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/pdb1a9g/pdb
pdb_00001a9g
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
8.217
1
19
A
1
B
22
-2.038
A_DC1:DG22_B
1
-5.756
0.299
0.201
-0.714
12.412
1
19
A
2
B
21
-1.342
A_DG2:DC21_B
2
3.592
-0.561
0.233
-0.517
11.292
1
19
A
3
B
20
-2.915
A_DC3:DG20_B
3
-4.399
0.429
-0.207
-0.476
8.783
1
19
A
4
B
19
0.264
A_DG4:DC19_B
4
-2.282
-0.654
0.310
-0.385
4.944
1
20
A
5
B
18
-3.803
A_DA5:DT18_B
5
-15.935
0.104
0.079
-0.130
14.611
1
20
A
7
B
16
-3.630
A_DA7:DT16_B
6
-27.826
0.247
0.204
-0.188
14.224
1
19
A
8
B
15
-1.532
A_DC8:DG15_B
7
-20.404
0.454
-0.157
-0.316
-1.709
1
19
A
9
B
14
-1.828
A_DG9:DC14_B
8
-2.324
-0.437
0.039
-0.369
-4.201
1
19
A
10
B
13
-0.176
A_DC10:DG13_B
9
-3.311
0.691
0.001
-0.445
-2.221
1
19
A
11
B
12
-2.271
A_DC11:DG12_B
10
2.483
0.690
0.142
-0.612
3.118
34.808
A
A
1
2
-1.169
B
B
22
21
3.109
-0.699
0.105
-1.014
AA_DC1DG2:DC21DG22_BB
1
-1.864
3.117
34.753
-1.594
-0.446
3.394
42.412
A
A
2
3
-4.670
B
B
21
20
3.345
-3.374
0.065
-0.797
AA_DG2DC3:DG20DC21_BB
2
2.479
-3.432
42.215
-0.747
0.170
3.804
29.461
A
A
3
4
-10.562
B
B
20
19
3.699
-5.330
0.267
-1.248
AA_DC3DG4:DC19DG20_BB
3
-3.560
7.055
28.771
-1.132
-1.407
3.624
47.444
A
A
4
5
-14.234
B
B
19
18
3.830
-11.353
-0.778
0.528
AA_DG4DA5:DT18DC19_BB
4
-0.885
1.110
46.134
1.718
0.885
6.003
85.144
A
A
5
7
8.510
B
B
18
16
5.861
11.485
-0.481
1.459
AA_DA5DA7:DT16DT18_BB
5
-5.556
4.116
84.363
0.597
0.122
3.243
36.981
A
A
7
8
-7.365
B
B
16
15
3.153
-4.653
0.858
-0.372
AA_DA7DC8:DG15DT16_BB
6
3.716
-5.882
36.515
0.030
-0.860
2.753
29.580
A
A
8
9
15.435
B
B
15
14
3.308
7.790
1.012
-1.562
AA_DC8DG9:DC14DG15_BB
7
-1.154
2.287
28.535
-4.616
-2.212
3.282
45.925
A
A
9
10
-3.139
B
B
14
13
3.238
-2.448
-0.017
-0.945
AA_DG9DC10:DG13DC14_BB
8
-0.216
0.277
45.863
-1.000
0.003
3.136
36.039
A
A
10
11
4.697
B
B
13
12
3.219
2.902
-0.241
-1.024
AA_DC10DC11:DG12DG13_BB
9
-1.400
2.266
35.899
-2.056
0.197
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 BACK CALCULATION 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
B
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
B
HO1'
H1
AAB
HOH
6
23
1.28
1
-4.23
0.70
102.20
97.97
A
A
A
C4'
C3'
C2'
DC
DC
DC
1
1
1
N
1
6.35
0.30
108.30
114.65
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
