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
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/pdb1n0k/pdb
pdb_00001n0k
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
1818.231
5'-D(*CP*CP*AP*AP*GP*G)-3'
1
syn
polymer
1840.227
5'-D(P*CP*TP*TP*GP*GP*G)-3'
1
syn
polymer
3952.574
5'-D(*CP*CP*CP*AP*AP*GP*GP*CP*CP*TP*TP*GP*G)-3'
1
syn
polymer
156.031
2-PHOSPHOGLYCOLIC ACID
1
man
non-polymer
no
no
(DC)(DC)(DA)(DA)(DG)(DG)
CCAAGG
A
polydeoxyribonucleotide
no
no
(DC)(DT)(DT)(DG)(DG)(DG)
CTTGGG
B
polydeoxyribonucleotide
no
no
(DC)(DC)(DC)(DA)(DA)(DG)(DG)(DC)(DC)(DT)(DT)(DG)(DG)
CCCAAGGCCTTGG
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
-0.681
1
22
A
1
C
26
-8.103
A_DC1:DG26_C
1
2.223
-0.702
-0.261
-1.437
-7.719
1
19
A
2
C
25
-1.150
A_DC2:DG25_C
2
-0.272
0.408
0.003
-0.204
-1.591
1
20
A
3
C
24
-4.763
A_DA3:DT24_C
3
-15.103
0.188
-0.237
-0.136
1.925
1
20
A
4
C
23
-1.861
A_DA4:DT23_C
4
-11.139
-0.205
0.395
-0.259
3.992
1
19
A
5
C
22
-0.420
A_DG5:DC22_C
5
-8.669
-0.526
0.164
-0.225
-9.570
1
19
A
6
C
21
-2.837
A_DG6:DC21_C
6
3.861
-0.163
-0.414
-0.200
-1.438
1
19
B
8
C
19
-4.880
B_DC8:DG19_C
7
-1.044
0.635
0.437
-0.361
5.622
1
20
B
9
C
18
-3.007
B_DT9:DA18_C
8
-6.228
0.195
0.409
-0.240
-4.145
1
20
B
10
C
17
-7.367
B_DT10:DA17_C
9
-7.672
-0.115
0.535
-0.413
11.291
1
19
B
11
C
16
-8.188
B_DG11:DC16_C
10
-17.548
-0.111
0.632
-0.392
-6.773
1
19
B
12
C
15
-6.810
B_DG12:DC15_C
11
-17.724
0.058
0.374
-0.319
-19.415
1
19
B
13
C
14
-17.920
B_DG13:DC14_C
12
-12.084
-1.015
-0.455
-0.780
4.185
58.590
A
A
1
2
-34.604
C
C
26
25
4.826
-32.266
0.323
-0.102
AA_DC1DC2:DG25DG26_CC
1
-0.597
0.641
49.573
2.452
-0.377
3.047
38.319
A
A
2
3
5.485
C
C
25
24
3.358
3.548
-0.313
-0.865
AA_DC2DA3:DT24DG25_CC
2
11.024
-17.042
36.590
-1.763
1.862
2.894
35.023
A
A
3
4
-1.208
C
C
24
23
2.966
-0.722
0.069
-0.026
AA_DA3DA4:DT23DT24_CC
3
-7.115
11.902
34.308
0.055
-1.084
3.342
34.957
A
A
4
5
-7.905
C
C
23
22
3.289
-4.733
0.188
-0.727
AA_DA4DG5:DC22DT23_CC
4
-1.930
3.224
34.593
-0.483
-0.610
3.869
34.642
A
A
5
6
-4.652
C
C
22
21
3.742
-2.758
0.399
-1.534
AA_DG5DG6:DC21DC22_CC
5
4.911
-8.282
34.194
-2.080
0.214
6.990
83.833
A
B
6
8
-1.364
C
C
21
19
6.963
-1.823
1.367
-0.467
AB_DG6DC8:DG19DC21_CC
6
1.583
-1.185
83.804
-0.257
-0.943
3.362
32.547
B
B
8
9
-18.452
C
C
19
18
3.293
-10.169
0.483
-0.662
BB_DC8DT9:DA18DG19_CC
7
2.195
-3.982
30.882
0.675
-0.462
3.489
36.366
B
B
9
10
8.817
C
C
18
17
3.595
5.482
-0.589
-0.294
BB_DT9DT10:DA17DA18_CC
8
1.410
-2.268
35.938
-1.303
1.158
2.952
38.196
B
B
10
11
-2.494
C
C
17
16
3.022
-1.625
-0.177
0.125
BB_DT10DG11:DC16DA17_CC
9
6.010
-9.223
37.703
0.380
0.967
3.840
44.092
B
B
11
12
-1.560
C
C
16
15
3.794
-1.167
0.710
0.526
BB_DG11DG12:DC15DC16_CC
10
6.168
-8.242
43.665
0.830
-0.266
3.353
41.878
B
B
12
13
-14.754
C
C
15
14
3.504
-10.400
-1.625
1.093
BB_DG12DG13:DC14DC15_CC
11
-6.834
9.696
40.066
2.695
1.507
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2003-01-07
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
_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
This entry is the ensemble model for PDB ENTRY 1N0K
ENSEMBLE: 1G5K is the structure of the oligonucleotide containing the phosphoglycolate lesion without the bleomycin bound.
