1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Beger, R.D.
Bolton, P.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C5 H11 O7 P
214.110
2'-DEOXY-RIBOFURANOSE-5'-MONOPHOSPHATE
ABASIC DEOXYRIBOSE
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
H2 O
18.015
WATER
non-polymer
N
1
N
P
N
2
N
O
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
R
C
N
10
N
O
N
11
N
C
N
12
S
C
N
13
N
O
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
H
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
O
N
26
N
P
N
27
N
O
N
28
N
O
N
29
N
O
N
30
N
C
N
31
R
C
N
32
N
O
N
33
S
C
N
34
N
O
N
35
N
C
N
36
R
C
Y
37
N
N
Y
38
N
C
Y
39
N
N
Y
40
N
C
Y
41
N
C
N
42
N
N
Y
43
N
N
Y
44
N
C
Y
45
N
N
Y
46
N
C
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
O
N
62
N
P
N
63
N
O
N
64
N
O
N
65
N
O
N
66
N
C
N
67
R
C
N
68
N
O
N
69
S
C
N
70
N
O
N
71
N
C
N
72
R
C
N
73
N
N
N
74
N
C
N
75
N
O
N
76
N
N
N
77
N
C
N
78
N
N
N
79
N
C
N
80
N
C
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
O
N
96
N
P
N
97
N
O
N
98
N
O
N
99
N
O
N
100
N
C
N
101
R
C
N
102
N
O
N
103
S
C
N
104
N
O
N
105
N
C
N
106
R
C
Y
107
N
N
Y
108
N
C
Y
109
N
N
Y
110
N
C
N
111
N
C
N
112
N
O
N
113
N
N
N
114
N
C
N
115
N
N
N
116
N
N
Y
117
N
C
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
O
N
133
N
P
N
134
N
O
N
135
N
O
N
136
N
O
N
137
N
C
N
138
R
C
N
139
N
O
N
140
S
C
N
141
N
O
N
142
N
C
N
143
R
C
N
144
N
N
N
145
N
C
N
146
N
O
N
147
N
N
N
148
N
C
N
149
N
O
N
150
N
C
N
151
N
C
N
152
N
C
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
O
N
169
N
H
N
170
N
H
N
1
N
sing
N
2
N
doub
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
doub
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
Y
48
N
sing
Y
49
N
sing
Y
50
N
doub
N
51
N
sing
Y
52
N
sing
Y
53
N
sing
Y
54
N
doub
N
55
N
sing
Y
56
N
doub
N
57
N
sing
N
58
N
sing
Y
59
N
sing
Y
60
N
doub
N
61
N
sing
Y
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
doub
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
doub
N
89
N
sing
N
90
N
doub
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
doub
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
doub
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
Y
121
N
sing
Y
122
N
sing
Y
123
N
doub
N
124
N
sing
Y
125
N
sing
N
126
N
sing
Y
127
N
doub
N
128
N
doub
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
doub
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
doub
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
doub
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
doub
N
167
N
sing
N
168
N
sing
N
169
N
doub
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
273
15565
15573
10.1074/jbc.273.25.15565
9624147
Structures of apurinic and apyrimidinic sites in duplex DNAs.
