1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Junker, H.-D.
Hoehn, S.T.
Bunt, R.C.
Marathius, V.
Chen, J.
Turner, C.J.
Stubbe, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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
C2 H5 O6 P
156.031
2-PHOSPHOGLYCOLIC ACID
non-polymer
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
N
P
N
145
N
O
N
146
N
O
N
147
N
O
N
148
N
O
N
149
N
C
N
150
N
C
N
151
N
O
N
152
N
O
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
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
doub
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
doub
N
161
N
sing
N
162
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
30
5497
5508
10.1093/nar/gkf681
12490718
Synthesis, Characterization and Solution Structure of Tethered Oligonucleotides Containing an Internal 3'-Phosphoglycolate, 5'-Phosphate Gapped Lesion
2002
10.2210/pdb1g5k/pdb
pdb_00001g5k
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
1802.232
5'-D(*CP*CP*AP*AP*AP*G)-3'
1
syn
polymer
1849.241
5'-D(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
156.031
2-PHOSPHOGLYCOLIC ACID
1
man
non-polymer
no
no
(DC)(DC)(DA)(DA)(DA)(DG)
CCAAAG
A
polydeoxyribonucleotide
no
no
(DA)(DC)(DT)(DG)(DG)(DG)
ACTGGG
B
polydeoxyribonucleotide
no
no
(DC)(DC)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DT)(DG)(DG)
CCCAGTACTTTGG
C
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
34.031
1
19
A
1
C
26
-1.125
A_DC1:DG26_C
1
-21.216
0.741
-0.282
-0.164
13.149
1
19
A
2
C
25
-5.105
A_DC2:DG25_C
2
-15.557
0.662
0.243
-0.383
-0.474
1
20
A
3
C
24
2.678
A_DA3:DT24_C
3
3.651
-0.012
0.484
-0.193
7.468
1
20
A
4
C
23
2.520
A_DA4:DT23_C
4
-4.579
0.040
0.824
-0.267
9.468
1
20
A
5
C
22
-4.115
A_DA5:DT22_C
5
-4.671
-0.180
0.655
-0.336
18.521
1
19
A
6
C
21
-2.836
A_DG6:DC21_C
6
-0.796
-0.906
0.945
-0.450
-8.449
1
20
B
8
C
19
5.930
B_DA8:DT19_C
7
4.043
-0.040
0.526
-0.247
-1.600
1
19
B
9
C
18
9.270
B_DC9:DG18_C
8
16.476
0.789
0.884
-0.359
6.801
1
20
B
10
C
17
2.400
B_DT10:DA17_C
9
6.494
0.005
0.425
-0.207
-12.553
1
19
B
11
C
16
1.238
B_DG11:DC16_C
10
-18.197
-0.866
-0.378
-0.339
-32.475
1
19
B
12
C
15
-6.156
B_DG12:DC15_C
11
-19.897
-0.657
-0.114
-0.227
-18.467
1
19
B
13
C
14
-9.319
B_DG13:DC14_C
12
-9.203
-0.612
0.034
-0.347
3.737
40.759
A
A
1
2
11.862
C
C
26
25
3.931
8.207
0.346
-0.515
AA_DC1DC2:DG25DG26_CC
1
-1.978
2.859
39.911
-1.813
-0.756
3.978
37.584
A
A
2
3
-17.424
C
C
25
24
3.817
-11.061
0.580
-1.306
AA_DC2DA3:DT24DG25_CC
2
-2.789
4.393
35.871
-0.266
-1.343
2.989
35.218
A
A
3
4
5.705
C
C
24
23
3.073
3.432
-0.420
-1.027
AA_DA3DA4:DT23DT24_CC
