1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Hoehn, S.T.
Turner, C.J.
Stubbe, J.
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
C5 H11 O7 P
214.110
2-DEOXY-5-PHOSPHONO-RIBOSE
saccharide
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
29
3413
3423
10.1093/nar/29.16.3413
11504879
Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation.
2001
10.2210/pdb1g5d/pdb
pdb_00001g5d
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
3892.526
5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*TP*GP*GP*G)-3'
1
syn
polymer
3942.572
5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'
1
syn
polymer
no
yes
(DC)(DC)(DA)(DA)(DA)(DG)(ORP)(DA)(DC)(DT)(DG)(DG)(DG)
CCAAAGXACTGGG
A
polydeoxyribonucleotide
no
no
(DC)(DC)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DT)(DG)(DG)
CCCAGTACTTTGG
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
39.797
1
19
A
1
B
26
-0.296
A_DC1:DG26_B
1
-28.551
0.654
-0.456
-0.110
27.111
1
19
A
2
B
25
-1.085
A_DC2:DG25_B
2
-23.866
0.406
-0.368
-0.181
-17.235
1
20
A
3
B
24
1.207
A_DA3:DT24_B
3
-11.896
0.074
-0.057
-0.178
-15.443
1
20
A
4
B
23
-0.261
A_DA4:DT23_B
4
-6.528
-0.041
0.037
-0.208
-13.876
1
20
A
5
B
22
-7.257
A_DA5:DT22_B
5
-1.433
-0.054
0.114
-0.187
1.014
1
19
A
6
B
21
-4.516
A_DG6:DC21_B
6
-9.657
-0.593
0.454
-0.369
8.826
1
20
A
8
B
19
-10.639
A_DA8:DT19_B
7
-5.710
0.114
0.270
-0.109
8.731
1
19
A
9
B
18
-1.124
A_DC9:DG18_B
8
-7.980
0.460
0.466
-0.270
8.515
1
20
A
10
B
17
-0.951
A_DT10:DA17_B
9
-7.538
-0.156
0.163
-0.198
-14.142
1
19
A
11
B
16
-1.219
A_DG11:DC16_B
10
-18.270
-0.234
0.033
-0.242
-29.166
1
19
A
12
B
15
-1.459
A_DG12:DC15_B
11
-22.952
-0.490
-0.065
-0.195
-25.304
1
19
A
13
B
14
-3.516
A_DG13:DC14_B
12
-10.436
-0.617
0.136
-0.260
3.694
38.501
A
A
1
2
2.924
B
B
26
25
3.693
1.927
0.760
-0.282
AA_DC1DC2:DG25DG26_BB
1
1.066
-1.617
38.440
-0.697
-1.003
3.754
45.563
A
A
2
3
16.133
B
B
25
24
4.071
12.353
0.310
-0.699
AA_DC2DA3:DT24DG25_BB
2
0.228
-0.298
43.942
-2.227
-0.376
3.230
37.019
A
A
3
4
-4.984
B
B
24
23
3.198
-3.161
-0.292
-0.457
AA_DA3DA4:DT23DT24_BB
3
-0.685
1.080
36.882
-0.302
0.369
3.278
33.985
A
A
4
5
-2.240
B
B
23
22
3.219
-1.308
-0.712
-0.469
AA_DA4DA5:DT22DT23_BB
4
-2.572
4.405
33.866
-0.594
0.809
2.999
34.918
A
A
5
6
-10.285
B
B
22
21
2.928
-6.136
-0.470
-0.515
AA_DA5DG6:DC21DT22_BB
5
-2.529
4.239
34.301
-0.010
0.434
6.114
84.547
A
A
6
8
-10.467
B
B
21
19
6.232
-14.027
-0.393
0.533
AA_DG6DA8:DT19DC21_BB
6
-7.416
5.534
83.322
1.021
-0.039
3.301
35.650
A
A
8
9
-4.212
B
B
19
18
3.334
-2.574
0.257
-0.063
AA_DA8DC9:DG18DT19_BB
7
-2.788
4.563
35.454
0.278
-0.831
3.460
36.266
A
A
9
10
-11.562
B
B
18
17
3.332
-7.150
0.161
-0.973
AA_DC9DT10:DA17DG18_BB
8
1.652
-2.671
35.541
-0.512
-0.015
3.619
41.548
A
A
10
11
4.618
B
B
17
16
3.691
3.270
-0.177
-0.872
AA_DT10DG11:DC16DA17_BB
9
-2.707
3.822
41.340
-1.618
-0.072
3.341
39.322
A
A
11
12
8.304
B
B
16
15
3.507
5.568
-0.132
-0.904
AA_DG11DG12:DC15DC16_BB
10
1.857
-2.769
38.898
-2.039
0.429
3.172
39.115
A
A
12
13
-0.454
B
B
15
14
3.146
-0.304
-0.617
-0.310
AA_DG12DG13:DC14DC15_BB
11
-1.750
2.615
39.076
-0.428
0.718
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
2001-08-22
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
Apyrimidinic Dna With Bound Water At The Damaged Site, Alpha Form, Nmr, 1 Structure
Apyrimidinic Dna With Bound Water At The Damaged Site, Beta Form, Nmr, 1 Structure
Minimized Average Structure: NMR Structure of an Oligonucleotide Containing an Abasic Site: Alpha Anomer
Ensemble: NMR Structure of an Oligonucleotide Containing an Abasic Site: Beta Anomer
Minimized average structure: NMR Structure of an Oligonucleotide Containing an Abasic Site: Beta Anomer
RCSB
Y
RCSB
2000-10-31
REL
The abasic site deoxyribose 1H-1H coupling constants and the DNA 31P-H3' coupling constants were experimentally determined. This information was used in the modeling protocol.
