0.022181
0.012806
0.000000
0.000000
0.025612
0.000000
0.000000
0.000000
0.023969
0.00000
0.00000
0.00000
Kennard, O.
Cruse, W.B.T.
Nachman, J.
Prange, T.
Shakked, Z.
Rabinovich, D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
45.084
45.084
41.720
C9 H12 Br N2 O8 P
387.078
n
5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
DNA linking
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
H2 O
18.015
WATER
non-polymer
N
1
N
N
N
2
N
C
N
3
N
N
N
4
N
C
N
5
N
C
N
6
N
C
N
7
N
O
N
8
N
O
N
9
N
BR
N
10
R
C
N
11
N
C
N
12
S
C
N
13
R
C
N
14
N
O
N
15
N
O
N
16
N
C
N
17
N
O
N
18
N
P
N
19
N
O
N
20
N
O
N
21
N
O
N
22
N
H
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
O
N
35
N
P
N
36
N
O
N
37
N
O
N
38
N
O
N
39
N
C
N
40
R
C
N
41
N
O
N
42
S
C
N
43
N
O
N
44
N
C
N
45
R
C
Y
46
N
N
Y
47
N
C
Y
48
N
N
Y
49
N
C
Y
50
N
C
N
51
N
N
Y
52
N
N
Y
53
N
C
Y
54
N
N
Y
55
N
C
N
56
N
H
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
O
N
71
N
P
N
72
N
O
N
73
N
O
N
74
N
O
N
75
N
C
N
76
R
C
N
77
N
O
N
78
S
C
N
79
N
O
N
80
N
C
N
81
R
C
N
82
N
N
N
83
N
C
N
84
N
O
N
85
N
N
N
86
N
C
N
87
N
N
N
88
N
C
N
89
N
C
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
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
O
N
105
N
P
N
106
N
O
N
107
N
O
N
108
N
O
N
109
N
C
N
110
R
C
N
111
N
O
N
112
S
C
N
113
N
O
N
114
N
C
N
115
R
C
Y
116
N
N
Y
117
N
C
Y
118
N
N
Y
119
N
C
N
120
N
C
N
121
N
O
N
122
N
N
N
123
N
C
N
124
N
N
N
125
N
N
Y
126
N
C
N
127
N
H
N
128
N
H
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
O
N
142
N
H
N
143
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
doub
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
doub
N
10
N
doub
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
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
doub
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
doub
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
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
Y
58
N
sing
Y
59
N
sing
Y
60
N
doub
N
61
N
sing
Y
62
N
sing
Y
63
N
sing
Y
64
N
doub
N
65
N
sing
Y
66
N
doub
N
67
N
sing
N
68
N
sing
Y
69
N
sing
Y
70
N
doub
N
71
N
sing
Y
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
doub
N
76
N
sing
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
N
97
N
sing
N
98
N
doub
N
99
N
sing
N
100
N
doub
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
doub
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
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
Y
131
N
sing
Y
132
N
sing
Y
133
N
doub
N
134
N
sing
Y
135
N
sing
N
136
N
sing
Y
137
N
doub
N
138
N
doub
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
doub
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
US
J.Biomol.Struct.Dyn.
JBSDD6
0646
0739-1102
3
623
647
3271041
Ordered water structure in an A-DNA octamer at 1.7 A resolution.