1998
10.2210/pdb1a9h/pdb
pdb_00001a9h
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3211.077
DNA (5'-D(*CP*GP*CP*GP*AP*AABP*AP*CP*GP*CP*C)-3')
1
syn
polymer
3366.184
DNA (5'-D(*GP*GP*CP*GP*TP*CP*TP*CP*GP*CP*G)-3')
1
syn
polymer
18.015
water
1
nat
water
no
yes
(DC)(DG)(DC)(DG)(DA)(AAB)(DA)(DC)(DG)(DC)(DC)
CGCGAXACGCC
A
polydeoxyribonucleotide
no
no
(DG)(DG)(DC)(DG)(DT)(DC)(DT)(DC)(DG)(DC)(DG)
GGCGTCTCGCG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-4.613
1
19
A
1
B
22
-0.630
A_DC1:DG22_B
1
-5.416
0.701
0.239
-0.594
-0.684
1
19
A
2
B
21
1.261
A_DG2:DC21_B
2
-7.385
-0.607
0.260
-0.545
-0.292
1
19
A
3
B
20
-0.516
A_DC3:DG20_B
3
-5.993
0.566
0.083
-0.452
5.628
1
19
A
4
B
19
-0.638
A_DG4:DC19_B
4
-12.971
-0.534
0.221
-0.344
19.268
1
20
A
5
B
18
-4.927
A_DA5:DT18_B
5
-4.457
0.106
0.393
-0.145
3.269
1
20
A
7
B
16
-1.102
A_DA7:DT16_B
6
-23.574
0.143
-0.184
-0.138
12.359
1
19
A
8
B
15
0.979
A_DC8:DG15_B
7
-18.542
0.359
-0.100
-0.226
5.726
1
19
A
9
B
14
0.168
A_DG9:DC14_B
8
-4.139
-0.430
0.298
-0.422
11.959
1
19
A
10
B
13
-0.178
A_DC10:DG13_B
9
-2.684
0.455
-0.153
-0.466
18.182
1
19
A
11
B
12
-3.311
A_DC11:DG12_B
10
-4.612
0.541
-0.490
-0.582
2.558
33.532
A
A
1
2
12.075
B
B
22
21
2.775
6.917
-0.427
-0.880
AA_DC1DG2:DC21DG22_BB
1
-1.518
2.650
32.796
-2.462
0.534
2.999
43.512
A
A
2
3
2.729
B
B
21
20
3.033
2.022
-0.300
-0.687
AA_DG2DC3:DG20DC21_BB
2
-0.014
0.019
43.467
-1.107
0.404
2.728
31.133
A
A
3
4
11.135
B
B
20
19
2.889
5.941
0.160
-0.593
AA_DC3DG4:DC19DG20_BB
3
-0.058
0.109
30.574
-2.088
-0.308
2.971
38.963
A
A
4
5
-1.508
B
B
19
18
2.887
-1.002
-0.823
-0.013
AA_DG4DA5:DT18DC19_BB
4
-5.555
8.355
38.568
0.090
0.628
2.933
35.495
A
A
7
8
-5.521
B
B
16
15
2.882
-3.360
1.162
-0.159
AA_DA7DC8:DG15DT16_BB
5
1.645
-2.703
35.303
0.178
-1.691
2.415
30.110
A
A
8
9
20.917
B
B
15
14
3.149
10.613
0.787
-1.202
AA_DC8DG9:DC14DG15_BB
6
-3.843
7.574
27.960
-4.231
-2.210
3.032
43.321
A
A
9
10
-1.765
B
B
14
13
3.038
-1.302
-0.421
-0.722
AA_DG9DC10:DG13DC14_BB
7
2.354
-3.191
43.241
-0.860
0.783
3.113
37.553
A
A
10
11
-3.773
B
B
13
12
3.070
-2.427
-0.504
-0.716
AA_DC10DC11:DG12DG13_BB
8
-0.339
0.526
37.476
-0.813
0.742
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Non-polymer description
Data collection
Database references
Derived calculations
Other
1
0
1998-07-15
1
1
2008-03-24
1
2
2011-07-13
1
3
2014-07-09
1
4
2024-04-10
_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
1998-04-06
REL
HOH
water