all calculated structures submitted
10
10
NOESY
PE-COSY
watergate-NOESY
31P-HCOSY
31P-decoupled-PE-COSY
31P-decoupled-J-scaled-DQCOSY
10 mM sodium phosphate buffer
6.8
ambient
293
K
10 mM sodium phosphate buffer
6.8
ambient
278
K
10 mM sodium phosphate buffer
6.8
ambient
298
K
The structure is based on 475 NOE-derived distance constraints and 101 dihedral angle restraints.
molecular dynamics
2.5 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer
D2O
2.5 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer
10% D2O, 90% H2O
3 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer
D2O
Brunger
structure solution
X-PLOR
3.851
MSI
processing
Felix
95.0
MSI
data analysis
Felix
95.0
Brunger
refinement
X-PLOR
3.851
750
Home-built
home-built
600
Home-built
home-built
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
A
3
n
3
DA
3
A
A
4
n
4
DA
4
A
A
5
n
5
DA
5
A
G
6
n
6
DG
6
A
D1P
7
n
7
ORP
7
A
A
8
n
8
DA
8
A
C
9
n
9
DC
9
A
T
10
n
10
DT
10
A
G
11
n
11
DG
11
A
G
12
n
12
DG
12
A
G
13
n
13
DG
13
A
C
14
n
1
DC
14
B
C
15
n
2
DC
15
B
C
16
n
3
DC
16
B
A
17
n
4
DA
17
B
G
18
n
5
DG
18
B
T
19
n
6
DT
19
B
A
20
n
7
DA
20
B
C
21
n
8
DC
21
B
T
22
n
9
DT
22
B
T
23
n
10
DT
23
B
T
24
n
11
DT
24
B
G
25
n
12
DG
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
DA
8
0.083
SIDE CHAIN
1
A
DC
9
0.072
SIDE CHAIN
1
A
DG
11
0.075
SIDE CHAIN
1
B
DA
20
0.057
SIDE CHAIN
1
B
DT
22
0.058
SIDE CHAIN
1
B
DT
23
0.063
SIDE CHAIN
1
B
DG
25
0.055
SIDE CHAIN
2
A
DG
6
0.082
SIDE CHAIN
2
A
DA
8
0.097
SIDE CHAIN
2
A
DT
10
0.068
SIDE CHAIN
2
A
DG
11
0.086
SIDE CHAIN
2
B
DC
16
0.071
SIDE CHAIN
2
B
DA
20
0.062
SIDE CHAIN
2
B
DG
25
0.082
SIDE CHAIN
3
A
DG
6
0.091
SIDE CHAIN
3
A
DA
8
0.105
SIDE CHAIN
3
A
DG
11
0.086
SIDE CHAIN
3
B
DC
16
0.068
SIDE CHAIN
3
B
DG
25
0.082
SIDE CHAIN
4
A
DG
6
0.088
SIDE CHAIN
4
A
DA
8
0.076
SIDE CHAIN
4
A
DC
9
0.081
SIDE CHAIN
4
A
DG
11
0.082
SIDE CHAIN
4
B
DG
25
0.076
SIDE CHAIN
5
A
DG
6
0.079
SIDE CHAIN
5
A
DG
11
0.085
SIDE CHAIN
5
B
DG
25
0.080
SIDE CHAIN
6
A
DG
6
0.093
SIDE CHAIN
6
A
DA
8
0.099
SIDE CHAIN
6
A
DC
9
0.076
SIDE CHAIN
6
A
DG
11
0.074
SIDE CHAIN
6
B
DA
20
0.058
SIDE CHAIN
6
B
DG
25
0.085
SIDE CHAIN
7
A
DG
6
0.091
SIDE CHAIN
7
A
DA
8
0.104
SIDE CHAIN
7
A
DG
11
0.086
SIDE CHAIN
7
B
DC
16
0.067
SIDE CHAIN
7
B
DG
25
0.077
SIDE CHAIN
8
A
DG
6
0.093
SIDE CHAIN
8
A
DA
8
0.098
SIDE CHAIN
8
A
DC
9
0.080
SIDE CHAIN
8
A
DG
11
0.073
SIDE CHAIN
8
A
DG
13
0.056
SIDE CHAIN
8
B
DA
20
0.057
SIDE CHAIN
8
B
DG
25
0.090
SIDE CHAIN
9
A
DG
6
0.079
SIDE CHAIN
9
A
DA
8
0.090
SIDE CHAIN
9
A
DT
10
0.068
SIDE CHAIN
9
A
DG
11
0.085
SIDE CHAIN
9
B
DC
16
0.076
SIDE CHAIN
9
B
DA
20
0.068
SIDE CHAIN
9
B
DG
25
0.081
SIDE CHAIN
10
A
DG
6
0.096
SIDE CHAIN
10
A
DA
8
0.108
SIDE CHAIN
10
A
DG
11
0.082
SIDE CHAIN
10
B
DG
25
0.077
SIDE CHAIN
1
4.03
0.60
118.60
122.63
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
1
5.45
