
A
C3'
DG
6
WRONG HAND
3
B
C3'
3DR
19
WRONG HAND
4
A
C3'
DG
6
WRONG HAND
4
B
C3'
3DR
19
WRONG HAND
5
A
C3'
DG
6
WRONG HAND
5
B
C3'
3DR
19
WRONG HAND
6
A
C3'
DG
6
WRONG HAND
6
B
C3'
3DR
19
WRONG HAND
1
-4.97
0.80
105.90
100.93
A
A
A
O4'
C1'
C2'
DG
DG
DG
2
2
2
N
1
3.13
0.50
113.10
116.23
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
2.24
0.30
108.30
110.54
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
3.14
0.30
108.30
111.44
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
1
-6.47
0.80
102.40
95.93
A
A
A
C3'
C2'
C1'
DG
DG
DG
6
6
6
N
1
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
3.01
0.50
113.10
116.11
A
A
A
N7
C8
N9
DG
DG
DG
6
6
6
N
1
3.28
0.50
113.10
116.38
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
1
3.86
0.50
113.80
117.66
A
A
A
N7
C8
N9
DA
DA
DA
10
10
10
N
1
-2.49
0.40
105.80
103.31
A
A
A
C8
N9
C4
DA
DA
DA
10
10
10
N
1
-5.88
0.70
102.20
96.32
A
A
A
C4'
C3'
C2'
DC
DC
DC
11
11
11
N
1
11.76
0.30
108.30
120.06
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
3.35
0.50
113.10
116.45
A
A
A
N7
C8
N9
DG
DG
DG
12
12
12
N
1
2.32
0.30
108.30
110.62
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
1
3.35
0.50
113.10
116.45
B
B
B
N7
C8
N9
DG
DG
DG
14
14
14
N
1
4.22
0.30
108.30
112.52
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
3.29
0.30
108.30
111.59
B
B
B
O4'
C1'
N9
DA
DA
DA
20
20
20
N
1
2.03
0.30
108.30
110.33
B
B
B
O4'
C1'
N1
DT
DT
DT
23
23
23
N
1
3.36
0.50
113.10
116.46
B
B
B
N7
C8
N9
DG
DG
DG
24
24
24
N
1
2.40
0.30
108.30
110.70
B
B
B
O4'
C1'
N1
DC
DC
DC
25
25
25
N
2
-6.59
1.00
110.10
103.51
A
A
A
C1'
O4'
C4'
DG
DG
DG
2
2
2
N
2
-5.02
0.80
105.90
100.88
A
A
A
O4'
C1'
C2'
DG
DG
DG
2
2
2
N
2
3.11
0.50
113.10
116.21
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
2
2.35
0.30
108.30
110.65
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
2
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
2
-6.19
0.80
102.40
96.21
A
A
A
C3'
C2'
C1'
DG
DG
DG
6
6
6
N
2
3.80
0.30
108.30
112.10
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
2
3.24
0.50
113.10
116.34
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
2
3.96
0.50
113.80
117.76
A
A
A
N7
C8
N9
DA
DA
DA
10
10
10
N
2
-2.56
0.40
105.80
103.24
A
A
A
C8
N9
C4
DA
DA
DA
10
10
10
N
2
-6.25
0.70
102.20
95.95
A
A
A
C4'
C3'
C2'
DC
DC
DC
11
11
11
N
2
11.80
0.30
108.30
120.10
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
2
2.28
0.30
108.30
110.58
A
A
A
O4'
C1'
N9
DG
DG
DG
12
12
12
N
2
3.23
0.50
113.10
116.33
A
A
A
N7
C8
N9
DG
DG
DG
12
12
12
N
2
8.23
0.30
108.30
116.53
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
2
3.20
0.50
113.10
116.30
B
B
B
N7
C8
N9
DG
DG
DG
14
14
14
N
2
4.70
0.30
108.30
113.00