100MS NOESY, 250MS NOESY 250MS QUIETNOESY 70MS BAND-SELECTIVE J TOCSY FOR PHOSPHOROUS "J SCALE" SET TO 2 AND 3
AVERAGE OF 5 STRUCTURES THAT THE NOESY BACKCALCULATION AGREES WITH EXPERIMENTAL NOESY
100
1
NOESY
PECOSY
TOCSY
ROESY
QUIET-NOESY
50 mM KCL
7.0
1
atm
300
K
matrix relaxation
TRIS
BRUNGER
refinement
X-PLOR
3.1
structure solution
VNMR
400
Varian
UNITY
500
Varian
INOVA
HOH
23
3
HOH
HOH
23
A
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
G
4
n
4
DG
4
A
A
5
n
5
DA
5
A
AAB
6
n
6
AAB
6
A
A
7
n
7
DA
7
A
C
8
n
8
DC
8
A
G
9
n
9
DG
9
A
C
10
n
10
DC
10
A
C
11
n
11
DC
11
A
G
12
n
1
DG
12
B
G
13
n
2
DG
13
B
C
14
n
3
DC
14
B
G
15
n
4
DG
15
B
T
16
n
5
DT
16
B
C
17
n
6
DC
17
B
T
18
n
7
DT
18
B
C
19
n
8
DC
19
B
G
20
n
9
DG
20
B
C
21
n
10
DC
21
B
G
22
n
11
DG
22
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
B
C3'
DG
22
WRONG HAND
1
A
A
O1'
H1
AAB
HOH
6
23
1.59
1
4.34
0.60
106.00
110.34
A
A
A
O4'
C4'
C3'
DC
DC
DC
1
1
1
N
1
-5.39
0.80
105.90
100.51
A
A
A
O4'
C1'
C2'
DC
DC
DC
1
1
1
N
1
2.55
0.40
120.30
122.85
A
A
A
C6
N1
C2
DC
DC
DC
1
1
1
N
1
5.54
0.60
118.90
124.44
A
A
A
N1
C2
O2
DC
DC
DC
1
1
1
N
1
3.76
0.60
106.00
109.76
A
A
A
O4'
C4'
C3'
DG
DG
DG
2
2
2
N
1
-6.00
0.70
102.20
96.20
A
A
A
C4'
C3'
C2'
DG
DG
DG
2
2
2
N
1
7.94
1.20
119.70
127.64
A
A
A
C3'
O3'
P
DG
DG
DC
2
2
3
Y
1
3.97
0.60
106.00
109.97
A
A
A
O4'
C4'
C3'
DC
DC
DC
3
3
3
N
1
-2.59
0.40
121.90
119.31
A
A
A
N3
C4
C5
DC
DC
DC
3
3
3
N
1
10.36
1.20
119.70
130.06
A
A
A
C3'
O3'
P
DC
DC
DG
3
3
4
Y
1
-4.87
0.80
105.90
101.03
A
A
A
O4'
C1'
C2'
DG
DG
DG
4
4
4
N
1
2.18
0.30
108.30
110.48
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
2.96
0.30
108.30
111.26
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
7.90
1.20
119.70
127.60
A
A
A
C3'
O3'
P
DA
DA
AAB
5
5
6
Y
1
10.92
1.20
119.70
130.62
A
A
A
C3'
O3'
P
AAB
AAB
DA
6
6
7
Y
1
-8.62
0.80
105.90
97.28
A
A
A
O4'
C1'
C2'
DC
DC
DC
8
8
8
N
1
-5.00
0.80
105.90
100.90
A
A
A
O4'
C1'
C2'
DG
DG
DG
9
9
9
N
1
3.47
0.30
108.30
111.77
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
1
16.26
1.60
120.90
137.16
A
A
A
P
O5'
C5'
DC
DC
DC
10
10
10
N
1
2.79
0.30
108.30
111.09
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
-4.42
0.70
102.20
97.78
A
A
A
C4'
C3'
C2'
DC
DC
DC
11
11
11
N
1
3.82
0.30
108.30
112.12
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
3.63
0.30
108.30
111.93
B
B
B
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
2.76
0.30
108.30
111.06
B
B
B
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
2.70
0.30
108.30
111.00
B
B
B
O4'
C1'
N1
DC
DC
DC
19