Minimized average structure: NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING A PHOSPHOGLYCOLATE LESION
RCSB
Y
RCSB
2002-10-14
REL
PGA
2-PHOSPHOGLYCOLIC ACID
minimum rmsd and nmr constraints violation
10
1
PECOSY
TOCSY
NOESY
HSQC
GE-HSQC
40 mM NaH2PO4
6.9
1
atm
293.15
K
conjugate gradient
minimized average structure
1.4 mM oligonucleotide
Brunger
refinement
XPLOR
3.851
Brunger
structure solution
XPLOR
3.851
500
custom build
600
custom build
750
custom build
C
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
G
5
n
5
DG
5
A
G
6
n
6
DG
6
A
C
7
n
1
DC
8
B
T
9
n
2
DT
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
A
18
n
5
DA
18
C
G
19
n
6
DG
19
C
G
20
n
7
DG
20
C
C
21
n
8
DC
21
C
C
22
n
9
DC
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
C
H41
O6
DC
DG
1
26
0.69
1
A
C
N3
H1
DC
DG
1
26
0.76
1
A
C
O2
H21
DC
DG
1
26
1.02
1
A
C
H41
C6
DC
DG
1
26
1.19
1
A
C
N4
O6
DC
DG
1
26
1.38
1
A
C
C4
H1
DC
DG
1
26
1.39
1
B
C
O4
H61
DT
DA
10
17
1.55
1
A
C
C2
H21
DC
DG
1
26
1.59
1
B
C
O6
H41
DG
DC
13
14
1.60
1
A
C
H42
O6
DC
DG
1
26
1.60
1
A
C
N3
N1
DC
DG
1
26
1.66
1
A
C
O2
N2
DC
DG
1
26
1.72
1
A
C
N4
C6
DC
DG
1
26
2.03
1
A
DA
3
0.162
SIDE CHAIN
1
A
DG
6
0.053
SIDE CHAIN
1
B
DT
9
0.080
SIDE CHAIN
1
B
DT
10
0.074
SIDE CHAIN
1
B
DG
11
0.075
SIDE CHAIN
1
C
DC
15
0.118
SIDE CHAIN
1
C
DC
16
0.188
SIDE CHAIN
1
C
DA
17
0.056
SIDE CHAIN
1
C
DG
19
0.060
SIDE CHAIN
1
C
DT
23
0.154
SIDE CHAIN
1
3.08
0.30
108.30
111.38
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
-3.41
0.40
120.30
116.89
A
A
A
C6
N1
C2
DC
DC
DC
1
1
1
N
1
3.40
0.50
117.40
120.80
A
A
A
C4
C5
C6
DC
DC
DC
1
1
1
N
1
-4.76
0.70
121.90
117.14
A
A
A
N3
C2
O2
DC
DC
DC
1
1
1
N
1
2.44
0.30
108.30
110.74
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
7.27
1.20
119.70
126.97
A
A
A
C3'
O3'
P
DC
DC
DA
2
2
3
Y
1
10.68
1.20
119.70
130.38
A
A
A
C3'
O3'
P
DA
DA
DA
3
3
4
Y
1
12.67
1.60
120.90
133.57
B
B
B
P
O5'
C5'
DC
DC
DC
8
8
8
N
1
3.76
0.30
108.30
112.06
B
B
B
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
4.68
0.60
118.90
123.58
B
B
B
N1
C2
O2
DC
DC
DC
8
8
8
N
1
9.60
1.20
119.70
129.30
B
B
B
C3'
O3'
P
DC
DC
DT
8
8
9
Y
1
5.18
0.30
108.30
113.48
B
B
B
O4'
C1'
N1
DT
DT
DT
9
9
9
N
1
-4.16
0.60
122.30
118.14
B
B
B
N3
C2
O2
DT
DT
DT
9
9
9
N
1
15.54
1.60
120.90
136.44
B
B
B
P
O5'
C5'
DT
DT
DT
10
10
10
N
1
4.36
0.70
110.30
114.66
B
B
B
C1'
O4'
C4'
DT
DT
DT
10
10
10
N
1
-4.59
0.60
122.30
117.71