1986
UK
Nature
NATUAS
0006
0028-0836
337
190
192
Coexistence of A-and B-Form DNA in a Single Crystal Lattice
1989
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
166
183
201
Sequence-Dependent Conformation of an A-DNA Double Helix. The Crystal Structure of the Octamer d(G-G-T-A-T-A-C-C)
1983
UK
Proc.R.Soc.London,Ser.B
PRLBA4
0338
0080-4649
213
479
487
Crystalline A-DNA. The X-Ray Analysis of the Fragment d(G-G-T-A-T-A-C-C)
1981
10.2210/pdb115d/pdb
pdb_0000115d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
ROOM TEMPERATURE
1
1
DIFFRACTOMETER
ENRAF-NONIUS CAD4
OSCILLATION CAMERA
PHILLIPS
M
x-ray
1
M
x-ray
2
1.0
1.0
SEALED TUBE
LURE
SYNCHROTRON
LURE
2556.357
DNA (5'-D(*GP*GP*(BRU)P*AP*(BRU)P*AP*CP*C)-3')
2
syn
polymer
18.015
water
85
nat
water
no
yes
(DG)(DG)(BRU)(DA)(BRU)(DA)(DC)(DC)
GGUAUACC
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
2.39
48.62
VAPOR DIFFUSION
7.00
pH 7.00, VAPOR DIFFUSION
WATER
1
MPD
1
MG ACETATE
1
SPERMINE_HCL
1
WATER
2
MPD
2
-7.835
1
19
A
1
B
16
-1.602
A_DG1:DC16_B
1
-5.405
-0.362
-0.143
-0.169
-11.372
1
19
A
2
B
15
1.223
A_DG2:DC15_B
2
-9.608
-0.287
-0.154
-0.071
-6.810
1
20
A
3
B
14
-2.419
A_BRU3:DA14_B
3
-9.201
-0.051
-0.022
-0.088
0.193
1
20
A
4
B
13
1.580
A_DA4:BRU13_B
4
-7.217
0.096
0.245
-0.074
7.768
1
20
A
5
B
12
4.237
A_BRU5:DA12_B
5
-9.279
-0.099
0.054
-0.077
8.299
1
20
A
6
B
11
0.947
A_DA6:BRU11_B
6
-13.438
0.023
-0.060
-0.097
8.276
1
19
A
7
B
10
3.192
A_DC7:DG10_B
7
-13.947
0.385
-0.106
-0.059
6.726
1
19
A
8
B
9
-1.053
A_DC8:DG9_B
8
-1.093
0.266
-0.094
-0.099
3.000
34.367
A
A
1
2
12.731
B
B
16
15
3.465
7.466
0.149
-1.834
AA_DG1DG2:DC15DC16_BB
1
-0.138
0.235
33.570
-4.270
-0.273
3.270
33.153
A
A
2
3
1.447
B
B
15
14
3.302
0.826
-0.592
-1.237
AA_DG2BRU3:DA14DC15_BB
2
0.044
-0.076
33.143
-2.308
1.045
2.537
31.961
A
A
3
4
19.007
B
B
14
13
3.103
10.280
0.248
-1.220
AA_BRU3DA4:BRU13DA14_BB
3
-2.276
4.208
30.220
-3.868
-0.817
3.113
30.446
A
A
4
5
6.487
B
B
13
12
3.238
3.399
0.364
-1.087
AA_DA4BRU5:DA12BRU13_BB
4
1.376
-2.627
30.229
-2.732
-0.425
2.633
33.088
A
A
5
6
20.653
B
B
12
11
3.270
11.528
-0.506
-1.295
AA_BRU5DA6:BRU11DA12_BB
5
0.147
-0.263
31.067
-4.089
0.912
3.123
33.869
A
A
6
7
8.088
B
B
11
10
3.333
4.697
0.641
-1.403
AA_DA6DC7:DG10BRU11_BB
6
0.484
-0.834
33.548
-3.158
-1.023
2.685
31.796
A
A
7
8
17.990
B
B
10
9
3.398
9.706
-0.299
-1.887
AA_DC7DC8:DG9DG10_BB
7
-0.443
0.822
30.311
-5.138
0.468
diffrn_detector
chem_comp_atom
chem_comp_bond
database_2
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Data collection
Database references
Derived calculations
1
0
1993-07-15
1
1
2008-05-22
1
2
2011-07-13
1
3
2018-04-18
1
4
2024-02-07
_diffrn_detector.detector
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
BNL
Y
NDB
1993-02-12
REL
HOH
water
HOH
18
2
HOH
HOH
18
A
HOH
19
2
HOH
HOH
19
A
HOH
20
2
HOH
HOH
20
A
HOH
24
2
HOH
HOH
24
A
HOH
27
2
HOH
HOH
27
A