19
19
N
1
12.23
1.20
119.70
131.93
B
B
B
C3'
O3'
P
DC
DC
DG
19
19
20
Y
1
2.67
0.30
108.30
110.97
B
B
B
O4'
C1'
N9
DG
DG
DG
20
20
20
N
1
3.63
0.60
118.90
122.53
B
B
B
N1
C2
O2
DC
DC
DC
21
21
21
N
1
8.17
1.20
119.70
127.87
B
B
B
C3'
O3'
P
DC
DC
DG
21
21
22
Y
1
-5.05
0.40
104.50
99.45
B
B
B
O4'
C4'
C3'
DG
DG
DG
22
22
22
N
1
6.65
1.10
109.80
116.45
B
B
B
C5'
C4'
O4'
DG
DG
DG
22
22
22
N
1
8.46
0.30
108.30
116.76
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
A
A
C5'
C4'
DC
DC
1
1
-0.085
0.011
1.509
1.424
N
1
A
A
C4'
C3'
DC
DC
1
1
-0.090
0.010
1.521
1.431
N
1
A
A
C3'
C2'
DC
DC
1
1
-0.131
0.008
1.516
1.385
N
1
A
A
C2'
C1'
DC
DC
1
1
-0.121
0.010
1.518
1.397
N
1
A
A
O4'
C4'
DC
DC
1
1
-0.158
0.010
1.446
1.288
N
1
A
A
C1'
N1
DC
DC
1
1
-0.085
0.014
1.468
1.383
N
1
A
A
C4
N4
DC
DC
1
1
-0.091
0.009
1.335
1.244
N
1
A
A
N1
C6
DC
DC
1
1
-0.037
0.006
1.367
1.330
N
1
A
A
C2
N3
DC
DC
1
1
-0.085
0.008
1.353
1.268
N
1
A
A
C5
C6
DC
DC
1
1
-0.082
0.008
1.339
1.257
N
1
A
A
P
OP1
DG
DG
2
2
-0.162
0.017
1.485
1.323
N
1
A
A
P
OP2
DG
DG
2
2
-0.177
0.017
1.485
1.308
N
1
A
A
P
O5'
DG
DG
2
2
-0.108
0.010
1.593
1.485
N
1
A
A
C5'
C4'
DG
DG
2
2
-0.089
0.011
1.509
1.420
N
1
A
A
C3'
C2'
DG
DG
2
2
-0.061
0.008
1.516
1.455
N
1
A
A
C2'
C1'
DG
DG
2
2
-0.063
0.010
1.518
1.455
N
1
A
A
O4'
C4'
DG
DG
2
2
-0.065
0.010
1.446
1.381
N
1
A
A
C2
N3
DG
DG
2
2
-0.054
0.008
1.323
1.269
N
1
A
A
C5
N7
DG
DG
2
2
-0.038
0.006
1.388
1.350
N
1
A
A
N9
C4
DG
DG
2
2
-0.070
0.008
1.375
1.305
N
1
A
A
P
OP2
DC
DC
3
3
-0.151
0.017
1.485
1.334
N
1
A
A
P
O5'
DC
DC
3
3
-0.104
0.010
1.593
1.489
N
1
A
A
C5'
C4'
DC
DC
3
3
-0.085
0.011
1.509
1.424
N
1
A
A
O3'
C3'
DC
DC
3
3
-0.037
0.006
1.419
1.382
N
1
A
A
C2
O2
DC
DC
3
3
-0.062
0.009
1.240
1.178
N
1
A
A
N1
C2
DC
DC
3
3
-0.065
0.010
1.397
1.332
N
1
A
A
N1
C6
DC
DC
3
3
-0.057
0.006
1.367
1.310
N
1
A
A
N3
C4
DC
DC
3
3
-0.055
0.007
1.335
1.280
N
1
A
A
C4
C5
DC
DC
3
3
-0.051
0.008
1.425
1.374
N
1
A
A
O3'
P
DC
DG
8
9
-0.079
0.012
1.607
1.528
Y
1
A
A
P
OP1
DG
DG
9
9
-0.103
0.017
1.485
1.382
N
1
A
A
P
OP2
DG
DG
9
9
-0.119
0.017
1.485
1.366
N
1
A
A
C3'
C2'
DG
DG
9
9
-0.090
0.008
1.516
1.426
N
1
A
A
C2'
C1'
DG
DG
9
9
-0.091
0.010
1.518
1.427
N
1
A
A
O4'
C1'
DG
DG
9
9
-0.077
0.012
1.418
1.341
N
1
A
A
O4'
C4'
DG
DG
9
9
-0.077
0.010
1.446
1.369
N
1
A
A
N1
C2
DG
DG
9
9
-0.058
0.008
1.373
1.315
N
1
A
A
C4
C5
DG
DG
9
9
-0.069
0.007
1.379
1.310
N
1
A
A
N7
C8
DG
DG
9
9
-0.048
0.006
1.305
1.257
N
1
A
A
C8
N9
DG
DG
9
9
-0.043
0.007
1.374
1.331
N
1
A
A
C6
O6
DG
DG
9
9
-0.061