3
-5.789
9.624
34.589
-2.174
-0.112
3.140
35.463
A
A
4
5
0.176
C
C
23
22
3.121
0.107
-0.636
-0.989
AA_DA4DA5:DT22DT23_CC
4
-1.382
2.270
35.436
-1.638
0.850
2.906
36.326
A
A
5
6
-2.935
C
C
22
21
2.876
-1.827
-0.075
-0.776
AA_DA5DG6:DC21DT22_CC
5
-3.262
5.240
36.140
-1.019
-0.284
6.468
91.225
A
B
6
8
-4.485
C
C
21
19
6.571
-6.390
0.487
-0.315
AB_DG6DA8:DT19DC21_CC
6
-14.333
10.059
90.160
0.031
-0.905
3.561
39.975
B
B
8
9
-2.275
C
C
19
18
3.532
-1.555
-0.045
-0.853
BB_DA8DC9:DG18DT19_CC
7
-1.106
1.618
39.931
-1.054
-0.071
3.345
28.835
B
B
9
10
-11.991
C
C
18
17
3.234
-5.914
-0.201
-1.136
BB_DC9DT10:DA17DG18_CC
8
3.712
-7.526
27.994
-0.934
1.250
3.884
36.281
B
B
10
11
-2.760
C
C
17
16
3.917
-1.711
-0.207
-1.158
BB_DT10DG11:DC16DA17_CC
9
5.946
-9.593
35.767
-1.572
1.332
3.953
42.874
B
B
11
12
-0.648
C
C
16
15
3.863
-0.473
-0.963
-0.189
BB_DG11DG12:DC15DC16_CC
10
-5.453
7.479
42.539
-0.202
0.667
3.042
39.151
B
B
12
13
-5.225
C
C
15
14
3.021
-3.494
-0.825
0.205
BB_DG12DG13:DC14DC15_CC
11
-2.788
4.169
38.904
0.696
0.920
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Data collection
1
0
2003-01-07
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
1
4
2024-05-22
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
ensemble model OF PDB ENTRY 1N0K
MINIMIZED AVERAGE STRUCTURE OF PDB ENTRY 1N0O
MINIMIZED AVERAGE STRUCTURE OF PDB ENTRY 1G5K
RCSB
Y
RCSB
2002-10-14
REL
PGA
2-PHOSPHOGLYCOLIC ACID
minimum rmsd and nmr constraints violation
10
10
PECOSY
TOCSY
NOESY
HSQC
GE-HSQC
%
40 mM NaHPO4
6.9
1.0
atm
293.15
K
CONJUGATE GRADIENT MINIMIZATION
Brunger
refinement
XPLOR
3.851
Brunger
structure solution
XPLOR
3.851
500
custom build
600
custom build
750
custom build
T
7
4
PGA
PGA
7
A
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
T
7
n
1
DA
8
B
C
9
n
2
DC
9
B
T
10
n
3
DT
10
B
G
11
n
4
DG
11
B
G
12
n
5
DG
12
B
G
13
n
6
DG
13
B
C
14
n
1
DC
14
C
C
15
n
2
DC
15
C
C
16
n
3
DC
16
C
A
17
n
4
DA
17
C
G
18
n
5
DG
18
C
T
19
n
6
DT
19
C
A
20
n
7
DA
20
C
C
21
n
8
DC
21
C
T
22
n
9
DT
22
C
T
23
n
10
DT
23
C
T
24
n
11
DT
24
C
G
25
n
12
DG
25
C
G
26
n
13
DG
26
C
author_defined_assembly
3
trimeric
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
DG
6
0.056
SIDE CHAIN
1
B
DC
9
0.095
SIDE CHAIN
1
B
DG
13
0.093
SIDE CHAIN
1
C
DA
20
0.053
SIDE CHAIN
1
C
DT
22
0.094
SIDE CHAIN
1
C
DT
23
0.096
SIDE CHAIN
1
C
DG
25
0.074
SIDE CHAIN
2
A
DC
2
0.075
SIDE CHAIN
2
B
DT
10
0.072
SIDE CHAIN
2
B
DG
11
0.078
SIDE CHAIN
2
B
DG
13
0.059
SIDE CHAIN
2
C
DC
14
0.082
SIDE CHAIN
2
C
DC
16
0.094
SIDE CHAIN
2
C
DG
18
0.081
SIDE CHAIN
2
C
DT
19
0.074
SIDE CHAIN
