0.024612
0.014210
0.000000
0.000000
0.028420
0.000000
0.000000
0.000000
0.018093
0.00000
0.00000
0.00000
Paukstelis, P.J.
Nowakowski, J.
Birktoft, J.J.
Seeman, N.C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
40.630
40.630
55.270
C9 H12 Br N2 O8 P
387.078
n
5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
DNA linking
C9 H13 Br N3 O7 P
386.093
n
5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-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
Mg 2
24.305
MAGNESIUM ION
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
BR
N
35
N
P
N
36
N
O
N
37
N
O
N
38
N
O
N
39
N
N
N
40
N
C
N
41
N
C
N
42
N
O
N
43
N
N
N
44
N
C
N
45
N
N
N
46
N
C
N
47
N
C
N
48
N
C
N
49
R
C
N
50
N
O
N
51
R
C
N
52
S
C
N
53
N
O
N
54
N
O
N
55
N
H
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
O
N
69
N
P
N
70
N
O
N
71
N
O
N
72
N
O
N
73
N
C
N
74
R
C
N
75
N
O
N
76
S
C
N
77
N
O
N
78
N
C
N
79
R
C
Y
80
N
N
Y
81
N
C
Y
82
N
N
Y
83
N
C
Y
84
N
C
N
85
N
N
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
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
144
N
MG
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
doub
N
37
N
sing
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
doub
N
46
N
sing
N
47
N
doub
N
48
N
sing
N
49
N
doub
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
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
doub
N
73
N
sing
N
74
N
sing
N
75
N
sing
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
Y
93
N
sing
Y
94
N
sing
Y
95
N
doub
N
96
N
sing
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
doub
N
102
N
sing
N
103
N
sing
Y
104
N
sing
Y
105
N
doub
N
106
N
sing
Y
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
UK
Chem.Biol.
CBOLE2
2050
1074-5521
11
1119
1126
10.1016/j.chembiol.2004.05.021
15324813
Crystal structure of a continuous three-dimensional DNA lattice.
2004
10.2210/pdb1p1y/pdb
pdb_00001p1y
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2002-08-04
ADSC QUANTUM 4
SINGLE WAVELENGTH
M
x-ray
1
0.92002
1.0
X8C
NSLS
0.92002
SYNCHROTRON
NSLS BEAMLINE X8C
4249.451
5'-D(*GP*GP*AP*(CBR)P*AP*GP*AP*(BRU)P*GP*GP*GP*AP*G)-3'
1
syn
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
23
nat
water
no
yes
(DG)(DG)(DA)(CBR)(DA)(DG)(DA)(BRU)(DG)(DG)(DG)(DA)(DG)
GGACAGAUGGGAG
X
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.97
58.52
VAPOR DIFFUSION, SITTING DROP
magnesium formate, mpd, lithium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K
295.5
magnesium formate
1
mpd
1
LiCl
1
mpd
2
LiCl
2
-2.683
4
7
X
1
X
10
-112.497
X_DG1:DG10_X
1
-6.650
-5.716
-0.213
-0.518
-0.455
12
4
X
2
X
11
174.581
X_DG2:DG11_X