-3.21
0.40
120.30
117.09
A
A
A
C6
N1
C2
DC
DC
DC
1
1
1
N
1
4.11
0.50
119.90
124.01
A
A
A
C2
N3
C4
DC
DC
DC
1
1
1
N
1
-3.91
0.40
121.90
117.99
A
A
A
N3
C4
C5
DC
DC
DC
1
1
1
N
1
3.38
0.50
121.00
124.38
A
A
A
C5
C6
N1
DC
DC
DC
1
1
1
N
1
8.04
1.20
119.70
127.74
A
A
A
C3'
O3'
P
DG
DG
DC
2
2
3
Y
1
5.30
0.60
106.00
111.30
A
A
A
O4'
C4'
C3'
DC
DC
DC
3
3
3
N
1
2.55
0.30
108.30
110.85
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
-4.41
0.70
102.20
97.79
A
A
A
C4'
C3'
C2'
DA
DA
DA
7
7
7
N
1
-4.44
0.70
108.00
103.56
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
1
-7.46
0.80
105.90
98.44
A
A
A
O4'
C1'
C2'
DC
DC
DC
8
8
8
N
1
5.92
0.30
108.30
114.22
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
5.96
0.30
108.30
114.26
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
1
9.25
1.20
119.70
128.95
A
A
A
C3'
O3'
P
DG
DG
DC
9
9
10
Y
1
2.46
0.30
108.30
110.76
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
3.81
0.60
118.90
122.71
A
A
A
N1
C2
O2
DC
DC
DC
10
10
10
N
1
7.25
1.20
119.70
126.95
A
A
A
C3'
O3'
P
DC
DC
DC
10
10
11
Y
1
-3.23
0.50
117.40
114.17
A
A
A
C4
C5
C6
DC
DC
DC
11
11
11
N
1
3.99
0.60
118.90
122.89
A
A
A
N1
C2
O2
DC
DC
DC
11
11
11
N
1
-4.36
0.70
102.20
97.84
B
B
B
C4'
C3'
C2'
DG
DG
DG
12
12
12
N
1
4.28
0.30
108.30
112.58
B
B
B
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
5.62
0.30
108.30
113.92
B
B
B
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
2.79
0.40
105.40
108.19
B
B
B
N9
C4
C5
DG
DG
DG
13
13
13
N
1
2.29
0.30
108.30
110.59
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
1
-4.20
0.70
121.90
117.70
B
B
B
N3
C2
O2
DC
DC
DC
14
14
14
N
1
7.49
1.20
119.70
127.19
B
B
B
C3'
O3'
P
DC
DC
DG
14
14
15
Y
1
7.81
1.20
119.70
127.51
B
B
B
C3'
O3'
P
DG
DG
DT
15
15
16
Y
1
2.04
0.30
108.30
110.34
B
B
B
O4'
C1'
N1
DC
DC
DC
17
17
17
N
1
-3.82
0.60
122.90
119.08
B
B
B
C6
C5
C7
DT
DT
DT
18
18
18
N
1
10.31
1.20
119.70
130.01
B
B
B
C3'
O3'
P
DT
DT
DC
18
18
19
Y
1
9.10
1.20
119.70
128.80
B
B
B
C3'
O3'
P
DC
DC
DG
19
19
20
Y
1
10.29
1.20
119.70
129.99
B
B
B
C3'
O3'
P
DG
DG
DC
20
20
21
Y
1
9.08
1.20
119.70
128.78
B
B
B
C3'
O3'
P
DC
DC
DG
21
21
22
Y
1
18.03
1.20
102.50
120.53
B
B
B
C3'
C2'
C1'
DG
DG
DG
22
22
22
N
1
-5.71
0.80
105.90
100.19
B
B
B
O4'
C1'
C2'
DG
DG
DG
22
22
22
