1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Li, Z.
Kim, H.Y.
Tamura, P.J.
Harris, C.M.
Harris, T.M.
Stone, M.P.
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
C18 H16 O3
280.318
8,9,10,11-TETRAHYDRO-BENZO[A]ANTHRACENE-8,9,10-TRIOL
non-polymer
US
Biochemistry
BICHAW
0033
0006-2960
38
14820
14832
10.1021/bi991607z
10555964
Role of a polycyclic aromatic hydrocarbon bay region ring in modulating DNA adduct structure: the non-bay region (8S,9R,10S, 11R)-N(6)-[11-(8,9,10,11-tetrahydro-8,9, 10-trihydroxybenz[a]anthracenyl)]-2' -deoxyadenosyl adduct in codon 61 of the human N-ras protooncogene
1999
10.2210/pdb1djd/pdb
pdb_00001djd
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3416.263
DNA(5'-D(*CT*GT*GT*AT*CT*AT*AT*GT*AT*AT*G)-3')
1
syn
polymer
3291.145
DNA(5'-D(*CT*TT*TT*CT*TT*TT*GT*TT*CT*CT*G)-3')
1
syn
polymer
280.318
8,9,10,11-TETRAHYDRO-BENZO[A]ANTHRACENE-8,9,10-TRIOL
1
syn
non-polymer
no
no
(DC)(DG)(DG)(DA)(DC)(DA)(DA)(DG)(DA)(DA)(DG)
CGGACAAGAAG
A
polydeoxyribonucleotide
no
no
(DC)(DT)(DT)(DC)(DT)(DT)(DG)(DT)(DC)(DC)(DG)
CTTCTTGTCCG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-6.085
1
19
A
1
B
22
-0.142
A_DC1:DG22_B
1
-6.767
0.173
0.036
-0.126
10.110
1
19
A
2
B
21
-3.796
A_DG2:DC21_B
2
-2.142
-0.124
0.208
-0.108
16.065
1
19
A
3
B
20
-0.594
A_DG3:DC20_B
3
-7.424
-0.198
0.103
-0.072
-3.027
1
20
A
4
B
19
1.149
A_DA4:DT19_B
4
-4.077
0.131
0.078
-0.129
17.830
1
19
A
5
B
18
1.855
A_DC5:DG18_B
5
6.796
0.177
0.477
-0.105
-24.992
A
6
B
17
-43.998
A_DA6:DT17_B
6
24.351
2.729
0.572
0.822
7.687
1
20
A
7
B
16
-2.788
A_DA7:DT16_B
7
-2.553
0.243
0.675
0.063
7.594
1
19
A
8
B
15
-3.364
A_DG8:DC15_B
8
-5.843
-0.143
0.074
-0.123
12.324
1
20
A
9
B
14
0.767
A_DA9:DT14_B
9
-9.549
0.127
-0.016
-0.076
10.109
1
20
A
10
B
13
4.197
A_DA10:DT13_B
10
-9.671
0.098
-0.074
-0.099
18.448
1
19
A
11
B
12
-2.985
A_DG11:DC12_B
11
-1.954
-0.139
0.260
-0.110
2.467
29.538
A
A
1
2
19.082
B
B
22
21
2.725
9.561
-0.316
-0.365
AA_DC1DG2:DC21DG22_BB
1
0.172
-0.343
27.979
-2.374
0.651
3.149
37.445
A
A
2
3
1.185
B
B
21
20
3.142
0.761
0.688
-0.057
AA_DG2DG3:DC20DC21_BB
2
0.511
-0.796
37.434
-0.185
-1.008
4.262
39.174
A
A
3
4
12.296
B
B
20
19
4.282
8.186
0.276
0.299
AA_DG3DA4:DT19DC20_BB
3
1.416
-2.127
38.317
-0.849
-0.188
3.168
32.458
A
A
4
5
2.375
B
B
19
18
3.178
1.327
-0.082
-0.041
AA_DA4DC5:DG18DT19_BB
4
1.393
-2.494
32.402
-0.299
0.384
1.933
19.336
A
A
6
7
-12.191
B
B
17
16
2.906
-3.979
2.431
-0.577
AA_DA6DA7:DT16DT17_BB
5
-6.770
20.745
17.684
-0.183
-9.849
3.352
32.383
A
A
7
8
5.787
B
B
16
15
3.443
3.221
-0.186
-0.661
AA_DA7DG8:DC15DT16_BB
6
1.375
-2.470
32.198
-1.776
0.587
3.160
35.520
A
A
8
9
4.260
B
B
15
14
3.192
2.597
-0.139
-0.344
AA_DG8DA9:DT14DC15_BB
7
-0.103
0.169
35.428
-0.932
0.214
3.034
34.587
A
A
9
10
12.241
B
B
14
13
3.225
7.227
-0.217
-0.580
AA_DA9DA10:DT13DT14_BB
8
0.846
-1.433
33.836
-2.055
0.491
2.988
30.052
A
A
10
11
0.376
B
B
13
12
2.988
0.195
-0.081
-0.146
AA_DA10DG11:DC12DT13_BB
9
-0.496
0.956
30.048
-0.317
0.063
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1999-12-16