2
C
DA
20
0.073
SIDE CHAIN
2
C
DC
21
0.063
SIDE CHAIN
2
C
DT
22
0.092
SIDE CHAIN
2
C
DT
23
0.100
SIDE CHAIN
2
C
DG
25
0.054
SIDE CHAIN
2
C
DG
26
0.060
SIDE CHAIN
3
A
DG
6
0.067
SIDE CHAIN
3
B
DG
11
0.054
SIDE CHAIN
3
C
DC
14
0.059
SIDE CHAIN
3
C
DC
15
0.065
SIDE CHAIN
3
C
DC
16
0.102
SIDE CHAIN
3
C
DT
23
0.080
SIDE CHAIN
3
C
DG
25
0.065
SIDE CHAIN
4
A
DC
1
0.090
SIDE CHAIN
4
A
DA
5
0.062
SIDE CHAIN
4
B
DG
11
0.075
SIDE CHAIN
4
C
DC
14
0.092
SIDE CHAIN
4
C
DC
16
0.100
SIDE CHAIN
4
C
DC
21
0.068
SIDE CHAIN
4
C
DT
23
0.126
SIDE CHAIN
5
A
DG
6
0.053
SIDE CHAIN
5
B
DG
11
0.072
SIDE CHAIN
5
C
DC
14
0.106
SIDE CHAIN
5
C
DC
16
0.095
SIDE CHAIN
5
C
DA
20
0.062
SIDE CHAIN
5
C
DT
22
0.063
SIDE CHAIN
5
C
DT
23
0.097
SIDE CHAIN
5
C
DG
25
0.062
SIDE CHAIN
6
A
DC
1
0.101
SIDE CHAIN
6
A
DG
6
0.051
SIDE CHAIN
6
B
DT
10
0.063
SIDE CHAIN
6
B
DG
11
0.080
SIDE CHAIN
6
C
DC
14
0.092
SIDE CHAIN
6
C
DC
16
0.103
SIDE CHAIN
6
C
DA
20
0.063
SIDE CHAIN
6
C
DT
23
0.098
SIDE CHAIN
6
C
DG
25
0.104
SIDE CHAIN
6
C
DG
26
0.089
SIDE CHAIN
7
A
DC
1
0.080
SIDE CHAIN
7
A
DA
5
0.061
SIDE CHAIN
7
B
DG
11
0.062
SIDE CHAIN
7
C
DC
14
0.092
SIDE CHAIN
7
C
DC
16
0.100
SIDE CHAIN
7
C
DA
20
0.058
SIDE CHAIN
7
C
DC
21
0.080
SIDE CHAIN
7
C
DT
23
0.085
SIDE CHAIN
7
C
DG
26
0.074
SIDE CHAIN
8
B
DG
11
0.054
SIDE CHAIN
8
B
DG
12
0.052
SIDE CHAIN
8
C
DC
14
0.090
SIDE CHAIN
8
C
DT
22
0.066
SIDE CHAIN
8
C
DT
23
0.101
SIDE CHAIN
8
C
DT
24
0.059
SIDE CHAIN
8
C
DG
25
0.066
SIDE CHAIN
9
A
DC
1
0.074
SIDE CHAIN
9
A
DA
5
0.053
SIDE CHAIN
9
B
DG
11
0.074
SIDE CHAIN
9
C
DC
14
0.094
SIDE CHAIN
9
C
DC
16
0.099
SIDE CHAIN
9
C
DT
23
0.125
SIDE CHAIN
10
A
DG
6
0.052
SIDE CHAIN
10
B
DT
10
0.065
SIDE CHAIN
10
B
DG
11
0.079
SIDE CHAIN
10
C
DC
14
0.103
SIDE CHAIN
10
C
DC
16
0.091
SIDE CHAIN
10
C
DA
20
0.058
SIDE CHAIN
10
C
DT
22
0.062
SIDE CHAIN
10
C
DT
23
0.090
SIDE CHAIN
10
C
DG
25
0.075
SIDE CHAIN
1
8.47
1.20
119.70
128.17
A
A
A
C3'
O3'
P
DC
DC
DA
2
2
3
Y
1
4.82
0.60
118.60
123.42
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
1
4.85
0.60
118.60
123.45
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
1
5.79
0.70
119.90
125.69
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
1
3.67
0.60
118.60
122.27
B
B
B
N1
C6
N6
DA
DA
DA
8
8
8
N
1
11.15
1.20
119.70
130.85
B
B
B
C3'
O3'
P
DT
DT
DG
10
10
11
Y
1
5.23
0.70
119.90
125.13
B
B
B
N3
C2
N2
DG
DG
DG
11
11
11
N
1
5.88
0.70
119.90
125.78
B
B
B
N3
C2
N2
DG
DG
DG
12
12
12
N
1
5.12
0.70
119.90
125.02
B
B
B
N3
C2
N2
DG
DG
DG
13
13
13
N
1
3.66
0.60
118.90
122.56
C
C
C
N1
C2
O2
DC
DC
DC
14
14
14
N
1
8.54
1.20
119.70
128.24
C
C
C
C3'
O3'
P
