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
C18 H16 O3
280.318
1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL
non-polymer
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
US
Biochemistry
BICHAW
0033
0006-2960
38
16045
16057
10.1021/bi9903650
10587427
Intercalation of the (1S,2R,3S,4R)-N6-[1-(1,2,3,4-tetrahydro-2,3, 4-trihydroxybenz[a]anthracenyl)]-2'-deoxyadenosyl adduct in an oligodeoxynucleotide containing the human N-ras codon 61 sequence.
1999
10.2210/pdb1dl4/pdb
pdb_00001dl4
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
BENZ[A]ANTHRACENE-MODIFIED ADENINE-6
3416.263
DNA (5'-D(*CP*GP*GP*AP*CP*(BZA)AP*AP*GP*AP*AP*G)-3')
1
syn
polymer
3291.145
DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3')
1
syn
polymer
280.318
1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-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
-8.158
1
19
A
1
B
22
-3.851
A_DC1:DG22_B
1
1.279
0.545
0.253
-0.314
-0.833
1
19
A
2
B
21
-3.087
A_DG2:DC21_B
2
-5.306
0.189
-0.084
-0.053
-0.979
1
19
A
3
B
20
-2.071
A_DG3:DC20_B
3
-3.857
-0.687
-0.030
-0.299
9.806
1
20
A
4
B
19
-7.108
A_DA4:DT19_B
4
1.774
0.358
0.204
-0.025
23.823
1
19
A
5
B
18
5.633
A_DC5:DG18_B
5
9.594
1.350
-0.127
-0.399
-28.810
1
20
A
7
B
16
-7.891
A_DA7:DT16_B
6
-5.666
1.418
-0.873
-0.240
-3.598
1
19
A
8
B
15
-5.336
A_DG8:DC15_B
7
2.328
-0.111
-0.111
-0.091
9.028
1
20
A
9
B
14
1.173
A_DA9:DT14_B
8
-2.321
0.466
-0.080
-0.094
21.548
1
20
A
10
B
13
-1.394
A_DA10:DT13_B
9
-9.349
0.196
0.095
0.025
9.620
1
19
A
11
B
12
-4.999
A_DG11:DC12_B
10
-1.487
-0.783
-0.052
-0.339
2.725
33.752
A
A
1
2
9.194
B
B
22
21
2.772
5.287
0.626
-0.535
AA_DC1DG2:DC21DG22_BB
1
6.330
-11.008
32.757
-1.653
-0.202
2.968
34.636
A
A
2
3
6.594
B
B
21
20
3.079
3.917
-0.112
-0.868
AA_DG2DG3:DC20DC21_BB
2
-1.522
2.562
34.388
-2.016
-0.029
2.977
39.422
A
A
3
4
0.315
B
B
20
19
2.969
0.213
-0.383
-0.291
AA_DG3DA4:DT19DC20_BB
3
-1.095
1.624
39.406
-0.454
0.451
3.021
35.372
A
A
4
5
-2.293
B
B
19
18
3.055
-1.391
0.687
-0.753
AA_DA4DC5:DG18DT19_BB
4
-2.768
4.561
35.240
-1.049
-1.510
2.380
26.844
A
A
7
8
7.499
B
B
16
15
2.444
3.453
0.188
0.231
AA_DA7DG8:DC15DT16_BB
5
-4.906
10.655
26.177
-0.167
-1.349
2.917
35.404
A
A
8
9
5.499
B
B
15
14
2.969
3.339
0.320
-0.324
AA_DG8DA9:DT14DC15_BB
6
-1.069
1.761
35.235
-0.976
-0.668
2.926
37.085
A
A
9
10
-1.793
B
B
14
13
2.893
-1.139
-0.660
0.033
AA_DA9DA10:DT13DT14_BB
7
-2.359
3.712
36.995
0.187
0.757
3.357
33.129
A
A
10
11
3.086
B
B
13
12
3.371
1.758
-0.711
-0.918
AA_DA10DG11:DC12DT13_BB
8
-2.187
3.840
33.013
-1.916
0.867
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
2000-01-12
1
1
2007-10-16
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
1999-12-08
REL
REL
BZA
1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL
THIS SEQUENCE WAS SYNTHESIZED BY CHEMICAL METHOD
sample
THIS SEQUENCE WAS SYNTHESIZED BY CHEMICAL METHOD
sample
THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES
structures with the lowest energy
7
1
2D NOESY
2D NOESY
2D NOESY
2D ROESY
DQF-COSY
0.1 M NACL
7.0
1
atm
278
K
0.1 M NACL
7.0
1
atm
283
K
0.1 M NACL
7.0
1
atm
298
K
THE STRUCTURE IS BASED ON A TOTAL OF 477 NOE-DERIVED DISTANCE CONSTRAINTS, 80 EMPIRICAL SUGAR PUCKER RESTRAINTS, 32 BACKBONE ANGLE DIHEDRAL RESTRAINTS, AND 18 EMPIRICAL PLANARITY RESTRAINTS.
