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
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
N
1
N
O
N
2
N
P
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
S
C
N
10
N
O
N
11
N
C
N
12
R
C
Y
13
N
N
Y
14
N
C
Y
15
N
N
Y
16
N
C
Y
17
N
C
N
18
N
N
Y
19
N
N
Y
20
N
C
Y
21
N
N
Y
22
N
C
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
O
N
38
N
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
N
C
N
48
R
C
N
49
N
N
N
50
N
C
N
51
N
O
N
52
N
N
N
53
N
C
N
54
N
N
N
55
N
C
N
56
N
C
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
O
N
72
N
P
N
73
N
O
N
74
N
O
N
75
N
O
N
76
N
C
N
77
R
C
N
78
N
O
N
79
S
C
N
80
N
O
N
81
N
C
N
82
R
C
Y
83
N
N
Y
84
N
C
Y
85
N
N
Y
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
N
N
92
N
N
Y
93
N
C
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
O
N
109
N
P
N
110
N
O
N
111
N
O
N
112
N
O
N
113
N
C
N
114
R
C
N
115
N
O
N
116
S
C
N
117
N
O
N
118
N
C
N
119
R
C
N
120
N
N
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
C
N
128
N
C
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
S
C
N
145
N
O
N
146
N
C
N
147
S
C
N
148
N
O
N
149
R
C
N
150
N
O
N
151
N
C
N
152
N
O
N
153
N
P
N
154
N
O
N
155
N
O
N
156
N
O
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
sing
N
3
N
doub
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
Y
24
N
sing
Y
25
N
sing
Y
26
N
doub
N
27
N
sing
Y
28
N
sing
Y
29
N
sing
Y
30
N
doub
N
31
N
sing
Y
32
N
doub
N
33
N
sing
N
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
doub
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
doub
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
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
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
sing
N
102
N
sing
Y
103
N
doub
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
doub
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
doub
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
doub
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
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
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/pdb1giz/pdb
pdb_00001giz
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
40.798
1
19
A
1
B
26
-0.782
A_DC1:DG26_B
1
-27.508
0.621
-0.502
-0.098
28.216
1
19
A
2
B
25
-1.766
A_DC2:DG25_B
2
-23.394
0.469
-0.326
-0.189
-20.727
1
20
A
3
B
24
0.238
A_DA3:DT24_B
3
-14.346
0.101
-0.227
-0.169
-15.997
1
20
A
4
B
23
-0.183
A_DA4:DT23_B
4
-5.372
-0.015
-0.011
-0.193
-11.401
1
20
A
5
B
22
-6.700
A_DA5:DT22_B
5
2.688
-0.093
0.166
-0.221
0.344
1
19
A
6
B
21
-4.072
A_DG6:DC21_B
6
-13.304
-0.637
0.409
-0.398
11.631
1
20
A
8
B
19
-11.575
A_DA8:DT19_B
7
-7.915
0.009
0.319
-0.133
15.359
1
19
A
9
B
18
2.689
A_DC9:DG18_B
8
-6.953
0.431
-0.043
-0.071
13.126
1
20
A
10
B
17
0.344
A_DT10:DA17_B
9
-10.034
-0.017
-0.170
-0.177
-16.905
1
19
A
11
B
16
-2.666
A_DG11:DC16_B
10
-18.127
-0.277
0.069
-0.267
-28.869
1
19
A
12
B
15
-0.635
A_DG12:DC15_B
11
-23.858
-0.490
-0.128
-0.174
-27.054
1
19
A
13
B
14
-2.827
A_DG13:DC14_B