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
2
1.97
0.30
108.30
110.27
B
B
B
O4'
C1'
N1
DT
DT
DT
17
17
17
N
2
2.68
0.30
108.30
110.98
B
B
B
O4'
C1'
N9
DA
DA
DA
20
20
20
N
2
-4.85
0.80
105.90
101.05
B
B
B
O4'
C1'
C2'
DC
DC
DC
21
21
21
N
2
2.04
0.30
108.30
110.34
B
B
B
O4'
C1'
N1
DC
DC
DC
21
21
21
N
2
3.22
0.50
113.10
116.32
B
B
B
N7
C8
N9
DG
DG
DG
24
24
24
N
2
2.01
0.30
108.30
110.31
B
B
B
O4'
C1'
N9
DG
DG
DG
26
26
26
N
3
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
3
-6.34
1.00
110.10
103.76
A
A
A
C1'
O4'
C4'
DG
DG
DG
2
2
2
N
3
-5.20
0.80
105.90
100.70
A
A
A
O4'
C1'
C2'
DG
DG
DG
2
2
2
N
3
3.22
0.50
113.10
116.32
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
3
2.26
0.30
108.30
110.56
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
3
3.08
0.30
108.30
111.38
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
3
-6.09
0.80
102.40
96.31
A
A
A
C3'
C2'
C1'
DG
DG
DG
6
6
6
N
3
4.34
0.30
108.30
112.64
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
3
3.06
0.50
113.10
116.16
A
A
A
N7
C8
N9
DG
DG
DG
6
6
6
N
3
2.92
0.30
108.30
111.22
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
3
3.90
0.50
113.80
117.70
A
A
A
N7
C8
N9
DA
DA
DA
10
10
10
N
3
-2.46
0.40
105.80
103.34
A
A
A
C8
N9
C4
DA
DA
DA
10
10
10
N
3
-5.56
0.70
102.20
96.64
A
A
A
C4'
C3'
C2'
DC
DC
DC
11
11
11
N
3
11.65
0.30
108.30
119.95
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
3
1.99
0.30
108.30
110.29
A
A
A
O4'
C1'
N9
DG
DG
DG
12
12
12
N
3
3.26
0.50
113.10
116.36
A
A
A
N7
C8
N9
DG
DG
DG
12
12
12
N
3
7.77
0.30
108.30
116.07
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
3
3.22
0.50
113.10
116.32
B
B
B
N7
C8
N9
DG
DG
DG
14
14
14
N
3
4.47
0.30
108.30
112.77
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
3
2.70
0.30
108.30
111.00
B
B
B
O4'
C1'
N1
DT
DT
DT
17
17
17
N
3
2.62
0.30
108.30
110.92
B
B
B
O4'
C1'
N9
DA
DA
DA
20
20
20
N
3
2.21
0.30
108.30
110.51
B
B
B
O4'
C1'
N1
DT
DT
DT
23
23
23
N
3
3.23
0.50
113.10
116.33
B
B
B
N7
C8
N9
DG
DG
DG
24
24
24
N
3
1.95
0.30
108.30
110.25
B
B
B
O4'
C1'
N1
DC
DC
DC
25
25
25
N
3
2.32
0.30
108.30
110.62
B
B
B
O4'
C1'
N9
DG
DG
DG
26
26
26
N
4
-5.00
0.80
105.90
100.90
A
A
A
O4'
C1'
C2'
DG
DG
DG
2
2
2
N
4
3.16
0.50
113.10
116.26
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
4
2.26
0.30
108.30
110.56
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
4
2.63
0.30
108.30
110.93
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
4
-5.74
0.80
102.40
96.66
A
A
A
C3'
C2'
C1'
DG
DG
DG
6
6
6
N
4
3.56
0.30
108.30
111.86
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
4
3.14
0.50
113.10
116.24
A
A
A
N7
C8
N9
DG
DG
DG
6
6
6
N
4
3.31
0.50
113.10
116.41
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