N
1
4.91
0.30
108.30
113.21
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
4.83
0.50
111.90
116.73
B
B
B
C2
N3
C4
DG
DG
DG
22
22
22
N
1
5.09
0.50
111.50
116.59
B
B
B
C5
C6
N1
DG
DG
DG
22
22
22
N
1
3.55
0.50
104.30
107.85
B
B
B
C5
N7
C8
DG
DG
DG
22
22
22
N
1
-4.25
0.50
113.10
108.85
B
B
B
N7
C8
N9
DG
DG
DG
22
22
22
N
1
3.31
0.40
106.40
109.71
B
B
B
C8
N9
C4
DG
DG
DG
22
22
22
N
1
4.02
0.60
130.40
134.42
B
B
B
C6
C5
N7
DG
DG
DG
22
22
22
N
1
-5.18
0.60
119.90
114.72
B
B
B
N1
C6
O6
DG
DG
DG
22
22
22
N
1
A
A
O5'
C5'
DC
DC
1
1
-0.183
0.025
1.418
1.235
N
1
A
A
C5'
C4'
DC
DC
1
1
-0.229
0.011
1.509
1.280
N
1
A
A
C4'
C3'
DC
DC
1
1
-0.163
0.010
1.521
1.358
N
1
A
A
C3'
C2'
DC
DC
1
1
-0.063
0.008
1.516
1.453
N
1
A
A
C2'
C1'
DC
DC
1
1
-0.176
0.010
1.518
1.342
N
1
A
A
O4'
C1'
DC
DC
1
1
-0.081
0.012
1.418
1.337
N
1
A
A
O4'
C4'
DC
DC
1
1
-0.118
0.010
1.446
1.328
N
1
A
A
O3'
C3'
DC
DC
1
1
-0.126
0.006
1.419
1.293
N
1
A
A
C2
O2
DC
DC
1
1
-0.126
0.009
1.240
1.114
N
1
A
A
C4
N4
DC
DC
1
1
-0.089
0.009
1.335
1.246
N
1
A
A
N1
C2
DC
DC
1
1
-0.173
0.010
1.397
1.224
N
1
A
A
N1
C6
DC
DC
1
1
-0.120
0.006
1.367
1.247
N
1
A
A
C2
N3
DC
DC
1
1
-0.076
0.008
1.353
1.277
N
1
A
A
N3
C4
DC
DC
1
1
-0.123
0.007
1.335
1.212
N
1
A
A
C4
C5
DC
DC
1
1
-0.165
0.008
1.425
1.260
N
1
A
A
C5
C6
DC
DC
1
1
-0.075
0.008
1.339
1.264
N
1
A
A
O3'
P
DC
DG
1
2
-0.201
0.012
1.607
1.406
Y
1
A
A
P
OP1
DG
DG
2
2
-0.140
0.017
1.485
1.345
N
1
A
A
P
OP2
DG
DG
2
2
-0.115
0.017
1.485
1.370
N
1
A
A
P
O5'
DG
DG
2
2
-0.162
0.010
1.593
1.431
N
1
A
A
C4
C5
DG
DG
2
2
-0.043
0.007
1.379
1.336
N
1
A
A
C6
N1
DG
DG
2
2
-0.048
0.007
1.391
1.343
N
1
A
A
N7
C8
DG
DG
2
2
-0.039
0.006
1.305
1.266
N
1
A
A
N9
C4
DG
DG
2
2
-0.053
0.008
1.375
1.322
N
1
A
A
P
OP1
DC
DC
3
3
-0.135
0.017
1.485
1.350
N
1
A
A
P
OP2
DC
DC
3
3
-0.188
0.017
1.485
1.297
N
1
A
A
P
O5'
DC
DC
3
3
-0.161
0.010
1.593
1.432
N
1
A
A
C5'
C4'
DC
DC
3
3
-0.139
0.011
1.509
1.370
N
1
A
A
C4'
C3'
DC
DC
3
3
-0.068
0.010
1.521
1.453
N
1
A
A
C3'
C2'
DC
DC
3
3
-0.049
0.008
1.516
1.467
N
1
A
A
O4'
C4'
DC
DC
3
3
-0.077
0.010
1.446
1.369
N
1
A
A
O3'
C3'
DC
DC
3
3
-0.049
0.006
1.419
1.370
N
1
A
A
P
O5'
DA
DA
5
5
-0.066
0.010
1.593
1.527
N
1
A
A
P
OP1
DA
DA
7
7
-0.130
0.017
1.485
1.355
N
1
A
A
P
O5'
DA
DA
7
7
-0.080
0.010
1.593
1.513
N
1
A
A
P