DC
DC
DT
21
21
22
Y
1
7.42
1.20
119.70
127.12
C
C
C
C3'
O3'
P
DT
DT
DG
24
24
25
Y
1
4.91
0.70
119.90
124.81
C
C
C
N3
C2
N2
DG
DG
DG
26
26
26
N
2
8.06
1.20
119.70
127.76
A
A
A
C3'
O3'
P
DC
DC
DA
2
2
3
Y
2
4.36
0.60
118.60
122.96
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
2
4.79
0.60
118.60
123.39
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
2
5.48
0.70
119.90
125.38
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
2
2.00
0.30
108.30
110.30
B
B
B
O4'
C1'
N9
DA
DA
DA
8
8
8
N
2
4.43
0.70
118.00
122.43
B
B
B
N3
C4
N4
DC
DC
DC
9
9
9
N
2
7.21
0.70
119.90
127.11
B
B
B
N3
C2
N2
DG
DG
DG
11
11
11
N
2
5.65
0.70
119.90
125.55
B
B
B
N3
C2
N2
DG
DG
DG
12
12
12
N
2
4.80
0.70
119.90
124.70
B
B
B
N3
C2
N2
DG
DG
DG
13
13
13
N
2
3.68
0.60
118.60
122.28
C
C
C
N1
C6
N6
DA
DA
DA
17
17
17
N
2
3.45
0.50
111.90
115.35
C
C
C
C2
N3
C4
DG
DG
DG
18
18
18
N
2
7.87
1.20
119.70
127.57
C
C
C
C3'
O3'
P
DC
DC
DT
21
21
22
Y
2
6.58
0.70
119.90
126.48
C
C
C
N3
C2
N2
DG
DG
DG
25
25
25
N
2
4.98
0.70
119.90
124.88
C
C
C
N3
C2
N2
DG
DG
DG
26
26
26
N
3
3.60
0.60
118.90
122.50
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
3
4.95
0.60
118.60
123.55
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
3
4.99
0.60
118.60
123.59
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
3
5.85
0.70
119.90
125.75
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
3
4.53
0.60
118.60
123.13
B
B
B
N1
C6
N6
DA
DA
DA
8
8
8
N
3
8.64
1.20
119.70
128.34
B
B
B
C3'
O3'
P
DT
DT
DG
10
10
11
Y
3
4.45
0.70
119.90
124.35
B
B
B
N3
C2
N2
DG
DG
DG
11
11
11
N
3
6.18
0.70
119.90
126.08
B
B
B
N3
C2
N2
DG
DG
DG
12
12
12
N
3
4.82
0.70
119.90
124.72
B
B
B
N3
C2
N2
DG
DG
DG
13
13
13
N
3
4.98
0.70
119.90
124.88
C
C
C
N3
C2
N2
DG
DG
DG
18
18
18
N
3
8.60
1.20
119.70
128.30
C
C
C
C3'
O3'
P
DT
DT
DT
22
22
23
Y
3
-3.93
0.60
122.90
118.97
C
C
C
C6
C5
C7
DT
DT
DT
23
23
23
N
3
4.45
0.70
119.90
124.35
C
C
C
N3
C2
N2
DG
DG
DG
26
26
26
N
4
3.72
0.60
118.60
122.32
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
4
4.54
0.60
118.60
123.14
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
4
5.74
0.60
118.60
124.34
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
4
-4.93
0.80
123.70
118.77
A
A
A
C5
C6
N6
DA
DA
DA
5
5
5
N
4
7.04
0.70
119.90
126.94
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
4
3.70
0.60
118.60
122.30
B
B
B
N1
C6
N6
DA
DA
DA
8
8
8
N
4
5.80
0.70
119.90
125.70
B
B
B
N3
C2
N2
DG
DG
DG
12
12
12
N
4
4.88
0.70
119.90
124.78
B
B
B
N3
C2
N2
DG
DG
DG
13
13
13
N
4
4.72
0.60
118.60
123.32
C
C
C
N1
C6
N6
DA
DA
DA
17
17
17
N
4
5.20
0.70
119.90
125.10
C
C
C