4
3.09
0.30
108.30
111.39
A
A
A
O4'
C1'
N1
DT
DT
DT
9
9
9
N
4
4.02
0.50
113.80
117.82
A
A
A
N7
C8
N9
DA
DA
DA
10
10
10
N
4
-2.51
0.40
105.80
103.29
A
A
A
C8
N9
C4
DA
DA
DA
10
10
10
N
4
-6.09
0.70
102.20
96.11
A
A
A
C4'
C3'
C2'
DC
DC
DC
11
11
11
N
4
12.08
0.30
108.30
120.38
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
4
2.00
0.30
108.30
110.30
A
A
A
O4'
C1'
N9
DG
DG
DG
12
12
12
N
4
3.34
0.50
113.10
116.44
A
A
A
N7
C8
N9
DG
DG
DG
12
12
12
N
4
3.24
0.50
113.10
116.34
B
B
B
N7
C8
N9
DG
DG
DG
14
14
14
N
4
4.49
0.30
108.30
112.79
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
4
2.82
0.30
108.30
111.12
B
B
B
O4'
C1'
N1
DT
DT
DT
17
17
17
N
4
2.53
0.30
108.30
110.83
B
B
B
O4'
C1'
N9
DA
DA
DA
20
20
20
N
4
1.94
0.30
108.30
110.24
B
B
B
O4'
C1'
N1
DT
DT
DT
23
23
23
N
4
3.29
0.50
113.10
116.39
B
B
B
N7
C8
N9
DG
DG
DG
24
24
24
N
4
2.87
0.30
108.30
111.17
B
B
B
O4'
C1'
N9
DG
DG
DG
26
26
26
N
5
-5.09
0.80
105.90
100.81
A
A
A
O4'
C1'
C2'
DG
DG
DG
2
2
2
N
5
3.08
0.50
113.10
116.18
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
5
2.27
0.30
108.30
110.57
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
5
3.23
0.30
108.30
111.53
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
5
-6.29
0.80
102.40
96.11
A
A
A
C3'
C2'
C1'
DG
DG
DG
6
6
6
N
5
5.11
0.30
108.30
113.41
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
5
3.16
0.30
108.30
111.46
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
5
3.78
0.50
113.80
117.58
A
A
A
N7
C8
N9
DA
DA
DA
10
10
10
N
5
-5.51
0.70
102.20
96.69
A
A
A
C4'
C3'
C2'
DC
DC
DC
11
11
11
N
5
11.54
0.30
108.30
119.84
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
5
2.43
0.30
108.30
110.73
A
A
A
O4'
C1'
N9
DG
DG
DG
12
12
12
N
5
3.18
0.50
113.10
116.28
A
A
A
N7
C8
N9
DG
DG
DG
12
12
12
N
5
8.59
0.30
108.30
116.89
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
5
3.19
0.50
113.10
116.29
B
B
B
N7
C8
N9
DG
DG
DG
14
14
14
N
5
4.28
0.30
108.30
112.58
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
5
-2.40
0.40
106.40
104.00
B
B
B
C8
N9
C4
DG
DG
DG
16
16
16
N
5
2.67
0.30
108.30
110.97
B
B
B
O4'
C1'
N1
DT
DT
DT
17
17
17
N
5
2.34
0.30
108.30
110.64
B
B
B
O4'
C1'
N9
DA
DA
DA
20
20
20
N
5
1.91
0.30
108.30
110.21
B
B
B
O4'
C1'
N1
DT
DT
DT
23
23
23
N
5
3.36
0.50
113.10
116.46
B
B
B
N7
C8
N9
DG
DG
DG
24
24
24
N
6
2.43
0.30
108.30
110.73
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
6
-5.40
0.80
105.90
100.50
A
A
A
O4'
C1'
C2'
DG
DG
DG
2
2
2
N
6
3.16
0.50
113.10
116.26
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
6
2.34
0.30
108.30
110.64
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
6
3.19
0.30
108.30
111.49
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