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_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_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
1999-12-02
REL
REL
TBT
8,9,10,11-TETRAHYDRO-BENZO[A]ANTHRACENE-8,9,10-TRIOL
Sequence Observed In human N-ras codon 61
sample
This structure was determined using 2D homonuclear techniques
back calculated data agree with experimental NOESY spectrum
1
1
2D NOESY
2D NOESY
DQF-COSY
TOCSY
0.1 M NaCl
7.0
1
atm
278
K
0.1 M NaCl
7.0
1
atm
293
K
The structure is based on a total of 475 NOE derived distance constraints, 55 empirical sugar pucker restraints, 35 empirical backbone angle restraints, and 18 empirical planarity restraints.
NOE-restrained molecular dynamics/simulated annealing
12
lowest energy
1.8 mM oligodeoxynucleotide; 10 mM phosphate buffer; 0.05 mM EDTA; 0.1 M NaCl
90% H2O/10% D2O
1.8 mM oligodeoxynucleotide; 10 mM phosphate buffer; 0.05 mM EDTA; 0.1 M NaCl
100% D2O
Bruker
collection
XwinNMR
2.0
Brunger
structure solution
X-PLOR
3.851
Biosym Technologies
processing
Felix
97.0
Borgias, Thomas, Li, Kumar, Tonelli
refinement
CORMA
5.2
Borgias, Thomas, Li, Kumar, Tonelli
iterative matrix relaxation
MARDIGRAS
3.0
500
Bruker
DMX
750
Bruker
DMX
ABA
6
3
TBT
TBT
25
A
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
G
3
n
3
DG
3
A
A
4
n
4
DA
4
A
C
5
n
5
DC
5
A
ABA
6
n
6
DA
6
A
A
7
n
7
DA
7
A
G
8
n
8
DG
8
A
A
9
n
9
DA
9
A
A
10
n
10
DA
10
A
G
11
n
11
DG
11
A
C
12
n
1
DC
12
B
T
13
n
2
DT
13
B
T
14
n
3
DT
14
B
C
15
n
4
DC
15
B
T
16
n
5
DT
16
B
T
17
n
6
DT
17
B
G
18
n
7
DG
18
B
T
19
n
8
DT
19
B
C
20
n
9
DC
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
3.33
0.30
108.30
111.63
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
2.97
0.30
108.30
111.27
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
4.49
0.50
113.10
117.59
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
-2.77
0.40
106.40
103.63
A
A
A
C8
N9
C4
DG
DG
DG
2
2
2
N
1
2.47
0.30
108.30
110.77
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
4.59
0.50
113.10
117.69
A
A
A
N7
C8
N9
DG
DG
DG
3
3
3
N
1
-2.64
0.40
106.40
103.76
A
A
A
C8
N9
C4
DG
DG
DG
3
3
3
N
1
3.11
0.30
108.30
111.41
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
3.70
0.50
113.80
117.50
A
A
A
N7
C8
N9
DA
DA
DA
4
4
4
N
1
2.94
0.30
108.30
111.24
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
3.82
0.50
113.80
117.62
A
A
A
N7
C8
N9
DA
DA
DA
6
6
6
N
1
3.17
0.30
108.30
111.47
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
1
3.88
0.50
113.80
117.68
A
A
A
N7
C8
N9
DA
DA
DA
7
7
7
N
1
3.02
0.30
108.30
111.32
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
4.57
0.50
113.10
117.67
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
1
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
1
3.66
0.50
113.80
117.46
A
A
A
N7
C8
N9
DA
DA
DA
9
9
9
N
1
2.48
0.30
108.30
110.78
A
A
A
O4'
C1'
N9
DA
DA
DA
10
10
10
N
1
3.81
0.50
113.80
117.61
A
A
A
N7
C8
N9
DA
DA
DA
10
10
10
N
1
2.77
0.30
108.30
111.07
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