2
24.789
3.179
-0.574
8.009
-7.038
7
2
X
3
X
12
-179.699
X_DA3:DA12_X
3
29.923
-5.402
0.167
5.487
-3.306
172.650
X
X
1
2
68.114
X
X
10
11
1.701
131.801
4.877
-0.870
XX_DG1DG2:DG11DG10_XX
1
-111.194
57.465
26.996
0.048
-2.035
4.480
173.704
X
X
2
3
0.875
X
X
11
12
4.480
1.746
0.032
0.071
XX_DG2DA3:DA12DG11_XX
2
-0.242
0.121
173.703
0.034
-0.016
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_conn_type
struct_site
repository
Initial release
Version format compliance
Version format compliance
Non-polymer description
Data collection
Database references
Derived calculations
1
0
2004-06-01
1
1
2008-04-29
1
2
2011-07-13
1
3
2011-11-02
1
4
2024-02-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_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_conn_type.id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2003-04-14
REL
REL
MG
MAGNESIUM ION
HOH
water
MO4
51
2
MG
MG
51
X
HOH
1
3
HOH
HOH
52
X
HOH
2
3
HOH
HOH
53
X
HOH
3
3
HOH
HOH
54
X
HOH
4
3
HOH
HOH
55
X
HOH
5
3
HOH
HOH
56
X
HOH
6
3
HOH
HOH
57
X
HOH
7
3
HOH
HOH
58
X
HOH
8
3
HOH
HOH
59
X
HOH
9
3
HOH
HOH
60
X
HOH
11
3
HOH
HOH
61
X
HOH
13
3
HOH
HOH
62
X
HOH
14
3
HOH
HOH
63
X
HOH
15
3
HOH
HOH
64
X
HOH
20
3
HOH
HOH
65
X
HOH
22
3
HOH
HOH
66
X
HOH
23
3
HOH
HOH
67
X
HOH
25
3
HOH
HOH
68
X
HOH
26
3
HOH
HOH
69
X
HOH
27
3
HOH
HOH
70
X
MO4
51
3
HOH
HOH
71
X
MO4
51
3
HOH
HOH
72
X
MO4
51
3
HOH
HOH
73
X
MO4
51
3
HOH
HOH
74
X
G
1
n
1
DG
1
X
G
2
n
2
DG
2
X
A
3
n
3
DA
3
X
CBR
4
n
4
CBR
4
X
A
5
n
5
DA
5
X
G
6
n
6
DG
6
X
A
7
n
7
DA
7
X
BRU
8
n
8
BRU
8
X
G
9
n
9
DG
9
X
G
10
n
10
DG
10
X
G
11
n
11
DG
11
X
A
12
n
12
DA
12
X
G
13
n
13
DG
13
X
author_defined_assembly
2
dimeric
X
HOH
71
C
O
HOH
1_555
X
MG
51
B
MG
MG
1_555
X
HOH
72
C
O
HOH
1_555
178.7
X
HOH
71
C
O
HOH
1_555
X
MG
51
B
MG
MG
1_555
X
HOH
73
C
O
HOH
1_555
93.5
X
HOH
72
C
O
HOH
1_555
X
MG
51
B
MG
MG
1_555
X
HOH
73
C
O
HOH
1_555
87.0
X
HOH
71
C
O
HOH
1_555
X
MG
51
B
MG
MG
1_555
X
HOH
74
C
O
HOH
1_555
83.8
X
HOH
72
C
O
HOH
1_555
X
MG
51
B
MG
MG
1_555
X
HOH
74
C
O
HOH
1_555
95.0
X
HOH
73
C
O
HOH
1_555
X
MG
51
B
MG
MG
1_555
X
HOH
74
C
O
HOH
1_555
93.7
X
CBR
4
A
CBR
4
DC
X
BRU
8
A
BRU
8
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
4_435
-x-1,-y-2,z
crystal symmetry operation
0.0000000000
-70.3732243115
0.0000000000
1
X
C5'
DG
13
A
C5'
DG
13
1
Y
1
X
C4'
DG
13
A
C4'
DG
13
1
Y
1
X
O4'
DG
13
A
O4'
DG
13
1
Y
1
X
C3'
DG
13
A
C3'
DG
13
1
Y
1
X
O3'
DG
13
A
O3'
DG
13
1
Y
1
X
C2'
DG
13
A
C2'
DG
13
1
Y
1
X
C1'
DG
13
A
C1'
DG
13
1
Y
1
X
N9
DG
13
A
N9
DG
13
1
Y
1
X
C8
DG
13
A
C8
DG
13
1
Y
1
X
N7
DG
13
A
N7
DG
13
1
Y
1
X
C5
DG
13
A
C5
DG
13
1
Y
1
X
C6
DG
13
A
C6
DG
13