N3
C2
N2
DG
DG
DG
18
18
18
N
4
-3.97
0.60
122.90
118.93
C
C
C
C6
C5
C7
DT
DT
DT
23
23
23
N
4
7.47
1.20
119.70
127.17
C
C
C
C3'
O3'
P
DT
DT
DG
24
24
25
Y
4
8.29
1.20
119.70
127.99
C
C
C
C3'
O3'
P
DG
DG
DG
25
25
26
Y
5
3.68
0.60
118.90
122.58
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
5
8.21
1.20
119.70
127.91
A
A
A
C3'
O3'
P
DC
DC
DA
2
2
3
Y
5
4.69
0.60
118.60
123.29
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
5
4.69
0.60
118.60
123.29
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
5
4.93
0.70
119.90
124.83
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
5
4.66
0.60
118.60
123.26
B
B
B
N1
C6
N6
DA
DA
DA
8
8
8
N
5
4.26
0.70
119.90
124.16
B
B
B
N3
C2
N2
DG
DG
DG
11
11
11
N
5
5.85
0.70
119.90
125.75
B
B
B
N3
C2
N2
DG
DG
DG
12
12
12
N
5
4.96
0.70
119.90
124.86
B
B
B
N3
C2
N2
DG
DG
DG
13
13
13
N
5
4.31
0.60
118.60
122.91
C
C
C
N1
C6
N6
DA
DA
DA
17
17
17
N
5
-3.75
0.60
122.90
119.15
C
C
C
C6
C5
C7
DT
DT
DT
23
23
23
N
5
4.91
0.70
119.90
124.81
C
C
C
N3
C2
N2
DG
DG
DG
26
26
26
N
6
4.03
0.60
118.60
122.63
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
6
4.68
0.60
118.60
123.28
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
6
4.79
0.60
118.60
123.39
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
6
4.44
0.70
119.90
124.34
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
6
5.84
0.60
118.60
124.44
B
B
B
N1
C6
N6
DA
DA
DA
8
8
8
N
6
-5.10
0.80
123.70
118.60
B
B
B
C5
C6
N6
DA
DA
DA
8
8
8
N
6
6.08
0.70
119.90
125.98
B
B
B
N3
C2
N2
DG
DG
DG
12
12
12
N
6
4.96
0.70
119.90
124.86
B
B
B
N3
C2
N2
DG
DG
DG
13
13
13
N
6
3.95
0.60
118.60
122.55
C
C
C
N1
C6
N6
DA
DA
DA
17
17
17
N
6
4.99
0.70
119.90
124.89
C
C
C
N3
C2
N2
DG
DG
DG
18
18
18
N
6
-4.34
0.60
122.90
118.56
C
C
C
C6
C5
C7
DT
DT
DT
23
23
23
N
6
5.31
0.70
119.90
125.21
C
C
C
N3
C2
N2
DG
DG
DG
25
25
25
N
6
10.84
1.20
119.70
130.54
C
C
C
C3'
O3'
P
DG
DG
DG
25
25
26
Y
7
3.70
0.60
118.60
122.30
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
7
4.08
0.60
118.60
122.68
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
7
5.45
0.60
118.60
124.05
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
7
5.82
0.70
119.90
125.72
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
7
3.73
0.60
118.60
122.33
B
B
B
N1
C6
N6
DA
DA
DA
8
8
8
N
7
5.84
0.70
119.90
125.74
B
B
B
N3
C2
N2
DG
DG
DG
12
12
12
N
7
4.93
0.70
119.90
124.83
B
B
B
N3
C2
N2
DG
DG
DG
13
13
13
N
7
4.04
0.60
118.60
122.64
C
C
C
N1
C6
N6
DA
DA
DA
17
17
17
N
7
5.37
0.70
119.90
125.27
C
C
C
N3
C2
N2
DG
DG
DG
18
18
18
N
7
8.20
1.20
119.70
127.90
C
C
C
C3'
O3'
P
DC
DC
DT
21
21
22
Y
7