6
-5.65
0.80
102.40
96.75
A
A
A
C3'
C2'
C1'
DG
DG
DG
6
6
6
N
6
3.38
0.30
108.30
111.68
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
6
3.03
0.50
113.10
116.13
A
A
A
N7
C8
N9
DG
DG
DG
6
6
6
N
6
3.29
0.50
113.10
116.39
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
6
4.02
0.50
113.80
117.82
A
A
A
N7
C8
N9
DA
DA
DA
10
10
10
N
6
-2.48
0.40
105.80
103.32
A
A
A
C8
N9
C4
DA
DA
DA
10
10
10
N
6
-5.99
0.70
102.20
96.21
A
A
A
C4'
C3'
C2'
DC
DC
DC
11
11
11
N
6
11.69
0.30
108.30
119.99
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
6
3.35
0.50
113.10
116.45
A
A
A
N7
C8
N9
DG
DG
DG
12
12
12
N
6
-2.45
0.40
106.40
103.95
A
A
A
C8
N9
C4
DG
DG
DG
12
12
12
N
6
7.69
0.30
108.30
115.99
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
6
3.15
0.50
113.10
116.25
B
B
B
N7
C8
N9
DG
DG
DG
14
14
14
N
6
4.34
0.30
108.30
112.64
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
6
-5.16
0.80
105.90
100.74
B
B
B
O4'
C1'
C2'
DA
DA
DA
18
18
18
N
6
3.22
0.50
113.80
117.02
B
B
B
N7
C8
N9
DA
DA
DA
18
18
18
N
6
2.13
0.30
108.30
110.43
B
B
B
O4'
C1'
N9
DA
DA
DA
20
20
20
N
6
2.37
0.30
108.30
110.67
B
B
B
O4'
C1'
N1
DC
DC
DC
21
21
21
N
6
3.21
0.50
113.10
116.31
B
B
B
N7
C8
N9
DG
DG
DG
24
24
24
N
6
-5.06
0.80
102.40
97.34
B
B
B
C3'
C2'
C1'
DG
DG
DG
26
26
26
N
6
2.84
0.30
108.30
111.14
B
B
B
O4'
C1'
N9
DG
DG
DG
26
26
26
N
1
A
A
C4
N4
DC
DC
1
1
0.094
0.009
1.335
1.429
N
1
A
A
C2
N2
DG
DG
2
2
0.083
0.010
1.341
1.424
N
1
A
A
C4
N4
DC
DC
3
3
0.093
0.009
1.335
1.428
N
1
A
A
C6
N6
DA
DA
4
4
0.093
0.008
1.335
1.428
N
1
A
A
C5
C7
DT
DT
5
5
0.037
0.006
1.496
1.533
N
1
A
A
C2
N2
DG
DG
6
6
0.086
0.010
1.341
1.427
N
1
A
A
C2
N2
DG
DG
8
8
0.078
0.010
1.341
1.419
N
1
A
A
C5
C7
DT
DT
9
9
0.036
0.006
1.496
1.532
N
1
A
A
C6
N6
DA
DA
10
10
0.092
0.008
1.335
1.427
N
1
A
A
C4
N4
DC
DC
11
11
0.096
0.009
1.335
1.431
N
1
A
A
C2
N2
DG
DG
12
12
0.084
0.010
1.341
1.425
N
1
A
A
C4
N4
DC
DC
13
13
0.093
0.009
1.335
1.428
N
1
B
B
C2
N2
DG
DG
14
14
0.081
0.010
1.341
1.422
N
1
B
B
C4
N4
DC
DC
15
15
0.093
0.009
1.335
1.428
N
1
B
B
C2
N2
DG
DG
16
16
0.080
0.010
1.341
1.421
N
1
B
B
C6
N6
DA
DA
18
18
0.096
0.008
1.335
1.431
N
1
B
B
C6
N6
DA
DA
20
20
0.094
0.008
1.335
1.429
N
1
B
B
C4
N4
DC
DC
21
21
0.094
0.009
1.335
1.429
N
1
B
B
C6
N6
DA
DA
22
22
0.092
0.008
1.335
1.427
N
1
B
B
C5
C7
DT
DT
23
23
0.038
0.006
1.496
1.534
N
1
B
B
C2
N2
DG
DG
24
24
0.084
0.010
1.341
1.425
N
1
B
B
C4
N4
DC
DC
25
25
0.093
0.009
1.335
1.428
N
1
B
B
C2
N2
DG
DG
26
26
0.085
0.010
1.341
1.426
N
2
A
A
C4
N4
DC
DC
1
1
0.095
0.009
1.335
1.430
N
2
A
A
C2
N2
DG
DG
2
2
0.081
0.010
1.341
1.422
N
2
A
A
C4
N4
DC
DC
3
3
0.093
0.009
1.335
1.428
N
2
A
A
C6
N6
DA
DA
4
4
0.094
0.008
1.335
1.429
N
2
A
A
C5
C7
DT
DT
5