HOH
29
2
HOH
HOH
29
A
HOH
30
2
HOH
HOH
30
A
HOH
31
2
HOH
HOH
31
A
HOH
33
2
HOH
HOH
33
A
HOH
34
2
HOH
HOH
34
A
HOH
35
2
HOH
HOH
35
A
HOH
36
2
HOH
HOH
36
A
HOH
38
2
HOH
HOH
38
A
HOH
39
2
HOH
HOH
39
A
HOH
40
2
HOH
HOH
40
A
HOH
43
2
HOH
HOH
43
A
HOH
44
2
HOH
HOH
44
A
HOH
46
2
HOH
HOH
46
A
HOH
49
2
HOH
HOH
49
A
HOH
56
2
HOH
HOH
56
A
HOH
57
2
HOH
HOH
57
A
HOH
58
2
HOH
HOH
58
A
HOH
60
2
HOH
HOH
60
A
HOH
61
2
HOH
HOH
61
A
HOH
66
2
HOH
HOH
66
A
HOH
70
2
HOH
HOH
70
A
HOH
72
2
HOH
HOH
72
A
HOH
79
2
HOH
HOH
79
A
HOH
80
2
HOH
HOH
80
A
HOH
81
2
HOH
HOH
81
A
HOH
82
2
HOH
HOH
82
A
HOH
83
2
HOH
HOH
83
A
HOH
84
2
HOH
HOH
84
A
HOH
86
2
HOH
HOH
86
A
HOH
87
2
HOH
HOH
87
A
HOH
89
2
HOH
HOH
89
A
HOH
90
2
HOH
HOH
90
A
HOH
91
2
HOH
HOH
91
A
HOH
92
2
HOH
HOH
92
A
HOH
93
2
HOH
HOH
93
A
HOH
94
2
HOH
HOH
94
A
HOH
96
2
HOH
HOH
96
A
HOH
98
2
HOH
HOH
98
A
HOH
100
2
HOH
HOH
100
A
HOH
101
2
HOH
HOH
101
A
HOH
17
2
HOH
HOH
17
B
HOH
21
2
HOH
HOH
21
B
HOH
22
2
HOH
HOH
22
B
HOH
23
2
HOH
HOH
23
B
HOH
25
2
HOH
HOH
25
B
HOH
26
2
HOH
HOH
26
B
HOH
28
2
HOH
HOH
28
B
HOH
32
2
HOH
HOH
32
B
HOH
37
2
HOH
HOH
37
B
HOH
41
2
HOH
HOH
41
B
HOH
42
2
HOH
HOH
42
B
HOH
45
2
HOH
HOH
45
B
HOH
47
2
HOH
HOH
47
B
HOH
48
2
HOH
HOH
48
B
HOH
50
2
HOH
HOH
50
B
HOH
51
2
HOH
HOH
51
B
HOH
52
2
HOH
HOH
52
B
HOH
53
2
HOH
HOH
53
B
HOH
54
2
HOH
HOH
54
B
HOH
55
2
HOH
HOH
55
B
HOH
59
2
HOH
HOH
59
B
HOH
62
2
HOH
HOH
62
B
HOH
63
2
HOH
HOH
63
B
HOH
64
2
HOH
HOH
64
B
HOH
65
2
HOH
HOH
65
B
HOH
67
2
HOH
HOH
67
B
HOH
68
2
HOH
HOH
68
B
HOH
69
2
HOH
HOH
69
B
HOH
71
2
HOH
HOH
71
B
HOH
73
2
HOH
HOH
73
B
HOH
74
2
HOH
HOH
74
B
HOH
75
2
HOH
HOH
75
B
HOH
76
2
HOH
HOH
76
B
HOH
77
2
HOH
HOH
77
B
HOH
78
2
HOH
HOH
78
B
HOH
85
2
HOH
HOH
85
B
HOH
88
2
HOH
HOH
88
B
HOH
95
2
HOH
HOH
95
B
HOH
97
2
HOH
HOH
97
B
HOH
99
2
HOH
HOH
99
B
G
1
n
1
DG
1
A
G
2
n
2
DG
2
A
+U
3
n
3
BRU
3
A
A
4
n
4
DA
4
A
+U
5
n
5
BRU
5
A
A
6
n
6
DA
6
A
C
7
n
7
DC
7
A
C
8
n
8
DC
8
A
G
9
n
1
DG
9
B
G
10
n
2
DG
10
B
+U
11
n
3
BRU
11
B
A
12
n
4
DA
12
B
+U
13
n
5
BRU
13
B
A
14
n
6
DA
14
B
C
15
n
7
DC
15
B
C
16
n
8
DC
16
B
author_defined_assembly
2
dimeric
A
BRU
3
A
BRU
3
DU
A
BRU
5
A
BRU
5
DU
B
BRU
11
B
BRU
3
DU
B
BRU
13
B
BRU
5
DU
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
A
C5'
O
DG
HOH
1
79
1.94
1
10.14
1.20
115.70
125.84
A
A
A
C5'
C4'
C3'
DG
DG
DG
1
1
1
N
1
9.69
1.50
119.60
129.29
A
A
A
OP1
P
OP2
DG
DG
DG
2
2
2
N
1
-7.57
0.90
105.70
98.13
A
A
A
O5'
P
OP1
DG
DG
DG
2
2
2
N
1
-2.66
0.40
104.50
101.84
A
A
A
O4'
C4'
C3'
DA
DA
DA
4
4
4
N
1
-4.95
0.70
108.00
103.05
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
9.82
1.10
110.50
120.32
A
A
A
O3'
P
OP2
BRU
DA
DA
5
6
6
Y
1
8.87
1.10
110.50
119.37
A
A
A
O3'
P
OP2
DA
DC
DC
6
7
7
Y
1
1.91
0.30
108.30
110.21
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
1
-4.72
0.40
104.50
99.78
A
A
A
O4'
C4'
C3'
DC
DC
DC
8
8
8
N
1
7.21
1.10
109.80
117.01
B
B
B
C5'
C4'
O4'
DG
DG
DG
9
9
9