B
B
B
N3
C2
O2
DT
DT
DT
10
10
10
N
1
-4.94
0.60
119.00
114.06
B
B
B
C4
C5
C7
DT
DT
DT
10
10
10
N
1
1.98
0.30
108.30
110.28
B
B
B
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
5.11
0.70
119.90
125.01
B
B
B
N3
C2
N2
DG
DG
DG
11
11
11
N
1
12.99
1.60
120.90
133.89
B
B
B
P
O5'
C5'
DG
DG
DG
12
12
12
N
1
1.85
0.30
108.30
110.15
B
B
B
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
5.76
0.70
119.90
125.66
B
B
B
N3
C2
N2
DG
DG
DG
12
12
12
N
1
6.18
0.70
110.30
116.48
B
B
B
C1'
O4'
C4'
DG
DG
DG
13
13
13
N
1
2.77
0.30
108.30
111.07
B
B
B
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
3.39
0.50
111.90
115.29
B
B
B
C2
N3
C4
DG
DG
DG
13
13
13
N
1
-3.34
0.50
128.60
125.26
B
B
B
N3
C4
C5
DG
DG
DG
13
13
13
N
1
-6.17
0.90
116.20
110.03
B
B
B
N1
C2
N2
DG
DG
DG
13
13
13
N
1
8.46
0.70
119.90
128.36
B
B
B
N3
C2
N2
DG
DG
DG
13
13
13
N
1
4.63
0.60
118.90
123.53
C
C
C
N1
C2
O2
DC
DC
DC
14
14
14
N
1
-3.49
0.40
120.30
116.81
C
C
C
C6
N1
C2
DC
DC
DC
15
15
15
N
1
7.28
1.20
119.70
126.98
C
C
C
C3'
O3'
P
DC
DC
DC
15
15
16
Y
1
-2.73
0.40
120.30
117.57
C
C
C
C6
N1
C2
DC
DC
DC
16
16
16
N
1
10.02
1.20
119.70
129.72
C
C
C
C3'
O3'
P
DC
DC
DA
16
16
17
Y
1
9.45
1.20
119.70
129.15
C
C
C
C3'
O3'
P
DA
DA
DA
17
17
18
Y
1
4.13
0.60
118.60
122.73
C
C
C
N1
C6
N6
DA
DA
DA
18
18
18
N
1
9.00
1.20
119.70
128.70
C
C
C
C3'
O3'
P
DA
DA
DG
18
18
19
Y
1
1.83
0.30
108.30
110.13
C
C
C
O4'
C1'
N9
DG
DG
DG
19
19
19
N
1
5.26
0.70
119.90
125.16
C
C
C
N3
C2
N2
DG
DG
DG
19
19
19
N
1
8.40
1.20
119.70
128.10
C
C
C
C3'
O3'
P
DG
DG
DG
19
19
20
Y
1
5.40
0.70
110.30
115.70
C
C
C
C1'
O4'
C4'
DG
DG
DG
20
20
20
N
1
9.30
1.20
102.50
111.80
C
C
C
C3'
C2'
C1'
DG
DG
DG
20
20
20
N
1
2.21
0.30
108.30
110.51
C
C
C
O4'
C1'
N9
DG
DG
DG
20
20
20
N
1
4.94
0.70
119.90
124.84
C
C
C
N3
C2
N2
DG
DG
DG
20
20
20
N
1
7.42
1.20
119.70
127.12
C
C
C
C3'
O3'
P
DC
DC
DC
21
21
22
Y
1
7.72
1.20
119.70
127.42
C
C
C
C3'
O3'
P
DC
DC
DT
22
22
23
Y
1
2.87
0.30
108.30
111.17
C
C
C
O4'
C1'
N1
DT
DT
DT
23
23
23
N
1
8.58
1.20
119.70
128.28
C
C
C
C3'
O3'
P
DT
DT
DG
24
24
25
Y
1
3.03
0.50
111.90
114.93
C
C
C
C2
N3
C4
DG
DG
DG
26
26
26
N
1
4.72
0.70
119.90
124.62
C
C
C
N3
C2
N2
DG
DG
DG
26
26
26
N
1
A
A
C2
O2
DC
DC
1
1
-0.057
0.009
1.240
1.183
N
1
A
A
N1
C6
DC
DC
1
1
-0.047
0.006
1.367
1.320
N
1
A
A
N3
C4
DC
DC
1
1
-0.067
0.007
1.335
1.268
N
1
A
A
N9
C4
DA
DA
4
4
0.037
0.006
1.374
1.411
N
1
B
B
P
OP1
DC
DC
8
8
0.124
0.017
1.485
1.609