-3.88
0.60
122.90
119.02
C
C
C
C6
C5
C7
DT
DT
DT
23
23
23
N
7
4.42
0.70
119.90
124.32
C
C
C
N3
C2
N2
DG
DG
DG
25
25
25
N
7
8.14
1.20
119.70
127.84
C
C
C
C3'
O3'
P
DG
DG
DG
25
25
26
Y
8
3.64
0.60
118.90
122.54
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
8
5.12
0.60
118.60
123.72
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
8
4.82
0.60
118.60
123.42
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
8
5.72
0.70
119.90
125.62
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
8
4.50
0.60
118.60
123.10
B
B
B
N1
C6
N6
DA
DA
DA
8
8
8
N
8
7.40
1.20
119.70
127.10
B
B
B
C3'
O3'
P
DT
DT
DG
10
10
11
Y
8
4.86
0.70
119.90
124.76
B
B
B
N3
C2
N2
DG
DG
DG
12
12
12
N
8
6.77
0.70
119.90
126.67
B
B
B
N3
C2
N2
DG
DG
DG
13
13
13
N
8
9.14
1.20
119.70
128.84
C
C
C
C3'
O3'
P
DC
DC
DC
15
15
16
Y
8
3.99
0.60
118.60
122.59
C
C
C
N1
C6
N6
DA
DA
DA
17
17
17
N
8
4.65
0.70
119.90
124.55
C
C
C
N3
C2
N2
DG
DG
DG
18
18
18
N
8
4.72
0.70
119.90
124.62
C
C
C
N3
C2
N2
DG
DG
DG
26
26
26
N
9
3.66
0.60
118.90
122.56
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
9
3.85
0.60
118.60
122.45
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
9
4.65
0.60
118.60
123.25
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
9
6.26
0.60
118.60
124.86
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
9
-5.50
0.80
123.70
118.20
A
A
A
C5
C6
N6
DA
DA
DA
5
5
5
N
9
7.12
0.70
119.90
127.02
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
9
5.83
0.70
119.90
125.73
B
B
B
N3
C2
N2
DG
DG
DG
12
12
12
N
9
4.95
0.70
119.90
124.85
B
B
B
N3
C2
N2
DG
DG
DG
13
13
13
N
9
4.81
0.60
118.60
123.41
C
C
C
N1
C6
N6
DA
DA
DA
17
17
17
N
9
5.14
0.70
119.90
125.04
C
C
C
N3
C2
N2
DG
DG
DG
18
18
18
N
9
3.74
0.60
118.90
122.64
C
C
C
N1
C2
O2
DC
DC
DC
21
21
21
N
9
8.07
1.20
119.70
127.77
C
C
C
C3'
O3'
P
DT
DT
DG
24
24
25
Y
9
4.49
0.70
119.90
124.39
C
C
C
N3
C2
N2
DG
DG
DG
26
26
26
N
10
3.66
0.60
118.90
122.56
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
10
7.38
1.20
119.70
127.08
A
A
A
C3'
O3'
P
DC
DC
DA
2
2
3
Y
10
5.01
0.60
118.60
123.61
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
10
4.78
0.60
118.60
123.38
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
10
4.98
0.70
119.90
124.88
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
10
4.81
0.60
118.60
123.41
B
B
B
N1
C6
N6
DA
DA
DA
8
8
8
N
10
4.25
0.70
119.90
124.15
B
B
B
N3
C2
N2
DG
DG
DG
11
11
11
N
10
5.86
0.70
119.90
125.76
B
B
B
N3
C2
N2
DG
DG
DG
12
12
12
N
10
4.89
0.70
119.90
124.79
B
B
B
N3
C2
N2
DG
DG
DG
13
13
13
N
10
4.51
0.60
118.60
123.11
C
C
C
N1
C6
N6
DA
DA
DA
17
17
17
N
10