N
1
-4.47
0.70
102.20
97.73
B
B
B
C4'
C3'
C2'
DG
DG
DG
9
9
9
N
1
3.25
0.50
111.50
114.75
B
B
B
C5
C6
N1
DG
DG
DG
9
9
9
N
1
6.83
1.10
110.50
117.33
B
B
B
O3'
P
OP2
BRU
DA
DA
11
12
12
Y
1
-5.88
0.90
105.70
99.82
B
B
B
O5'
P
OP2
DA
DA
DA
12
12
12
N
1
-2.88
0.40
104.50
101.62
B
B
B
O4'
C4'
C3'
DA
DA
DA
14
14
14
N
1
17.20
1.50
119.60
136.80
B
B
B
OP1
P
OP2
DC
DC
DC
16
16
16
N
1
A
A
P
O5'
DA
DA
4
4
0.064
0.010
1.593
1.657
N
1
A
A
O3'
P
DA
BRU
4
5
-0.083
0.012
1.607
1.524
Y
1
B
B
P
OP2
DC
DC
16
16
-0.110
0.017
1.485
1.375
N
1
B
A
OP1
O
DC
HOH
15
83
1.86
1_555
6_655
1
A
B
O
O
HOH
HOH
35
88
1.94
1_555
3_664
1
A
B
O
O
HOH
HOH
35
26
2.00
1_555
5_564
0.14
1.700
10.000
4428
1
2.000
TR
isotropic
TR
isotropic
1.700
10.000
85
407
4
318
0
fix
fix
1.700
115D
4669
2.000
1,2
refinement
NUCLSQ
ORDERED WATER STRUCTURE IN AN A-DNA OCTAMER AT 1.7 ANGSTROMS RESOLUTION
1
N
N
1
N
N
2
N
N
2
N
N
covale
1.602
both
A
DG
2
A
O3'
DG
2
1_555
A
BRU
3
A
P
BRU
3
1_555
covale
1.586
both
A
BRU
3
A
O3'
BRU
3
1_555
A
DA
4
A
P
DA
4
1_555
covale
1.524
both
A
DA
4
A
O3'
DA
4
1_555
A
BRU
5
A
P
BRU
5
1_555
covale
1.536
both
A
BRU
5
A
O3'
BRU
5
1_555
A
DA
6
A
P
DA
6
1_555
covale
1.540
both
B
DG
10
B
O3'
DG
2
1_555
B
BRU
11
B
P
BRU
3
1_555
covale
1.567
both
B
BRU
11
B
O3'
BRU
3
1_555
B
DA
12
B
P
DA
4
1_555
covale
1.625
both
B
DA
12
B
O3'
DA
4
1_555
B
BRU
13
B
P
BRU
5
1_555
covale
1.658
both
B
BRU
13
B
O3'
BRU
5
1_555
B
DA
14
B
P
DA
6
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
B
DC
16
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
B
DC
16
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
B
DC
16
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
15
B
N3
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
15
B
O2
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
15
B
N4
DC
7
1_555
hydrog
WATSON-CRICK
A
BRU
3
A
N3
BRU
3
1_555
B
DA
14
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
BRU
3
A
O4
BRU
3
1_555
B
DA
14
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
BRU
13
B
N3
BRU
5
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
BRU
13
B
O4
BRU
5
1_555
hydrog
WATSON-CRICK
A
BRU
5
A
N3
BRU
5
1_555
B
DA
12
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
BRU
5
A
O4
BRU
5
1_555
B
DA
12
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
BRU
11
B
N3
BRU
3
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
BRU
11
B
O4
BRU
3
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
B
DG
10
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
B
DG
10
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
B
DG
10
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
DG
9
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
DG
9
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
DG
9
B
N2
DG
1
1_555
DNA
A-DNA, DOUBLE HELIX, MODIFIED, DNA
115D
PDB
1
115D
1
8
115D
1
8
115D
A
1
1
8
9
16
115D
9
16
115D
B
1
1
8
169
P 61