4.84
0.50
113.10
117.94
A
A
A
N7
C8
N9
DG
DG
DG
11
11
11
N
1
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
DG
DG
DG
11
11
11
N
1
3.21
0.30
108.30
111.51
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
2.70
0.30
108.30
111.00
B
B
B
O4'
C1'
N1
DT
DT
DT
13
13
13
N
1
3.03
0.30
108.30
111.33
B
B
B
O4'
C1'
N1
DT
DT
DT
14
14
14
N
1
3.27
0.30
108.30
111.57
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
3.13
0.30
108.30
111.43
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
1
-3.65
0.60
122.90
119.25
B
B
B
C6
C5
C7
DT
DT
DT
16
16
16
N
1
2.74
0.30
108.30
111.04
B
B
B
O4'
C1'
N1
DT
DT
DT
17
17
17
N
1
2.29
0.30
108.30
110.59
B
B
B
O4'
C1'
N9
DG
DG
DG
18
18
18
N
1
4.52
0.50
113.10
117.62
B
B
B
N7
C8
N9
DG
DG
DG
18
18
18
N
1
-2.71
0.40
106.40
103.69
B
B
B
C8
N9
C4
DG
DG
DG
18
18
18
N
1
2.35
0.30
108.30
110.65
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
3.01
0.30
108.30
111.31
B
B
B
O4'
C1'
N1
DC
DC
DC
20
20
20
N
1
3.27
0.30
108.30
111.57
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
4.71
0.50
113.10
117.81
B
B
B
N7
C8
N9
DG
DG
DG
22
22
22
N
1
-2.42
0.40
106.40
103.98
B
B
B
C8
N9
C4
DG
DG
DG
22
22
22
N
THE SOLUTION STRUCTURE OF A NON-BAY REGION 11R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE
1
N
N
2
N
N
3
N
N
covale
1.343
none
A
DA
6
A
N6
DA
6
1_555
A
TBT
25
C
C4C
TBT
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
DG
3
A
N1
DG
3
1_555
B
DC
20
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
DC
20
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
DC
20
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
19
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
19
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
18
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
18
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
18
B
N2
DG
7
1_555
hydrog
DA-DT PAIR
A
DA
6
A
N6
DA
6
1_555
B
DT
17
B
O4
DT
6
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
DG
8
A
N1
DG
8
1_555
B
DC
15
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
8
A
N2
DG
8
1_555
B
DC
15
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
8
A
O6
DG
8
1_555
B
DC
15
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
A
DA
9
A
N1
DA
9
1_555
B
DT
14
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
9
A
N6
DA
9
1_555
B
DT
14
B
O4
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N1
DA
10
1_555
B
DT
13
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N6
DA
10
1_555
B
DT
13
B
O4
DT
2
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N1
DG
11
1_555
B
DC
12
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N2
DG
11
1_555
B
DC
12
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
11
A
O6
DG
11
1_555
B
DC
12
B
N4
DC
1
1_555
DNA
BENZ[A]ANTHRACENE-DNA DUPLEX, DNA
1DJD
PDB
1
1DJD
1DJD
PDB
2
1DJD
1
11
1DJD
1
11
1DJD
A
1
1
11
12
22
1DJD
12
22
1DJD
B
2
1
11
BINDING SITE FOR RESIDUE TBT A 25
A
TBT
25
Software
5
A
DA
6
A
DA
6
5
1_555
A
DA
7
A
DA
7
5
1_555
B
DT
16
B
DT
5
5
1_555
B
DT
17
B
DT
6
5
1_555
B
DG
18
B
DG
7
5
1_555
1
P 1