12
-12.701
-0.701
0.133
-0.258
3.682
38.965
A
A
1
2
2.636
B
B
26
25
3.700
1.757
0.698
-0.341
AA_DC1DC2:DG25DG26_BB
1
0.006
-0.009
38.927
-0.752
-1.045
3.834
46.045
A
A
2
3
17.202
B
B
25
24
4.190
13.279
0.251
-0.739
AA_DC2DA3:DT24DG25_BB
2
2.101
-2.721
44.140
-2.378
-0.094
3.119
36.896
A
A
3
4
-6.200
B
B
24
23
3.084
-3.916
-0.259
-0.433
AA_DA3DA4:DT23DT24_BB
3
-1.304
2.065
36.672
-0.180
0.241
3.176
32.857
A
A
4
5
-1.490
B
B
23
22
3.115
-0.842
-0.687
-0.513
AA_DA4DA5:DT22DT23_BB
4
-3.002
5.314
32.712
-0.767
0.720
3.145
35.865
A
A
5
6
-12.739
B
B
22
21
3.082
-7.786
-0.361
-0.599
AA_DA5DG6:DC21DT22_BB
5
-0.562
0.920
35.033
0.102
0.508
6.383
80.681
A
A
6
8
-13.802
B
B
21
19
6.542
-17.766
0.394
0.209
AA_DG6DA8:DT19DC21_BB
6
-1.940
1.507
79.009
1.088
-0.405
3.275
35.372
A
A
8
9
-5.728
B
B
19
18
3.272
-3.473
0.651
0.196
AA_DA8DC9:DG18DT19_BB
7
2.473
-4.079
35.123
0.836
-0.706
3.311
36.620
A
A
9
10
-2.129
B
B
18
17
3.286
-1.337
0.181
-0.644
AA_DC9DT10:DA17DG18_BB
8
1.141
-1.817
36.579
-0.839
-0.129
3.754
41.726
A
A
10
11
7.312
B
B
17
16
3.885
5.181
-0.215
-0.829
AA_DT10DG11:DC16DA17_BB
9
-5.627
7.941
41.050
-1.806
-0.395
3.316
39.252
A
A
11
12
7.214
B
B
16
15
3.470
4.829
-0.109
-0.915
AA_DG11DG12:DC15DC16_BB
10
3.334
-4.980
38.828
-1.963
0.577
3.225
38.702
A
A
12
13
-1.140
B
B
15
14
3.184
-0.755
-0.644
-0.286
AA_DG12DG13:DC14DC15_BB
11
-2.745
4.146
38.601
-0.341
0.642
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: 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.
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
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
0.070
SIDE CHAIN
1
A
DG
11
0.087
SIDE CHAIN
1
B
DT
22
0.077
SIDE CHAIN
1
B
DG
25
0.065
SIDE CHAIN
1
4.02
0.60
118.60
122.62
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
1
5.80
0.60
118.60
124.40
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
1
-5.24
0.80
123.70
118.46
A
A
A
C5
C6
N6
DA
DA
DA
5
5
5
N
1
5.16
0.70
119.90
125.06
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
1
5.01
0.60
118.60
123.61
A
A
A
N1
C6
N6
DA
DA
DA
8
8
8
N
1
-4.89
0.80
123.70
118.81
A
A
A
C5
C6
N6
DA
DA
DA
8
8
8
N
1
5.34
0.70
119.90
125.24
A
A
A
N3
C2
N2
DG
DG
DG
12
12
12
N
1
4.65
0.70
119.90
124.55
A
A
A
N3
C2
N2
DG
DG
DG
13
13
13
N
1
3.94
0.60
118.60
122.54
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
1
8.05
1.20
119.70
127.75
B
B
B
C3'
O3'
P
DC
DC
DT
21
21
22
Y
1
7.65
1.20
119.70
127.35
B
B
B
C3'
O3'
P
DT
DT
DT
22
22
23
Y
1
4.50
0.70
119.90
124.40
B
B
B
N3
C2
N2
DG
DG
DG
25
25
25
N
1
4.86
0.70
119.90
124.76
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
N9
C4
DA
DA
8
8
0.038
0.006
1.374
1.412
N
1
B
B
C8
N9
DG
DG
25
25
-0.042
0.007
1.374
1.332
N
NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: ALPHA ANOMER
1
N
N
2
N
N
covale
1.577
both
A
DG
6
A
O3'
DG
6
1_555
A
ORP
7
A
P
ORP
7
1_555
covale
1.581
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
1GIZ
PDB
1
1GIZ
1GIZ
PDB
2
1GIZ
1
13
1GIZ
1
13
1GIZ
A
1
1
13
14
26
1GIZ
14
26
1GIZ
B
2
1
13
1
P 1