N
1
B
B
P
OP2
DC
DC
8
8
0.125
0.017
1.485
1.610
N
1
B
B
P
O5'
DC
DC
8
8
-0.153
0.010
1.593
1.440
N
1
B
B
O3'
C3'
DC
DC
8
8
-0.055
0.006
1.419
1.364
N
1
B
B
O3'
P
DC
DT
8
9
-0.127
0.012
1.607
1.480
Y
1
B
B
P
OP1
DT
DT
9
9
-0.121
0.017
1.485
1.364
N
1
B
B
P
OP2
DT
DT
9
9
-0.108
0.017
1.485
1.377
N
1
B
B
C6
N1
DT
DT
9
9
0.044
0.007
1.378
1.422
N
1
B
B
P
O5'
DT
DT
10
10
-0.086
0.010
1.593
1.507
N
1
B
B
O4'
C1'
DT
DT
10
10
-0.073
0.012
1.418
1.345
N
1
B
B
O3'
C3'
DT
DT
10
10
-0.044
0.006
1.419
1.375
N
1
B
B
C5
C7
DT
DT
10
10
-0.038
0.006
1.496
1.458
N
1
B
B
O3'
P
DT
DG
10
11
-0.090
0.012
1.607
1.517
Y
1
B
B
C4'
C3'
DG
DG
13
13
-0.064
0.010
1.521
1.457
N
1
B
B
O3'
C3'
DG
DG
13
13
-0.077
0.006
1.419
1.342
N
1
C
C
O5'
C5'
DC
DC
14
14
-0.231
0.025
1.418
1.187
N
1
C
C
O3'
P
DC
DC
14
15
-0.090
0.012
1.607
1.517
Y
1
C
C
P
O5'
DC
DC
15
15
-0.070
0.010
1.593
1.523
N
1
C
C
O3'
P
DC
DC
15
16
-0.075
0.012
1.607
1.532
Y
1
C
C
O5'
C5'
DC
DC
21
21
-0.167
0.025
1.418
1.251
N
1
C
C
C2'
C1'
DC
DC
21
21
0.066
0.010
1.519
1.585
N
1
C
C
N1
C2
DT
DT
24
24
0.055
0.008
1.376
1.431
N
minimized average
NMR Structure of duplex DNA d(CCAAGGXCTTGGG), X is a 3' phosphoglycolate, 5'phosphate gapped lesion
1
N
N
2
N
N
3
N
N
4
N
N
covale
1.621
one
A
DG
6
A
O3'
DG
6
1_555
A
PGA
7
D
P
PGA
1_555
hydrog
REVERSED WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
C
DG
26
C
N2
DG
13
1_555
hydrog
REVERSED WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
C
DG
26
C
N1
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
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
DG
5
A
N1
DG
5
1_555
C
DC
22
C
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
C
DC
22
C
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
C
DC
22
C
N4
DC
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
DC
8
B
N3
DC
1
1_555
C
DG
19
C
N1
DG
6
1_555
hydrog
WATSON-CRICK
B
DC
8
B
N4
DC
1
1_555
C
DG
19
C
O6
DG
6
1_555
hydrog
WATSON-CRICK
B
DC
8
B
O2
DC
1
1_555
C
DG
19
C
N2
DG
6
1_555
hydrog
WATSON-CRICK
B
DT
9
B
N3
DT
2
1_555
C
DA
18
C
N1
DA
5
1_555
hydrog
WATSON-CRICK
B
DT
9
B
O4
DT
2
1_555
C
DA
18
C
N6
DA
5
1_555
hydrog
DT-DC MISPAIR
B
DT
10
B
O4
DT
3
1_555
C
DC
16
C
N4
DC
3
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
1N0K
PDB
1
1N0K
1N0K
PDB
2
1N0K
1N0K
PDB
3
1N0K
1
6
1N0K
1
6
1N0K
A
1
1
6
8
13
1N0K
8
13
1N0K
B
2
1
6
14
26
1N0K
14
26
1N0K
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