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/pdb1a9j/pdb
pdb_00001a9j
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
3390.209
DNA (5'-D(*GP*GP*CP*GP*TP*AP*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)(DA)(DT)(DC)(DG)(DC)(DG)
GGCGTATCGCG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-4.550
1
19
A
1
B
22
1.380
A_DC1:DG22_B
1
-6.800
0.656
0.293
-0.340
-2.412
1
19
A
2
B
21
-1.676
A_DG2:DC21_B
2
-1.357
-0.575
-0.003
-0.396
-10.122
1
19
A
3
B
20
0.613
A_DC3:DG20_B
3
-2.231
0.530
0.508
-0.377
7.739
1
19
A
4
B
19
-0.357
A_DG4:DC19_B
4
-2.184
-0.488
0.141
-0.306
1.680
1
20
A
5
B
18
-5.544
A_DA5:DT18_B
5
-18.341
0.050
-0.084
-0.204
8.371
1
20
A
7
B
16
-7.168
A_DA7:DT16_B
6
-21.806
0.132
0.283
-0.200
9.592
1
19
A
8
B
15
-1.028
A_DC8:DG15_B
7
-1.698
0.575
0.001
-0.312
8.141
1
19
A
9
B
14
-0.779
A_DG9:DC14_B
8
-4.529
-0.562
0.266
-0.366
2.561
1
19
A
10
B
13
0.170
A_DC10:DG13_B
9
-8.335
0.580
0.238
-0.371
4.417
1
19
A
11
B
12
-0.649
A_DC11:DG12_B
10
-1.399
0.523
0.171
-0.346
2.091
28.270
A
A
1
2
24.271
B
B
22
21
2.886
11.516
-0.082
-1.356
AA_DC1DG2:DC21DG22_BB
1
1.641
-3.459
25.811
-4.908
0.472
3.476
46.146
A
A
2
3
-2.668
B
B
21
20
3.448
-2.090
0.007
-0.900
AA_DG2DC3:DG20DC21_BB
2
-2.946
3.762
46.012
-0.959
-0.276
2.699
29.536
A
A
3
4
-0.088
B
B
20
19
2.700
-0.045
0.157
-0.493
AA_DC3DG4:DC19DG20_BB
3
3.719
-7.314
29.306
-0.959
0.346
3.361
48.922
A
A
4
5
-0.756
B
B
19
18
3.371
-0.626
-0.751
0.471
AA_DG4DA5:DT18DC19_BB
4
0.257
-0.311
48.917
0.617
0.927
5.961
83.556
A
A
5
7
3.823
B
B
18
16
5.920
5.087
-0.080
1.171
AA_DA5DA7:DT16DT18_BB
5
-7.698
5.785
83.138
0.656
-0.276
3.379
40.122
A
A
7
8
-7.127
B
B
16
15
3.341
-4.877
1.133
-0.108
AA_DA7DC8:DG15DT16_BB
6
1.918
-2.803
39.792
0.416
-1.425
3.616
31.684
A
A
8
9
-9.418
B
B
15
14
3.445
-5.120
0.243
-1.427
AA_DC8DG9:DC14DG15_BB
7
-1.171
2.154
31.257
-1.589
-0.680
3.325
49.959
A
A
9
10
-5.948
B
B
14
13
3.282
-5.016
-0.028
-0.606
AA_DG9DC10:DG13DC14_BB
8
-0.105
0.124
49.723
-0.349
0.026
3.265
37.617
A
A
10
11
-4.823
B
B
13
12
3.189
-3.106
-0.110
-1.060
AA_DC10DC11:DG12DG13_BB
9
-1.230
1.910
37.474
-1.245
0.012
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Structure summary
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
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
A
17
n
6
DA
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
A
A
O1'
H1
AAB
HOH
6
23
1.59
1
-4.61
0.70
121.90
117.29
A
A
A
N3
C2
O2
DC
DC
DC
1
1
1
N
1
-5.80
0.80
105.90
100.10
A
A
A
O4'
C1'
C2'
DG
DG
DG
2
2
2
N
1
4.10
0.30
108.30
112.40