0.60
118.60
124.05
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
1
-4.91
0.80
123.70
118.79
A
A
A
C5
C6
N6
DA
DA
DA
5
5
5
N
1
5.38
0.70
119.90
125.28
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
1
5.26
0.60
118.60
123.86
A
A
A
N1
C6
N6
DA
DA
DA
8
8
8
N
1
-5.06
0.80
123.70
118.64
A
A
A
C5
C6
N6
DA
DA
DA
8
8
8
N
1
5.12
0.70
119.90
125.02
A
A
A
N3
C2
N2
DG
DG
DG
12
12
12
N
1
4.91
0.70
119.90
124.81
A
A
A
N3
C2
N2
DG
DG
DG
13
13
13
N
1
4.31
0.60
118.60
122.91
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
1
7.72
1.20
119.70
127.42
B
B
B
C3'
O3'
P
DA
DA
DG
17
17
18
Y
1
4.71
0.70
119.90
124.61
B
B
B
N3
C2
N2
DG
DG
DG
18
18
18
N
1
5.12
0.60
118.60
123.72
B
B
B
N1
C6
N6
DA
DA
DA
20
20
20
N
1
9.66
1.20
119.70
129.36
B
B
B
C3'
O3'
P
DC
DC
DT
21
21
22
Y
1
4.48
0.70
119.90
124.38
B
B
B
N3
C2
N2
DG
DG
DG
25
25
25
N
1
4.85
0.70
119.90
124.75
B
B
B
N3
C2
N2
DG
DG
DG
26
26
26
N
2
3.89
0.60
118.60
122.49
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
2
5.06
0.60
118.60
123.66
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
2
4.49
0.70
119.90
124.39
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
2
4.88
0.60
118.60
123.48
A
A
A
N1
C6
N6
DA
DA
DA
8
8
8
N
2
4.49
0.70
119.90
124.39
A
A
A
N3
C2
N2
DG
DG
DG
12
12
12
N
2
4.96
0.70
119.90
124.86
A
A
A
N3
C2
N2
DG
DG
DG
13
13
13
N
2
2.70
0.30
108.30
111.00
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
2
4.21
0.60
118.60
122.81
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
2
7.49
1.20
119.70
127.19
B
B
B
C3'
O3'
P
DA
DA
DG
17
17
18
Y
2
4.38
0.70
119.90
124.28
B
B
B
N3
C2
N2
DG
DG
DG
18
18
18
N
2
9.31
1.20
119.70
129.01
B
B
B
C3'
O3'
P
DC
DC
DT
21
21
22
Y
2
4.66
0.70
119.90
124.56
B
B
B
N3
C2
N2
DG
DG
DG
26
26
26
N
3
3.94
0.60
118.60
122.54
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
3
4.94
0.60
118.60
123.54
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
3
5.37
0.70
119.90
125.27
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
3
4.25
0.60
118.60
122.85
A
A
A
N1
C6
N6
DA
DA
DA
8
8
8
N
3
4.45
0.70
119.90
124.35
A
A
A
N3
C2
N2
DG
DG
DG
12
12
12
N
3
5.01
0.70
119.90
124.91
A
A
A
N3
C2
N2
DG
DG
DG
13
13
13
N
3
2.98
0.30
108.30
111.28
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
3
3.85
0.60
118.60
122.45
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
3
4.39
0.70
119.90
124.29
B
B
B
N3
C2
N2
DG
DG
DG
18
18
18
N
3
4.19
0.60
118.60
122.79
B
B
B
N1
C6
N6
DA
DA
DA
20
20
20
N
3
9.29
1.20
119.70
128.99
B
B
B
C3'
O3'
P
DC
DC
DT
21
21
22
Y
3
5.06
0.70
119.90
124.96
B
B
B
N3
C2
N2
DG
DG
DG
26
26
26
N
4
4.01
0.60
118.60
122.61
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
4
5.07
0.60
118.60
123.67
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
4
5.17
0.70
119.90
125.07
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
4
5.20
0.60
118.60
123.80
A
A
A
N1
C6
N6
DA
DA
DA
8
8
8