OP2
DC
DC
8
8
-0.107
0.017
1.485
1.378
N
1
A
A
O3'
C3'
DC
DC
8
8
-0.041
0.006
1.419
1.378
N
1
A
A
P
OP2
DC
DC
10
10
-0.111
0.017
1.485
1.374
N
1
A
A
P
O5'
DC
DC
10
10
-0.066
0.010
1.593
1.527
N
1
A
A
C3'
C2'
DC
DC
10
10
-0.061
0.008
1.516
1.455
N
1
A
A
O4'
C4'
DC
DC
10
10
-0.067
0.010
1.446
1.379
N
1
A
A
C3'
C2'
DC
DC
11
11
-0.061
0.008
1.516
1.455
N
1
A
A
C4
N4
DC
DC
11
11
-0.074
0.009
1.335
1.261
N
1
A
A
N1
C2
DC
DC
11
11
-0.087
0.010
1.397
1.310
N
1
A
A
C2
N3
DC
DC
11
11
-0.064
0.008
1.353
1.289
N
1
A
A
C4
C5
DC
DC
11
11
-0.073
0.008
1.425
1.352
N
1
A
A
C5
C6
DC
DC
11
11
-0.051
0.008
1.339
1.288
N
1
B
B
C5'
C4'
DG
DG
12
12
-0.123
0.011
1.509
1.386
N
1
B
B
C4'
C3'
DG
DG
12
12
-0.118
0.010
1.521
1.403
N
1
B
B
C3'
C2'
DG
DG
12
12
-0.050
0.008
1.516
1.466
N
1
B
B
C2'
C1'
DG
DG
12
12
-0.151
0.010
1.518
1.367
N
1
B
B
O4'
C1'
DG
DG
12
12
-0.099
0.012
1.418
1.319
N
1
B
B
O4'
C4'
DG
DG
12
12
-0.087
0.010
1.446
1.359
N
1
B
B
O3'
C3'
DG
DG
12
12
-0.061
0.006
1.419
1.358
N
1
B
B
N3
C4
DG
DG
12
12
-0.042
0.007
1.350
1.308
N
1
B
B
C4
C5
DG
DG
12
12
-0.043
0.007
1.379
1.336
N
1
B
B
C6
N1
DG
DG
12
12
-0.058
0.007
1.391
1.333
N
1
B
B
C5
N7
DG
DG
12
12
-0.042
0.006
1.388
1.346
N
1
B
B
N9
C4
DG
DG
12
12
-0.054
0.008
1.375
1.321
N
1
B
B
C2
N2
DG
DG
12
12
-0.064
0.010
1.341
1.277
N
1
B
B
O3'
P
DG
DG
12
13
-0.078
0.012
1.607
1.529
Y
1
B
B
P
OP1
DG
DG
13
13
-0.109
0.017
1.485
1.376
N
1
B
B
P
OP2
DG
DG
13
13
-0.130
0.017
1.485
1.355
N
1
B
B
N3
C4
DG
DG
13
13
-0.049
0.007
1.350
1.301
N
1
B
B
C6
N1
DG
DG
13
13
-0.064
0.007
1.391
1.327
N
1
B
B
C5
N7
DG
DG
13
13
-0.046
0.006
1.388
1.342
N
1
B
B
C8
N9
DG
DG
13
13
-0.046
0.007
1.374
1.328
N
1
B
B
C2
N2
DG
DG
13
13
-0.076
0.010
1.341
1.265
N
1
B
B
P
OP1
DC
DC
14
14
-0.120
0.017
1.485
1.365
N
1
B
B
P
OP2
DC
DC
14
14
-0.128
0.017
1.485
1.357
N
1
B
B
P
O5'
DC
DC
14
14
-0.074
0.010
1.593
1.519
N
1
B
B
O3'
C3'
DC
DC
14
14
-0.048
0.006
1.419
1.371
N
1
B
B
C2
O2
DC
DC
14
14
-0.062
0.009
1.240
1.178
N
1
B
B
N1
C6
DC
DC
14
14
-0.053
0.006
1.367
1.314
N
1
B
B
N3
C4
DC
DC
14
14
-0.057
0.007
1.335
1.278
N
1
B
B
O3'
P
DG
DT
15
16
-0.099
0.012
1.607
1.508
Y
1
B
B
P
OP1
DT
DT
16
16
-0.119
0.017
1.485
1.366
N
1
B
B
P
OP2
DT
DT
16
16
-0.110
0.017
1.485
1.375
N
1
B
B
P
O5'
DT
DT
16
16
-0.112
0.010
1.593
1.481
N
1