5
0.036
0.006
1.496
1.532
N
2
A
A
C2
N2
DG
DG
6
6
0.085
0.010
1.341
1.426
N
2
A
A
C2
N2
DG
DG
8
8
0.078
0.010
1.341
1.419
N
2
A
A
C5
C7
DT
DT
9
9
0.038
0.006
1.496
1.534
N
2
A
A
C6
N6
DA
DA
10
10
0.092
0.008
1.335
1.427
N
2
A
A
C4
N4
DC
DC
11
11
0.098
0.009
1.335
1.433
N
2
A
A
C2
N2
DG
DG
12
12
0.083
0.010
1.341
1.424
N
2
A
A
C4
N4
DC
DC
13
13
0.093
0.009
1.335
1.428
N
2
B
B
C2
N2
DG
DG
14
14
0.079
0.010
1.341
1.420
N
2
B
B
C4
N4
DC
DC
15
15
0.092
0.009
1.335
1.427
N
2
B
B
C2
N2
DG
DG
16
16
0.080
0.010
1.341
1.421
N
2
B
B
C6
N6
DA
DA
18
18
0.095
0.008
1.335
1.430
N
2
B
B
C6
N6
DA
DA
20
20
0.096
0.008
1.335
1.431
N
2
B
B
C4
N4
DC
DC
21
21
0.095
0.009
1.335
1.430
N
2
B
B
C6
N6
DA
DA
22
22
0.095
0.008
1.335
1.430
N
2
B
B
C5
C7
DT
DT
23
23
0.038
0.006
1.496
1.534
N
2
B
B
C2
N2
DG
DG
24
24
0.084
0.010
1.341
1.425
N
2
B
B
C4
N4
DC
DC
25
25
0.095
0.009
1.335
1.430
N
2
B
B
C2
N2
DG
DG
26
26
0.084
0.010
1.341
1.425
N
3
A
A
C4
N4
DC
DC
1
1
0.093
0.009
1.335
1.428
N
3
A
A
C2
N2
DG
DG
2
2
0.083
0.010
1.341
1.424
N
3
A
A
C4
N4
DC
DC
3
3
0.094
0.009
1.335
1.429
N
3
A
A
C6
N6
DA
DA
4
4
0.093
0.008
1.335
1.428
N
3
A
A
C2
N2
DG
DG
6
6
0.086
0.010
1.341
1.427
N
3
A
A
C2
N2
DG
DG
8
8
0.068
0.010
1.341
1.409
N
3
A
A
C5
C7
DT
DT
9
9
0.037
0.006
1.496
1.533
N
3
A
A
C6
N6
DA
DA
10
10
0.092
0.008
1.335
1.427
N
3
A
A
C4
N4
DC
DC
11
11
0.096
0.009
1.335
1.431
N
3
A
A
C2
N2
DG
DG
12
12
0.083
0.010
1.341
1.424
N
3
A
A
C4
N4
DC
DC
13
13
0.094
0.009
1.335
1.429
N
3
B
B
C2
N2
DG
DG
14
14
0.078
0.010
1.341
1.419
N
3
B
B
C4
N4
DC
DC
15
15
0.093
0.009
1.335
1.428
N
3
B
B
C2
N2
DG
DG
16
16
0.080
0.010
1.341
1.421
N
3
B
B
C5
C7
DT
DT
17
17
0.037
0.006
1.496
1.533
N
3
B
B
C6
N6
DA
DA
18
18
0.094
0.008
1.335
1.429
N
3
B
B
C6
N6
DA
DA
20
20
0.093
0.008
1.335
1.428
N
3
B
B
C4
N4
DC
DC
21
21
0.094
0.009
1.335
1.429
N
3
B
B
C6
N6
DA
DA
22
22
0.094
0.008
1.335
1.429
N
3
B
B
C5
C7
DT
DT
23
23
0.038
0.006
1.496
1.534
N
3
B
B
C2
N2
DG
DG
24
24
0.084
0.010
1.341
1.425
N
3
B
B
C4
N4
DC
DC
25
25
0.093
0.009
1.335
1.428
N
3
B
B
C2
N2
DG
DG
26
26
0.083
0.010
1.341
1.424
N
4
A
A
C4
N4
DC
DC
1
1
0.096
0.009
1.335
1.431
N
4
A
A
C2
N2
DG
DG
2
2
0.083
0.010
1.341
1.424
N
4
A
A
C4
N4
DC
DC
3
3
0.093
0.009
1.335
1.428
N
4
A
A
C6
N6
DA
DA
4
4
0.093
0.008
1.335
1.428
N
4
A
A
C5
C7
DT
DT
5
5
0.037
0.006
1.496
1.533
N
4
A
A
C2
N2
DG
DG
6
6
0.085
0.010
1.341
1.426
N
4
A
A
C2
N2
DG
DG
8
8
0.076
0.010
1.341
1.417
N
4
A
A
C5
C7
DT
DT
9
9
0.038
0.006
1.496
1.534
N
4
A
A
C6
N6
DA
DA
10
10
0.090
0.008
1.335
1.425
N
4
A
A
C4
N4
DC
DC
11
11
0.096
0.009
1.335
1.431
N
4
A
A
C2
N2
DG
DG
12
12
0.084
0.010
1.341
1.425
N
4
A
A
C4
N4
DC
DC
13
13
0.094
0.009
1.335
1.429
N
4
B
B
C2
N2
DG
DG
14
14
0.079
0.010