0.009
1.237
1.176
N
1
A
A
P
O5'
DC
DC
10
10
-0.073
0.010
1.593
1.520
N
1
A
A
O5'
C5'
DC
DC
10
10
-0.238
0.025
1.418
1.180
N
1
A
A
C3'
C2'
DC
DC
10
10
-0.073
0.008
1.516
1.443
N
1
A
A
C2'
C1'
DC
DC
10
10
-0.084
0.010
1.518
1.434
N
1
A
A
O4'
C4'
DC
DC
10
10
-0.081
0.010
1.446
1.365
N
1
A
A
N1
C2
DC
DC
10
10
-0.068
0.010
1.397
1.329
N
1
A
A
C4
C5
DC
DC
10
10
-0.058
0.008
1.425
1.367
N
1
A
A
O3'
P
DC
DC
10
11
-0.076
0.012
1.607
1.531
Y
1
A
A
C3'
C2'
DC
DC
11
11
-0.053
0.008
1.516
1.463
N
1
A
A
C2
O2
DC
DC
11
11
-0.060
0.009
1.240
1.180
N
1
A
A
N1
C2
DC
DC
11
11
-0.072
0.010
1.397
1.325
N
1
A
A
N1
C6
DC
DC
11
11
-0.044
0.006
1.367
1.323
N
1
A
A
N3
C4
DC
DC
11
11
-0.053
0.007
1.335
1.282
N
1
A
A
C4
C5
DC
DC
11
11
-0.069
0.008
1.425
1.356
N
1
B
B
C5'
C4'
DG
DG
12
12
-0.072
0.011
1.509
1.437
N
1
B
B
C4'
C3'
DG
DG
12
12
-0.106
0.010
1.521
1.415
N
1
B
B
C3'
C2'
DG
DG
12
12
-0.087
0.008
1.516
1.429
N
1
B
B
C2'
C1'
DG
DG
12
12
-0.122
0.010
1.518
1.396
N
1
B
B
O4'
C1'
DG
DG
12
12
-0.084
0.012
1.418
1.334
N
1
B
B
O4'
C4'
DG
DG
12
12
-0.097
0.010
1.446
1.349
N
1
B
B
N1
C2
DG
DG
12
12
-0.061
0.008
1.373
1.312
N
1
B
B
C2
N3
DG
DG
12
12
-0.054
0.008
1.323
1.269
N
1
B
B
C4
C5
DG
DG
12
12
-0.069
0.007
1.379
1.310
N
1
B
B
C5
C6
DG
DG
12
12
-0.072
0.010
1.419
1.347
N
1
B
B
C6
N1
DG
DG
12
12
-0.044
0.007
1.391
1.347
N
1
B
B
N7
C8
DG
DG
12
12
-0.073
0.006
1.305
1.232
N
1
B
B
N9
C4
DG
DG
12
12
-0.065
0.008
1.375
1.310
N
1
B
B
C6
O6
DG
DG
12
12
-0.070
0.009
1.237
1.167
N
1
B
B
O3'
P
DG
DG
12
13
-0.113
0.012
1.607
1.494
Y
1
B
B
P
OP2
DG
DG
13
13
-0.106
0.017
1.485
1.379
N
1
B
B
P
O5'
DG
DG
13
13
-0.132
0.010
1.593
1.461
N
1
B
B
C5'
C4'
DG
DG
13
13
-0.090
0.011
1.509
1.419
N
1
B
B
O3'
C3'
DG
DG
13
13
-0.048
0.006
1.419
1.371
N
1
B
B
C4'
C3'
DC
DC
21
21
-0.064
0.010
1.521
1.457
N
1
B
B
C3'
C2'
DC
DC
21
21
-0.070
0.008
1.516
1.446
N
1
B
B
O4'
C4'
DC
DC
21
21
-0.064
0.010
1.446
1.382
N
1
B
B
O3'
C3'
DC
DC
21
21
-0.038
0.006
1.419
1.381
N
1
B
B
O3'
P
DC
DG
21
22
-0.109
0.012
1.607
1.498
Y
1
B
B
P
O5'
DG
DG
22
22
-0.061
0.010
1.593
1.532
N
1
B
B
C5'
C4'
DG
DG
22
22
-0.110
0.011
1.509
1.399
N
1
B
B
C4'
C3'
DG
DG
22
22
-0.187
0.010
1.521
1.334
N
1
B
B
C3'
C2'
DG
DG
22
22
-0.126
0.008
1.516
1.390
N
1
B
B
C2'
C1'
DG
DG
22
22
-0.195
0.010
1.518
1.323
N
1
B
B
O4'
C1'
DG
DG
22
22
-0.075
0.012
1.418
1.343
N
1
B
B
O4'
C4'
DG
DG
22
22
-0.101
0.010
1.446
1.345
N
1
B
B
O3'
C3'
DG
DG
22
22
-0.163
0.006
1.419
1.256
N
1
B
B
N3
C4
DG
DG
22
22
-0.064
0.007
1.350
1.286
N
1
B
B
C4
C5
DG