7.37
1.20
119.70
127.07
C
C
C
C3'
O3'
P
DA
DA
DG
17
17
18
Y
10
-3.84
0.60
122.90
119.06
C
C
C
C6
C5
C7
DT
DT
DT
23
23
23
N
1
B
B
P
OP3
DA
DA
8
8
-0.124
0.012
1.607
1.483
N
1
C
C
C5'
C4'
DT
DT
19
19
0.044
0.007
1.512
1.556
N
1
C
C
C5'
C4'
DA
DA
20
20
0.046
0.007
1.512
1.558
N
1
C
C
C5'
C4'
DT
DT
23
23
0.043
0.007
1.512
1.555
N
2
B
B
P
OP3
DA
DA
8
8
-0.124
0.012
1.607
1.483
N
2
B
B
C5'
C4'
DG
DG
11
11
0.044
0.007
1.512
1.556
N
2
C
C
C5'
C4'
DA
DA
20
20
0.052
0.007
1.512
1.564
N
2
C
C
C5'
C4'
DT
DT
22
22
0.042
0.007
1.512
1.554
N
2
C
C
C5'
C4'
DT
DT
23
23
0.044
0.007
1.512
1.556
N
3
B
B
P
OP3
DA
DA
8
8
-0.121
0.012
1.607
1.486
N
3
B
B
N1
C2
DT
DT
10
10
0.049
0.008
1.376
1.425
N
3
C
C
C5'
C4'
DC
DC
21
21
0.042
0.007
1.512
1.554
N
3
C
C
C5'
C4'
DT
DT
22
22
0.044
0.007
1.512
1.556
N
4
A
A
C5'
C4'
DA
DA
3
3
0.044
0.007
1.512
1.556
N
4
B
B
P
OP3
DA
DA
8
8
-0.124
0.012
1.607
1.483
N
4
B
B
C5'
C4'
DG
DG
11
11
0.044
0.007
1.512
1.556
N
4
C
C
C5'
C4'
DT
DT
19
19
0.046
0.007
1.512
1.558
N
4
C
C
C5'
C4'
DT
DT
22
22
0.046
0.007
1.512
1.558
N
4
C
C
N1
C2
DT
DT
22
22
0.052
0.008
1.376
1.428
N
5
B
B
P
OP3
DA
DA
8
8
-0.130
0.012
1.607
1.477
N
5
C
C
C5'
C4'
DC
DC
21
21
0.042
0.007
1.512
1.554
N
5
C
C
C5'
C4'
DT
DT
22
22
0.044
0.007
1.512
1.556
N
6
A
A
C5'
C4'
DA
DA
3
3
0.045
0.007
1.512
1.557
N
6
A
A
C5'
C4'
DA
DA
4
4
0.044
0.007
1.512
1.556
N
6
B
B
P
OP3
DA
DA
8
8
-0.124
0.012
1.607
1.483
N
6
C
C
N1
C2
DT
DT
19
19
0.048
0.008
1.376
1.424
N
6
C
C
C5'
C4'
DT
DT
22
22
0.042
0.007
1.512
1.554
N
7
A
A
C5'
C4'
DA
DA
3
3
0.048
0.007
1.512
1.560
N
7
B
B
P
OP3
DA
DA
8
8
-0.122
0.012
1.607
1.485
N
7
B
B
C5'
C4'
DG
DG
11
11
0.044
0.007
1.512
1.556
N
7
C
C
C5'
C4'
DT
DT
19
19
0.045
0.007
1.512
1.557
N
7
C
C
C5'
C4'
DC
DC
21
21
0.042
0.007
1.512
1.554
N
7
C
C
C5'
C4'
DT
DT
22
22
0.051
0.007
1.512
1.563
N
7
C
C
N1
C2
DT
DT
22
22
0.053
0.008
1.376
1.429
N
8
B
B
P
OP3
DA
DA
8
8
-0.124
0.012
1.607
1.483
N
8
C
C
C5'
C4'
DT
DT
22
22
0.045
0.007
1.512
1.557
N
8
C
C
C5'
C4'
DT
DT
23
23
0.044
0.007
1.512
1.556
N
9
B
B
P
OP3
DA
DA
8
8
-0.125
0.012
1.607
1.482
N
9
B
B
C5'
C4'
DG
DG
11
11
0.043
0.007
1.512
1.555
N
9
C
C
C5'
C4'
DT
DT
19
19
0.047
0.007
1.512
1.559
N
9
C
C
C5'
C4'
DA
DA
20
20
0.042
0.007
1.512
1.554
N
9
C
C
C5'
C4'
DT
DT
22
22
0.043
0.007
1.512
1.555
N
9
C
C
N1
C2
DT
DT
22
22
0.051
0.008
1.376
1.427
N
10
B
B
P
OP3
DA
DA
8
8
-0.130
0.012
1.607
1.477
N
10
C
C
C5'
C4'
DC
DC
21
21
0.044
0.007
1.512
1.556
N
10
C
C
C5'
C4'
DT
DT
22
22
0.045
0.007
1.512
1.557
N
10
C
C
C5'
C4'
DT
DT
23
23
0.042
0.007
1.512
1.554
N