NOE-RESTRAINTED MOLECULAR DYNAMICS /SIMULATED ANNEALING
1
lowest energy
1.7 MM OLIGODEOXYNUCLEOTIDE; 10 MM PHOSPHATE BUFFER; 0.05 MM EDTA; 0.1 M NACL
1.7 MM OLIGODEOXYNUCLEOTIDE; 10 MM PHOSPHATE BUFFER; 0.05 MM EDTA; 0.1 M NACL
BRUKER
collection
XwinNMR
2.0
A.BRUNGER
structure solution
X-PLOR
3.851
BIOSYM TECHNOLOGIES
processing
Felix
97.0
BORGIAS, B.A., THOMAS, P.D., LI, H., KUMAR, A., AND TONELLI, M.
refinement
CORMA
5.2
BORGIAS, B.A., THOMAS, P.D., LI, H., KUMAR, A., AND TONELLI, M.
iterative matrix relaxation
MARDIGRAS
3.0
750
Bruker
DRX
500
Bruker
DRX
ABA
6
3
BZA
BZA
12
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
A
C9C
BZA
12
WRONG HAND
1
A
C3B
BZA
12
WRONG HAND
1
A
DA
6
0.061
SIDE CHAIN
1
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
4.13
0.30
108.30
112.43
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
4.35
0.50
113.10
117.45
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
-2.57
0.40
106.40
103.83
A
A
A
C8
N9
C4
DG
DG
DG
2
2
2
N
1
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
4.62
0.50
113.10
117.72
A
A
A
N7
C8
N9
DG
DG
DG
3
3
3
N
1
-2.48
0.40
106.40
103.92
A
A
A
C8
N9
C4
DG
DG
DG
3
3
3
N
1
2.68
0.30
108.30
110.98
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
3.89
0.50
113.80
117.69
A
A
A
N7
C8
N9
DA
DA
DA
4
4
4
N
1
2.63
0.30
108.30
110.93
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
3.40
0.50
113.80
117.20
A
A
A
N7
C8
N9
DA
DA
DA
6
6
6
N
1
3.01
0.30
108.30
111.31
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
1
3.62
0.50
113.80
117.42
A
A
A
N7
C8
N9
DA
DA
DA
7
7
7
N
1
3.21
0.30
108.30
111.51
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
4.41
0.50
113.10
117.51
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
1
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
1
2.97
0.30
108.30
111.27
A
A
A
O4'
C1'
N9
DA
DA
DA
9
9
9
N
1
3.81
0.50
113.80
117.61
A
A
A
N7
C8
N9
DA
DA
DA
9
9
9
N
1
2.10
0.30
108.30
110.40
A
A
A
O4'
C1'
N9
DA
DA
DA
10
10
10
N
1
3.92
0.50
113.80
117.72
A
A
A
N7
C8
N9
DA
DA
DA
10
10
10
N
1
2.31
0.30
108.30
110.61
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
4.66
0.50
113.10
117.76
A
A
A
N7
C8
N9
DG
DG
DG
11
11
11
N
1
-2.51
0.40
106.40
103.89
A
A
A
C8
N9
C4
DG
DG
DG
11
11
11
N
1
1.93
0.30
108.30
110.23
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
2.98
0.30
108.30
111.28
B
B
B
O4'
C1'
N1
DT
DT
DT
13
13
13
N
1
3.38
0.30
108.30
111.68
B
B
B
O4'
C1'
N1
DT
DT
DT
14
14
14
N
1
2.86
0.30
108.30
111.16
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
3.59
0.30
108.30
111.89
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
1
-3.86
0.60
122.90
119.04
B
B
B
C6
C5
C7
DT
DT
DT
16
16
16
N
1
3.20
0.30
108.30
111.50
B
B
B
O4'
C1'
N1
DT
DT
DT
17
17
17
N
1
5.09
0.30
108.30
113.39
B
B
B
O4'
C1'
N9
DG
DG
DG
18
18
18
N
1
4.59
0.50
113.10
117.69
B
B
B
N7
C8
N9
DG
DG
DG
18
18
18
N
1
-3.03
0.40
106.40
103.37
B
B
B
C8
N9
C4
DG
DG
DG
18
18
18
N
1
2.94
0.30
108.30
111.24
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
2.87
0.30
108.30
111.17
B
B
B
O4'
C1'
N1
DC
DC
DC
20
20
20
N
1
2.98
0.30
108.30
111.28
B
B
B
O4'
C1'
N1
DC
DC
DC
21
21
21
N
1
1.87
0.30
108.30
110.17
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
4.72
0.50
113.10
117.82
B
B
B
N7
C8
N9
DG
DG
DG
22
22
22
N
1
-2.43
0.40
106.40
103.97
B
B
B
C8
N9
C4
DG
DG
DG
22
22
22
N
THE SOLUTION STRUCTURE OF A BAY-REGION 1S-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
BZA
12
C
C4C
BZA
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
DC-DA MISPAIR
A
DC
5
A
N3
DC
5
1_555
A
DA
6
A
N6
DA
6
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
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
DG-DT MISPAIR
A
DG
8
A
N2
DG
8
1_555
B
DT
16
B
O2
DT
5
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
1DL4
PDB
1
1DL4
1DL4
PDB
2
1DL4
1
11
1DL4
1
11
1DL4
A
1
1
11
12
22
1DL4
12
22
1DL4
B
2
1
11
BINDING SITE FOR RESIDUE BZA A 12
A
BZA
12
Software
6
A
DC
5
A
DC
5
6
1_555
A
DA
6
A
DA
6
6
1_555
A
DA
7
A
DA
7
6
1_555
B
DT
16
B
DT
5
6
1_555
B
DT
17
B
DT
6
6
1_555
B
DG
18
B
DG
7
6
1_555
1
P 1