1.341
1.420
N
4
B
B
C4
N4
DC
DC
15
15
0.093
0.009
1.335
1.428
N
4
B
B
C2
N2
DG
DG
16
16
0.080
0.010
1.341
1.421
N
4
B
B
C6
N6
DA
DA
18
18
0.096
0.008
1.335
1.431
N
4
B
B
C6
N6
DA
DA
20
20
0.095
0.008
1.335
1.430
N
4
B
B
C4
N4
DC
DC
21
21
0.093
0.009
1.335
1.428
N
4
B
B
C6
N6
DA
DA
22
22
0.092
0.008
1.335
1.427
N
4
B
B
C2
N2
DG
DG
24
24
0.084
0.010
1.341
1.425
N
4
B
B
C4
N4
DC
DC
25
25
0.094
0.009
1.335
1.429
N
4
B
B
C2
N2
DG
DG
26
26
0.082
0.010
1.341
1.423
N
5
A
A
C4
N4
DC
DC
1
1
0.095
0.009
1.335
1.430
N
5
A
A
C2
N2
DG
DG
2
2
0.083
0.010
1.341
1.424
N
5
A
A
C4
N4
DC
DC
3
3
0.093
0.009
1.335
1.428
N
5
A
A
C6
N6
DA
DA
4
4
0.092
0.008
1.335
1.427
N
5
A
A
C5
C7
DT
DT
5
5
0.036
0.006
1.496
1.532
N
5
A
A
C2
N2
DG
DG
6
6
0.086
0.010
1.341
1.427
N
5
A
A
C2
N2
DG
DG
8
8
0.069
0.010
1.341
1.410
N
5
A
A
C5
C7
DT
DT
9
9
0.037
0.006
1.496
1.533
N
5
A
A
C6
N6
DA
DA
10
10
0.091
0.008
1.335
1.426
N
5
A
A
C4
N4
DC
DC
11
11
0.095
0.009
1.335
1.430
N
5
A
A
C2
N2
DG
DG
12
12
0.082
0.010
1.341
1.423
N
5
A
A
C4
N4
DC
DC
13
13
0.093
0.009
1.335
1.428
N
5
B
B
C2
N2
DG
DG
14
14
0.079
0.010
1.341
1.420
N
5
B
B
C4
N4
DC
DC
15
15
0.093
0.009
1.335
1.428
N
5
B
B
C2
N2
DG
DG
16
16
0.080
0.010
1.341
1.421
N
5
B
B
C6
N6
DA
DA
18
18
0.092
0.008
1.335
1.427
N
5
B
B
C6
N6
DA
DA
20
20
0.095
0.008
1.335
1.430
N
5
B
B
C4
N4
DC
DC
21
21
0.094
0.009
1.335
1.429
N
5
B
B
C6
N6
DA
DA
22
22
0.093
0.008
1.335
1.428
N
5
B
B
C5
C7
DT
DT
23
23
0.037
0.006
1.496
1.533
N
5
B
B
C2
N2
DG
DG
24
24
0.085
0.010
1.341
1.426
N
5
B
B
C4
N4
DC
DC
25
25
0.093
0.009
1.335
1.428
N
5
B
B
C2
N2
DG
DG
26
26
0.084
0.010
1.341
1.425
N
6
A
A
C4
N4
DC
DC
1
1
0.095
0.009
1.335
1.430
N
6
A
A
C2
N2
DG
DG
2
2
0.083
0.010
1.341
1.424
N
6
A
A
C4
N4
DC
DC
3
3
0.094
0.009
1.335
1.429
N
6
A
A
C6
N6
DA
DA
4
4
0.093
0.008
1.335
1.428
N
6
A
A
C5
C7
DT
DT
5
5
0.036
0.006
1.496
1.532
N
6
A
A
C2
N2
DG
DG
6
6
0.086
0.010
1.341
1.427
N
6
A
A
C2
N2
DG
DG
8
8
0.079
0.010
1.341
1.420
N
6
A
A
C5
C7
DT
DT
9
9
0.039
0.006
1.496
1.535
N
6
A
A
C6
N6
DA
DA
10
10
0.091
0.008
1.335
1.426
N
6
A
A
C4
N4
DC
DC
11
11
0.097
0.009
1.335
1.432
N
6
A
A
C2
N2
DG
DG
12
12
0.083
0.010
1.341
1.424
N
6
A
A
C4
N4
DC
DC
13
13
0.094
0.009
1.335
1.429
N
6
B
B
C2
N2
DG
DG
14
14
0.079
0.010
1.341
1.420
N
6
B
B
C4
N4
DC
DC
15
15
0.093
0.009
1.335
1.428
N
6
B
B
C2
N2
DG
DG
16
16
0.080
0.010
1.341
1.421
N
6
B
B
C6
N6
DA
DA
18
18
0.094
0.008
1.335
1.429
N
6
B
B
C6
N6
DA
DA
20
20
0.093
0.008
1.335
1.428
N
6
B
B
C4
N4
DC
DC
21
21
0.091
0.009
1.335
1.426
N
6
B
B
C6
N6
DA
DA
22
22
0.092
0.008
1.335
1.427
N
6
B
B
C5
C7
DT
DT
23
23
0.037
0.006
1.496
1.533
N
6
B
B
C2
N2
DG
DG
24
24
0.084
0.010
1.341
1.425
N
6
B
B
C4
N4
DC
DC
25
25
0.093
0.009
1.335
1.428
N