NMR Structrure of d(CCAAAGXACTGGG), X is a 3'-phosphoglycolate, 5'-phosphate gapped lesion, 10 structures
1
N
N
2
N
N
3
N
N
4
N
N
covale
1.578
one
A
DG
6
A
O3'
DG
6
1_555
A
PGA
7
D
P
PGA
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
C
DG
26
C
N1
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
C
DG
26
C
O6
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
C
DG
26
C
N2
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
C
DG
25
C
N1
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
C
DG
25
C
O6
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
C
DG
25
C
N2
DG
12
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
C
DT
24
C
N3
DT
11
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
C
DT
24
C
O4
DT
11
1_555
hydrog
DA-DT PAIR
A
DA
4
A
N6
DA
4
1_555
C
DT
22
C
O4
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
C
DT
23
C
N3
DT
10
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
C
DT
23
C
O4
DT
10
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
C
DT
22
C
N3
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
C
DT
22
C
O4
DT
9
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
C
DC
21
C
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
C
DC
21
C
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
C
DC
21
C
N4
DC
8
1_555
hydrog
WATSON-CRICK
B
DA
8
B
N1
DA
1
1_555
C
DT
19
C
N3
DT
6
1_555
hydrog
WATSON-CRICK
B
DA
8
B
N6
DA
1
1_555
C
DT
19
C
O4
DT
6
1_555
hydrog
WATSON-CRICK
B
DC
9
B
N3
DC
2
1_555
C
DG
18
C
N1
DG
5
1_555
hydrog
WATSON-CRICK
B
DC
9
B
N4
DC
2
1_555
C
DG
18
C
O6
DG
5
1_555
hydrog
WATSON-CRICK
B
DC
9
B
O2
DC
2
1_555
C
DG
18
C
N2
DG
5
1_555
hydrog
WATSON-CRICK
B
DT
10
B
N3
DT
3
1_555
C
DA
17
C
N1
DA
4
1_555
hydrog
WATSON-CRICK
B
DT
10
B
O4
DT
3
1_555
C
DA
17
C
N6
DA
4
1_555
hydrog
WATSON-CRICK
B
DG
11
B
N1
DG
4
1_555
C
DC
16
C
N3
DC
3
1_555
hydrog
WATSON-CRICK
B
DG
11
B
N2
DG
4
1_555
C
DC
16
C
O2
DC
3
1_555
hydrog
WATSON-CRICK
B
DG
11
B
O6
DG
4
1_555
C
DC
16
C
N4
DC
3
1_555
hydrog
WATSON-CRICK
B
DG
12
B
N1
DG
5
1_555
C
DC
15
C
N3
DC
2
1_555
hydrog
WATSON-CRICK
B
DG
12
B
N2
DG
5
1_555
C
DC
15
C
O2
DC
2
1_555
hydrog
WATSON-CRICK
B
DG
12
B
O6
DG
5
1_555
C
DC
15
C
N4
DC
2
1_555
hydrog
WATSON-CRICK
B
DG
13
B
N1
DG
6
1_555
C
DC
14
C
N3
DC
1
1_555
hydrog
WATSON-CRICK
B
DG
13
B
N2
DG
6
1_555
C
DC
14
C
O2
DC
1
1_555
hydrog
WATSON-CRICK
B
DG
13
B
O6
DG
6
1_555
C
DC
14
C
N4
DC
1
1_555
DNA
DNA, bleomycin, phosphoglycolate
1G5K
PDB
1
1G5K
1G5K
PDB
2
1G5K
1G5K
PDB
3
1G5K
1
6
1G5K
1
6
1G5K
A
1
1
6
8
13
1G5K
8
13
1G5K
B
2
1
6
14
26
1G5K
14
26
1G5K
C
3
1
13
BINDING SITE FOR RESIDUE PGA A 7
A
PGA
7
Software
1
A
DG
6
A
DG
6
1
1_555