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
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
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
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
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/pdb1gj0/pdb
pdb_00001gj0
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*(AAB)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)(AAB)(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
38.542
1
19
A
1
B
26
-0.227
A_DC1:DG26_B
1
-28.248
0.624
-0.434
-0.110
28.087
1
19
A
2
B
25
-1.851
A_DC2:DG25_B
2
-23.620
0.423
-0.277
-0.173
-17.364
1
20
A
3
B
24
1.364
A_DA3:DT24_B
3
-13.891
0.053
-0.085
-0.170
-16.265
1
20
A
4
B
23
0.710
A_DA4:DT23_B
4
-7.987
-0.069
0.099
-0.195
-13.970
1
20
A
5
B
22
-7.135
A_DA5:DT22_B
5
0.848
-0.037
0.189
-0.183
4.582
1
19
A
6
B
21
-5.540
A_DG6:DC21_B
6
-7.884
-0.766
0.433
-0.419
15.212
1
20
A
8
B
19
-12.776
A_DA8:DT19_B
7
-13.405
0.118
0.642
-0.180
11.427
1
19
A
9
B
18
-1.158
A_DC9:DG18_B
8
-9.862
0.387
0.347
-0.239
12.116
1
20
A
10
B
17
-1.371
A_DT10:DA17_B
9
-8.401
-0.073
-0.011
-0.168
-17.032
1
19
A
11
B
16
-2.798
A_DG11:DC16_B
10
-18.866
-0.148
0.040
-0.253
-30.101
1
19
A
12
B
15
-0.012
A_DG12:DC15_B
11
-24.057
-0.555
-0.088
-0.145
-25.713
1
19
A
13
B
14
-3.742
A_DG13:DC14_B
12
-13.889
-0.666
0.240
-0.258
3.602
38.731
A
A
1
2
3.386
B
B
26
25
3.622
2.244
0.684
-0.335
AA_DC1DC2:DG25DG26_BB
1
0.266
-0.402
38.668
-0.809
-0.996
3.815
45.347
A
A
2
3
15.559
B
B
25
24
4.126
11.868
0.358
-0.755
AA_DC2DA3:DT24DG25_BB
2
1.157
-1.516
43.831
-2.282
-0.337
3.219
36.937
A
A
3
4
-5.108
B
B
24
23
3.182
-3.232
-0.262
-0.479
AA_DA3DA4:DT23DT24_BB
3
-1.699
2.686
36.763
-0.329
0.189
3.211
33.261
A
A
4
5
-1.490
B
B
23
22
3.154
-0.852
-0.735
-0.575
AA_DA4DA5:DT22DT23_BB
4
-2.373
4.149
33.168
-0.866
0.898
2.969
32.557
A
A
5
6
-14.223
B
B
22
21
2.885
-7.898
-0.233
-0.728
AA_DA5DG6:DC21DT22_BB
5
0.762
-1.372
31.600
-0.046
0.536
6.056
85.039
A
A
6
8
-8.018
B
B
21
19
6.132
-10.814
0.044
0.343
AA_DG6DA8:DT19DC21_BB
6
-4.728
3.505
84.371
0.721
-0.237
3.376
38.338
A
A
8
9
-9.412
B
B
19
18
3.446
-6.156
0.606
0.279
AA_DA8DC9:DG18DT19_BB
7
0.975
-1.491
37.847
1.233
-0.795
3.320
37.508
A
A
9
10
-5.620
B
B
18
17
3.247
-3.604
0.358
-0.733
AA_DC9DT10:DA17DG18_BB
8
3.365
-5.248
37.194
-0.665
-0.112
3.716
42.039
A
A
10
11
7.144
B
B
17
16
3.839
5.109
-0.240
-0.899
AA_DT10DG11:DC16DA17_BB
9
-3.321
4.644
41.615
-1.867
-0.065
3.281
38.961
A
A
11
12
7.065
B
B
16
15
3.418
4.699
-0.110
-0.877
AA_DG11DG12:DC15DC16_BB
10
2.334
-3.509
38.619
-1.900
0.456
3.192
39.873
A
A
12
13
-2.243
B
B
15
14
3.142
-1.528
-0.647
-0.348
AA_DG12DG13:DC14DC15_BB
11
-3.073
4.511
39.731
-0.339
0.604
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Data collection
1
0
2001-08-22
1
1
2008-04-26
1
2
2011-07-13
1
3
2022-02-23
1
4
2023-12-27
_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
Ensemble: NMR Structure of an Oligonucleotide Containing an Abasic Site: Beta Anomer
Ensemble: NMR Structure of an Oligonucleotide Containing an Abasic Site: Alpha Anomer
Minimized Average Structure: NMR Structure of an Oligonucleotide Containing an Abasic Site: Alpha 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.
1
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
AAB
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
0.079
SIDE CHAIN
1
A
DG
11
0.090
SIDE CHAIN
1
B
DT
22
0.075
SIDE CHAIN
1
B
DG
25
0.065
SIDE CHAIN
1
4.18
0.60
118.60
122.78
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
1
5.48
0.60
118.60
124.08
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
1
-5.02
0.80
123.70
118.68
A
A
A
C5
C6
N6
DA
DA
DA
5
5
5
N
1
4.66
0.70
119.90
124.56
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
1
5.69
0.60
118.60
124.29
A
A
A
N1
C6
N6
DA
DA
DA
8
8
8
N
1
4.76
0.70
119.90
124.66
A
A
A
N3
C2
N2
DG
DG
DG
12
12
12
N
1
5.31
0.70
119.90
125.21
A
A
A
N3
C2
N2
DG
DG
DG
13
13
13
N
1
4.69
0.60
118.60
123.29
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
1
7.75
1.20
119.70
127.45
B
B
B
C3'
O3'
P
DA
DA
DG
17
17
18
Y
1
5.00
0.70
119.90
124.90
B
B
B
N3
C2
N2
DG
DG
DG
18
18
18
N
1
4.33
0.60
118.60
122.93
B
B
B
N1
C6
N6
DA
DA
DA
20
20
20
N
1
3.74
0.60
118.90
122.64
B
B
B
N1
C2
O2
DC
DC
DC
21
21
21
N
1
9.30
1.20
119.70
129.00
B
B
B
C3'
O3'
P
DC
DC
DT
21
21
22
Y
1
7.61
1.20
119.70
127.31
B
B
B
C3'
O3'
P
DT
DT
DT
22
22
23
Y
1
4.46
0.70
119.90
124.36
B
B
B
N3
C2
N2
DG
DG
DG
25
25
25
N
1
4.96
0.70
119.90
124.86
B
B
B
N3
C2
N2
DG
DG
DG
26
26
26
N
1
A
A
N9
C4
DA
DA
4
4
0.039
0.006
1.374
1.413
N
1
A
A
C5'
C4'
DT
DT
10
10
0.043
0.007
1.512
1.555
N
1
B
B
N1
C2
DT
DT
22
22
0.049
0.008
1.376
1.425
N
NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: BETA ANOMER
1
N
N
2
N
N
covale
1.585
one
A
DG
6
A
O3'
DG
6
1_555
A
AAB
7
A
P
AAB
7
1_555
covale
1.582
one
A
AAB
7
A
O3'
AAB
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
1GJ0
PDB
1
1GJ0
1GJ0
PDB
2
1GJ0
1
13
1GJ0
1
13
1GJ0
A
1
1
13
14
26
1GJ0
14
26
1GJ0
B
2
1
13
1
P 1