DG
22
22
-0.054
0.007
1.379
1.325
N
1
B
B
C6
N1
DG
DG
22
22
-0.082
0.007
1.391
1.309
N
1
B
B
C5
N7
DG
DG
22
22
-0.061
0.006
1.388
1.327
N
1
B
B
C8
N9
DG
DG
22
22
-0.070
0.007
1.374
1.304
N
1
B
B
N9
C4
DG
DG
22
22
-0.066
0.008
1.375
1.309
N
1
B
B
C2
N2
DG
DG
22
22
-0.086
0.010
1.341
1.255
N
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
X-PLOR
3.1
APURINIC DNA WITH BOUND WATER AT THE DAMAGED SITE AND O2 OF CYTOSINE, BETA FORM, NMR, 1 STRUCTURE
1
N
N
2
N
N
3
N
N
covale
1.585
one
A
DA
5
A
O3'
DA
5
1_555
A
AAB
6
A
P
AAB
6
1_555
covale
1.578
one
A
AAB
6
A
O3'
AAB
6
1_555
A
DA
7
A
P
DA
7
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
22
B
N1
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
22
B
O6
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
22
B
N2
DG
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
21
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
21
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
21
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
20
B
N1
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
20
B
O6
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
20
B
N2
DG
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
19
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
19
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
19
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
18
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
18
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
B
DT
16
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
B
DT
16
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
DG
15
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
DG
15
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
DG
15
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
B
DC
14
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
B
DC
14
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
B
DC
14
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N3
DC
10
1_555
B
DG
13
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N4
DC
10
1_555
B
DG
13
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
10
A
O2
DC
10
1_555
B
DG
13
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
12
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
12
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
12
B
N2
DG
1
1_555
DNA
DAMAGED DNA, APURINIC DNA, WATER, DNA
1A9H
PDB
1
1A9H
1A9H
PDB
2
1A9H
1
11
1A9H
1
11
1A9H
A
1
1
11
12
22
1A9H
12
22
1A9H
B
2
1
11
1
P 1