B
B
C3'
C2'
DC
DC
17
17
-0.056
0.008
1.516
1.460
N
1
B
B
N1
C6
DC
DC
17
17
-0.042
0.006
1.367
1.325
N
1
B
B
N3
C4
DC
DC
17
17
-0.043
0.007
1.335
1.292
N
1
B
B
P
OP1
DT
DT
18
18
-0.106
0.017
1.485
1.379
N
1
B
B
P
O5'
DT
DT
18
18
-0.082
0.010
1.593
1.511
N
1
B
B
P
O5'
DC
DC
19
19
-0.104
0.010
1.593
1.489
N
1
B
B
C3'
C2'
DG
DG
20
20
-0.084
0.008
1.516
1.432
N
1
B
B
C2'
C1'
DG
DG
20
20
-0.067
0.010
1.518
1.451
N
1
B
B
O3'
C3'
DG
DG
20
20
-0.037
0.006
1.419
1.382
N
1
B
B
P
OP1
DC
DC
21
21
-0.134
0.017
1.485
1.351
N
1
B
B
P
OP2
DC
DC
21
21
-0.131
0.017
1.485
1.354
N
1
B
B
P
O5'
DC
DC
21
21
-0.060
0.010
1.593
1.533
N
1
B
B
C3'
C2'
DC
DC
21
21
-0.068
0.008
1.516
1.448
N
1
B
B
C2'
C1'
DC
DC
21
21
-0.074
0.010
1.518
1.444
N
1
B
B
O4'
C4'
DC
DC
21
21
-0.083
0.010
1.446
1.363
N
1
B
B
O3'
C3'
DC
DC
21
21
-0.100
0.006
1.419
1.319
N
1
B
B
O3'
P
DC
DG
21
22
-0.116
0.012
1.607
1.491
Y
1
B
B
P
OP2
DG
DG
22
22
-0.106
0.017
1.485
1.379
N
1
B
B
C4'
C3'
DG
DG
22
22
-0.129
0.010
1.521
1.392
N
1
B
B
C3'
C2'
DG
DG
22
22
-0.221
0.008
1.516
1.295
N
1
B
B
C2'
C1'
DG
DG
22
22
-0.266
0.010
1.518
1.252
N
1
B
B
O4'
C1'
DG
DG
22
22
-0.125
0.012
1.418
1.293
N
1
B
B
O4'
C4'
DG
DG
22
22
-0.097
0.010
1.446
1.349
N
1
B
B
O3'
C3'
DG
DG
22
22
-0.300
0.006
1.419
1.119
N
1
B
B
C1'
N9
DG
DG
22
22
-0.182
0.014
1.468
1.286
N
1
B
B
N1
C2
DG
DG
22
22
-0.178
0.008
1.373
1.195
N
1
B
B
C2
N3
DG
DG
22
22
-0.078
0.008
1.323
1.245
N
1
B
B
N3
C4
DG
DG
22
22
-0.102
0.007
1.350
1.248
N
1
B
B
C4
C5
DG
DG
22
22
-0.186
0.007
1.379
1.193
N
1
B
B
C5
C6
DG
DG
22
22
-0.086
0.010
1.419
1.333
N
1
B
B
C6
N1
DG
DG
22
22
-0.117
0.007
1.391
1.274
N
1
B
B
C5
N7
DG
DG
22
22
-0.068
0.006
1.388
1.320
N
1
B
B
N7
C8
DG
DG
22
22
-0.131
0.006
1.305
1.174
N
1
B
B
C8
N9
DG
DG
22
22
-0.152
0.007
1.374
1.222
N
1
B
B
N9
C4
DG
DG
22
22
-0.078
0.008
1.375
1.297
N
1
B
B
C2
N2
DG
DG
22
22
-0.112
0.010
1.341
1.229
N
1
B
B
C6
O6
DG
DG
22
22
-0.161
0.009
1.237
1.076
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 N3 OF CYTOSINE, BETA FORM, NMR, 1 STRUCTURE
1
N
N
2
N
N
3
N
N
covale
1.544
one
A
DA
5
A
O3'
DA
5
1_555
A
AAB
6
A
P
AAB
6
1_555
covale
1.567
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
1A9G
PDB
1
1A9G
1A9G
PDB
2
1A9G
1
11
1A9G
1
11
1A9G
A
1
1
11
12
22
1A9G
12
22
1A9G
B
2
1
11
1
P 1