N
4
5.04
0.70
119.90
124.94
A
A
A
N3
C2
N2
DG
DG
DG
12
12
12
N
4
5.92
0.70
119.90
125.82
A
A
A
N3
C2
N2
DG
DG
DG
13
13
13
N
4
3.86
0.30
108.30
112.16
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
4
4.83
0.60
118.60
123.43
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
4
4.94
0.70
119.90
124.84
B
B
B
N3
C2
N2
DG
DG
DG
18
18
18
N
4
3.87
0.60
118.60
122.47
B
B
B
N1
C6
N6
DA
DA
DA
20
20
20
N
4
9.16
1.20
119.70
128.86
B
B
B
C3'
O3'
P
DC
DC
DT
21
21
22
Y
4
4.75
0.70
119.90
124.65
B
B
B
N3
C2
N2
DG
DG
DG
26
26
26
N
5
4.05
0.60
118.60
122.65
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
5
3.70
0.60
118.60
122.30
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
5
5.25
0.60
118.60
123.85
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
5
5.28
0.70
119.90
125.18
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
5
5.61
0.60
118.60
124.21
A
A
A
N1
C6
N6
DA
DA
DA
8
8
8
N
5
-5.33
0.80
123.70
118.37
A
A
A
C5
C6
N6
DA
DA
DA
8
8
8
N
5
5.59
0.70
119.90
125.49
A
A
A
N3
C2
N2
DG
DG
DG
12
12
12
N
5
5.93
0.70
119.90
125.83
A
A
A
N3
C2
N2
DG
DG
DG
13
13
13
N
5
4.15
0.30
108.30
112.45
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
5
4.37
0.60
118.60
122.97
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
5
7.32
1.20
119.70
127.02
B
B
B
C3'
O3'
P
DT
DT
DA
19
19
20
Y
5
10.48
1.20
119.70
130.18
B
B
B
C3'
O3'
P
DC
DC
DT
21
21
22
Y
5
4.95
0.70
119.90
124.85
B
B
B
N3
C2
N2
DG
DG
DG
26
26
26
N
6
3.91
0.60
118.60
122.51
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
6
5.02
0.60
118.60
123.62
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
6
5.10
0.70
119.90
125.00
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
6
4.50
0.60
118.60
123.10
A
A
A
N1
C6
N6
DA
DA
DA
8
8
8
N
6
5.77
0.70
119.90
125.67
A
A
A
N3
C2
N2
DG
DG
DG
13
13
13
N
6
3.17
0.30
108.30
111.47
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
6
3.70
0.60
118.90
122.60
B
B
B
N1
C2
O2
DC
DC
DC
14
14
14
N
6
4.08
0.60
118.60
122.68
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
6
4.95
0.70
119.90
124.85
B
B
B
N3
C2
N2
DG
DG
DG
18
18
18
N
6
3.97
0.60
118.60
122.57
B
B
B
N1
C6
N6
DA
DA
DA
20
20
20
N
6
8.69
1.20
119.70
128.39
B
B
B
C3'
O3'
P
DC
DC
DT
21
21
22
Y
6
4.79
0.70
119.90
124.69
B
B
B
N3
C2
N2
DG
DG
DG
26
26
26
N
7
3.98
0.60
118.60
122.58
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
7
5.13
0.60
118.60
123.73
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
7
5.48
0.70
119.90
125.38
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
7
4.20
0.60
118.60
122.80
A
A
A
N1
C6
N6
DA
DA
DA
8
8
8
N
7
4.42
0.70
119.90
124.32
A
A
A
N3
C2
N2
DG
DG
DG
12
12
12
N
7
4.95
0.70
119.90
124.85
A
A
A
N3
C2
N2
DG
DG
DG
13
13
13
N
7
2.98
0.30
108.30
111.28
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
7
3.83
0.60
118.60
122.43
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
7
4.22