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
7.24
1.20
119.70
126.94
A
A
A
C3'
O3'
P
DC
DC
DG
3
3
4
Y
1
1.97
0.30
108.30
110.27
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
7.74
1.20
119.70
127.44
A
A
A
C3'
O3'
P
DA
DA
AAB
5
5
6
Y
1
2.81
0.30
108.30
111.11
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
13.69
1.20
119.70
133.39
A
A
A
C3'
O3'
P
DC
DC
DG
8
8
9
Y
1
3.25
0.30
108.30
111.55
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
1
3.66
0.30
108.30
111.96
B
B
B
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
3.70
0.30
108.30
112.00
B
B
B
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
8.77
1.20
119.70
128.47
B
B
B
C3'
O3'
P
DG
DG
DT
15
15
16
Y
1
2.93
0.30
108.30
111.23
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
1
2.91
0.30
108.30
111.21
B
B
B
O4'
C1'
N1
DT
DT
DT
18
18
18
N
1
7.20
1.20
119.70
126.90
B
B
B
C3'
O3'
P
DT
DT
DC
18
18
19
Y
1
11.62
1.20
119.70
131.32
B
B
B
C3'
O3'
P
DG
DG
DC
20
20
21
Y
1
-4.99
0.70
102.20
97.21
B
B
B
C4'
C3'
C2'
DG
DG
DG
22
22
22
N
1
3.29
0.30
108.30
111.59
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
A
A
C4'
C3'
DC
DC
1
1
-0.080
0.010
1.521
1.441
N
1
A
A
C3'
C2'
DC
DC
1
1
-0.073
0.008
1.516
1.443
N
1
A
A
O3'
C3'
DC
DC
1
1
-0.087
0.006
1.419
1.332
N
1
A
A
C2
O2
DC
DC
1
1
-0.060
0.009
1.240
1.180
N
1
A
A
N1
C6
DC
DC
1
1
-0.051
0.006
1.367
1.316
N
1
A
A
N3
C4
DC
DC
1
1
-0.055
0.007
1.335
1.280
N
1
A
A
O3'
P
DC
DG
1
2
-0.112
0.012
1.607
1.495
Y
1
A
A
P
OP1
DG
DG
2
2
-0.244
0.017
1.485
1.241
N
1
A
A
P
OP2
DG
DG
2
2
-0.229
0.017
1.485
1.256
N
1
A
A
P
O5'
DG
DG
2
2
-0.091
0.010
1.593
1.502
N
1
A
A
P
OP1
DC
DC
8
8
-0.129
0.017
1.485
1.356
N
1
A
A
P
OP2
DC
DC
8
8
-0.113
0.017
1.485
1.372
N
1
A
A
P
O5'
DC
DC
8
8
-0.075
0.010
1.593
1.518
N
1
A
A
C3'
C2'
DC
DC
8
8
-0.050
0.008
1.516
1.466
N
1
A
A
O3'
P
DC
DG
8
9
-0.092
0.012
1.607
1.515
Y
1
B
B
C3'
C2'
DC
DC
21
21
-0.056
0.008
1.516
1.460
N
1
B
B
P
OP2
DG
DG
22
22
-0.156
0.017
1.485
1.329
N
1
B
B
P
O5'
DG
DG
22
22
-0.141
0.010
1.593
1.452
N
1
B
B
O3'
C3'
DG
DG
22
22
-0.042
0.006
1.419
1.377
N
1
B
B
C6
N1
DG
DG
22
22
-0.046
0.007
1.391
1.345
N
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
X-PLOR
3.1
APYRIMIDINIC DNA WITH BOUND WATER AT THE DAMAGED SITE, BETA FORM, NMR, 1 STRUCTURE
1
N
N
2
N
N
3
N
N
covale
1.561
one
A
DA
5
A
O3'
DA
5
1_555
A
AAB
6
A
P
AAB
6
1_555
covale
1.597
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, APYRIMIDINIC DNA, WATER, DNA
1A9J
PDB
1
1A9J
1A9J
PDB
2
1A9J
1
11
1A9J
1
11
1A9J
A
1
1
11
12
22
1A9J
12
22
1A9J
B
2
1
11
1
P 1