6
B
B
C2
N2
DG
DG
26
26
0.084
0.010
1.341
1.425
N
STRUCTURE OF A DNA DUPLEX CONTAINING A BISTRAND ABASIC SITE LESION STAGGERED IN A 5'-ORIENTATION.
1
N
N
2
N
N
covale
1.616
both
A
DG
6
A
O3'
DG
6
1_555
A
3DR
7
A
P
3DR
7
1_555
covale
1.617
both
A
3DR
7
A
O3'
3DR
7
1_555
A
DG
8
A
P
DG
8
1_555
covale
1.619
both
B
DA
18
B
O3'
DA
5
1_555
B
3DR
19
B
P
3DR
6
1_555
covale
1.616
both
B
3DR
19
B
O3'
3DR
6
1_555
B
DA
20
B
P
DA
7
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
26
B
N1
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
26
B
O6
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
26
B
N2
DG
13
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
25
B
N3
DC
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
25
B
O2
DC
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
25
B
N4
DC
12
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
24
B
N1
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
24
B
O6
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
24
B
N2
DG
11
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
23
B
N3
DT
10
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
23
B
O4
DT
10
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
DA
22
B
N1
DA
9
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
DA
22
B
N6
DA
9
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
DC
21
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
21
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
21
B
N4
DC
8
1_555
hydrog
DG-DA MISPAIR
A
DG
8
A
N2
DG
8
1_555
B
DA
18
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
9
A
N3
DT
9
1_555
B
DA
18
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
9
1_555
B
DA
18
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N1
DA
10
1_555
B
DT
17
B
N3
DT
4
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N6
DA
10
1_555
B
DT
17
B
O4
DT
4
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
16
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
16
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
16
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N1
DG
12
1_555
B
DC
15
B
N3
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N2
DG
12
1_555
B
DC
15
B
O2
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
12
A
O6
DG
12
1_555
B
DC
15
B
N4
DC
2
1_555
hydrog
WATSON-CRICK
A
DC
13
A
N3
DC
13
1_555
B
DG
14
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
13
A
N4
DC
13
1_555
B
DG
14
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
13
A
O2
DC
13
1_555
B
DG
14
B
N2
DG
1
1_555
DNA
double helix, abasic sites, clustered damage, extruded residues., DNA
1HT7
PDB
1
1HT7
1HT7
PDB
2
1HT7
1
13
1HT7
1
13
1HT7
A
1
1
13
14
26
1HT7
14
26
1HT7
B
2
1
13
1
P 1