0.70
119.90
124.12
B
B
B
N3
C2
N2
DG
DG
DG
18
18
18
N
7
4.42
0.60
118.60
123.02
B
B
B
N1
C6
N6
DA
DA
DA
20
20
20
N
7
8.98
1.20
119.70
128.68
B
B
B
C3'
O3'
P
DC
DC
DT
21
21
22
Y
7
4.72
0.70
119.90
124.62
B
B
B
N3
C2
N2
DG
DG
DG
26
26
26
N
8
3.88
0.60
118.60
122.48
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
8
5.04
0.60
118.60
123.64
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
8
5.12
0.70
119.90
125.02
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
8
4.50
0.60
118.60
123.10
A
A
A
N1
C6
N6
DA
DA
DA
8
8
8
N
8
5.60
0.70
119.90
125.50
A
A
A
N3
C2
N2
DG
DG
DG
13
13
13
N
8
3.30
0.30
108.30
111.60
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
8
4.40
0.60
118.60
123.00
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
8
5.03
0.70
119.90
124.93
B
B
B
N3
C2
N2
DG
DG
DG
18
18
18
N
8
3.98
0.60
118.60
122.58
B
B
B
N1
C6
N6
DA
DA
DA
20
20
20
N
8
8.61
1.20
119.70
128.31
B
B
B
C3'
O3'
P
DC
DC
DT
21
21
22
Y
8
4.24
0.70
119.90
124.14
B
B
B
N3
C2
N2
DG
DG
DG
25
25
25
N
8
4.81
0.70
119.90
124.71
B
B
B
N3
C2
N2
DG
DG
DG
26
26
26
N
9
3.93
0.60
118.60
122.53
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
9
5.04
0.60
118.60
123.64
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
9
4.49
0.70
119.90
124.39
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
9
5.10
0.60
118.60
123.70
A
A
A
N1
C6
N6
DA
DA
DA
8
8
8
N
9
5.40
0.70
119.90
125.30
A
A
A
N3
C2
N2
DG
DG
DG
12
12
12
N
9
4.69
0.70
119.90
124.59
A
A
A
N3
C2
N2
DG
DG
DG
13
13
13
N
9
4.54
0.60
118.60
123.14
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
9
7.38
1.20
119.70
127.08
B
B
B
C3'
O3'
P
DA
DA
DG
17
17
18
Y
9
4.39
0.70
119.90
124.29
B
B
B
N3
C2
N2
DG
DG
DG
18
18
18
N
9
9.24
1.20
119.70
128.94
B
B
B
C3'
O3'
P
DC
DC
DT
21
21
22
Y
9
4.86
0.70
119.90
124.76
B
B
B
N3
C2
N2
DG
DG
DG
26
26
26
N
10
3.97
0.60
118.60
122.57
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
10
5.11
0.60
118.60
123.71
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
10
5.35
0.70
119.90
125.25
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
10
4.63
0.60
118.60
123.23
A
A
A
N1
C6
N6
DA
DA
DA
8
8
8
N
10
4.64
0.70
119.90
124.54
A
A
A
N3
C2
N2
DG
DG
DG
12
12
12
N
10
5.47
0.70
119.90
125.37
A
A
A
N3
C2
N2
DG
DG
DG
13
13
13
N
10
1.81
0.30
108.30
110.11
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
10
4.30
0.60
118.60
122.90
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
10
4.54
0.70
119.90
124.44
B
B
B
N3
C2
N2
DG
DG
DG
18
18
18
N
10
4.17
0.60
118.60
122.77
B
B
B
N1
C6
N6
DA
DA
DA
20
20
20
N
10
9.19
1.20
119.70
128.89
B
B
B
C3'
O3'
P
DC
DC
DT
21
21
22
Y
10
4.24
0.70
119.90
124.14
B
B
B
N3
C2
N2
DG
DG
DG
25
25
25
N
10
4.84
0.70
119.90
124.74
B
B
B
N3
C2
N2
DG
DG
DG
26
26
26
N
1
A
A
N9
C4
DA
DA
4
4
0.037
0.006
1.374
1.411
N
1
A
A
C5'
C4'
DT
DT
10
10
0.044
0.007
1.512
1.556
N
1
B
B
C8
N9
DG
DG
25
25
-0.043
0.007
1.374
1.331
N
2
A
A
N9
C4
DA
DA
4
4
0.036
0.006
1.374
1.410
N
2
A
A
C5'
C4'
DT
DT
10
10
0.043
0.007
1.512
1.555
N
2
B
B
C5'
C4'
DT
DT
24
24
0.043
0.007
1.512
1.555
N
3
A
A
N9
C4
DA
DA
4
4
0.037
0.006
1.374
1.411
N
4
A
A
N9
C4
DA
DA
4
4
0.036
0.006
1.374
1.410
N
4
A
A
C5'
C4'
DT
DT
10
10
0.043
0.007
1.512
1.555
N
4
B
B
C5'
C4'
DC
DC
16
16
0.042
0.007
1.512
1.554
N
4
B
B
C5'
C4'
DT
DT
24
24
0.043
0.007
1.512
1.555
N
5
A
A
N9
C4
DA
DA
4
4
0.036
0.006
1.374
1.410
N
5
B
B
C5'
C4'
DC
DC
16
16
0.042
0.007
1.512
1.554
N
5
B
B
C5'
C4'
DA
DA
17
17
0.042
0.007
1.512
1.554
N
6
B
B
C5'
C4'
DT
DT
24
24
0.043
0.007
1.512
1.555
N
7
B
B
C5'
C4'
DT
DT
24
24
0.043
0.007
1.512
1.555
N
8
A
A
N9
C4
DA
DA
4
4
0.036
0.006
1.374
1.410
N
8
A
A
C5'
C4'
DT
DT
10
10
0.043
0.007
1.512
1.555
N
9
A
A
C5'
C4'
DT
DT
10
10
0.043
0.007
1.512
1.555
N
9
B
B
C5'
C4'
DA
DA
20
20
0.043
0.007
1.512
1.555
N
9
B
B
C5'
C4'
DT
DT
24
24
0.043
0.007
1.512
1.555
N
10
A
A
N9
C4
DA
DA
4
4
0.038
0.006
1.374
1.412
N
NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: ALPHA ANOMER
1
N
N
2
N
N
covale
1.580
both
A
DG
6
A
O3'
DG
6
1_555
A
ORP
7
A
P
ORP
7
1_555
covale
1.586
one
A
ORP
7
A
O3
ORP
7
1_555
A
DA
8
A
P
DA
8
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
DC
2
A
N3
DC
2
1_555
B
DG
25
B
N1
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
25
B
O6
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
25
B
N2
DG
12
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
24
B
N3
DT
11
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
24
B
O4
DT
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
DA
5
A
N1
DA
5
1_555
B
DT
22
B
N3
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
22
B
O4
DT
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
WATSON-CRICK
A
DA
8
A
N1
DA
8
1_555
B
DT
19
B
N3
DT
6
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N6
DA
8
1_555
B
DT
19
B
O4
DT
6
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
DG
18
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
18
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
18
B
N2
DG
5
1_555
hydrog
WATSON-CRICK
A
DT
10
A
N3
DT
10
1_555
B
DA
17
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
10
A
O4
DT
10
1_555
B
DA
17
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N1
DG
11
1_555
B
DC
16
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N2
DG
11
1_555
B
DC
16
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
11
A
O6
DG
11
1_555
B
DC
16
B
N4
DC
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
DG
13
A
N1
DG
13
1_555
B
DC
14
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
13
A
N2
DG
13
1_555
B
DC
14
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
13
A
O6
DG
13
1_555
B
DC
14
B
N4
DC
1
1_555
DNA
damaged DNA, apyrimidinic site, DNA
1G5D
PDB
1
1G5D
1G5D
PDB
2
1G5D
1
13
1G5D
1
13
1G5D
A
1
1
13
14
26
1G5D
14
26
1G5D
B
2
1
13