1
Y
1
X
O6
DG
13
A
O6
DG
13
1
Y
1
X
N1
DG
13
A
N1
DG
13
1
Y
1
X
C2
DG
13
A
C2
DG
13
1
Y
1
X
N2
DG
13
A
N2
DG
13
1
Y
1
X
N3
DG
13
A
N3
DG
13
1
Y
1
X
C4
DG
13
A
C4
DG
13
1
Y
1
1.89
0.30
108.30
110.19
X
X
X
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
-6.15
0.80
105.90
99.75
X
X
X
O4'
C1'
C2'
DG
DG
DG
2
2
2
N
1
-7.70
0.40
104.50
96.80
X
X
X
O4'
C4'
C3'
DA
DA
DA
3
3
3
N
1
8.69
0.70
110.30
118.99
X
X
X
C1'
O4'
C4'
DA
DA
DA
3
3
3
N
1
-7.51
0.80
105.90
98.39
X
X
X
O4'
C1'
C2'
DA
DA
DA
3
3
3
N
1
-8.35
0.70
108.00
99.65
X
X
X
O4'
C1'
N9
DA
DA
DA
3
3
3
N
1
-4.12
0.50
129.30
125.18
X
X
X
N1
C2
N3
DA
DA
DA
3
3
3
N
1
6.07
0.50
110.60
116.67
X
X
X
C2
N3
C4
DA
DA
DA
3
3
3
N
1
-3.12
0.50
110.70
107.58
X
X
X
C4
C5
N7
DA
DA
DA
5
5
5
N
1
-4.41
0.60
118.60
114.19
X
X
X
N1
C6
N6
DA
DA
DA
5
5
5
N
1
-5.79
0.80
102.40
96.61
X
X
X
C3'
C2'
C1'
DG
DG
DG
6
6
6
N
1
5.93
0.30
108.30
114.23
X
X
X
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
-3.87
0.60
123.90
120.03
X
X
X
N1
C2
N3
DG
DG
DG
6
6
6
N
1
2.92
0.30
108.30
111.22
X
X
X
O4'
C1'
N9
DA
DA
DA
7
7
7
N
1
-8.92
0.80
102.40
93.48
X
X
X
C3'
C2'
C1'
DG
DG
DG
9
9
9
N
1
2.49
0.30
108.30
110.79
X
X
X
O4'
C1'
N9
DG
DG
DG
9
9
9
N
1
-3.84
0.60
128.60
124.76
X
X
X
C5
C6
O6
DG
DG
DG
9
9
9
N
1
-2.80
0.40
104.50
101.70
X
X
X
O4'
C4'
C3'
DG
DG
DG
11
11
11
N
1
4.44
0.70
110.30
114.74
X
X
X
C1'
O4'
C4'
DG
DG
DG
11
11
11
N
1
-6.42
0.60
119.90
113.48
X
X
X
N1
C6
O6
DG
DG
DG
11
11
11
N
1
3.61
0.60
128.60
132.21
X
X
X
C5
C6
O6
DG
DG
DG
11
11
11
N
1
8.02
1.20
110.70
118.72
X
X
X
O5'
P
OP1
DA
DA
DA
12
12
12
N
1
-3.41
0.50
110.70
107.29
X
X
X
C4
C5
N7
DA
DA
DA
12
12
12
N
1
4.54
0.50
103.90
108.44
X
X
X
C5
N7
C8
DA
DA
DA
12
12
12
N
1
-4.03
0.60
118.60
114.57
X
X
X
N1
C6
N6
DA
DA
DA
12
12
12
N
1
10.52
1.50
119.60
130.12
X
X
X
OP1
P
OP2
DG
DG
DG
13
13
13
N
1
X
X
N3
C4
DA
DA
3
3
-0.048
0.006
1.344
1.296
N
1
X
X
O3'
C3'
DG
DG
9
9
-0.041
0.006
1.419
1.378
N
1
X
X
N3
C4
DA
DA
12
12
-0.039
0.006
1.344
1.305
N
39.727
-1.50
-0.75
0.00
-1.50
0.00
2.24
0.956
0.940
0.23256
0.20332
0.20485
0.20485
2.10
35.14
161
2907
2870
5.3
98.70
3.627
0.096
RANDOM
1
THROUGHOUT
2
SAD
0.163
0.156
0.80
0.80
1.40
MAXIMUM LIKELIHOOD WITH PHASES
BABINET MODEL WITH MASK
2.10
35.14
23
281
1
257
0
0.020
0.021
292
3.133
3.000
451
0.120
0.200
36
0.013
0.020
142
0.381
0.200
74
0.187
0.200
11
0.113
0.200
20
0.065
0.200
5
0.258
0.228
2.155
16
217
20
1.8
50
1P1Y
5957
3066
0
0.071
0.071
1
20.7
99
0.22
2.10
2.18
13.76
307
1
99.4
refinement
REFMAC
5.1.24
data reduction
HKL-2000
data scaling
SCALEPACK
phasing
CNS
Crystal structure of a continuous three-dimensional DNA lattice from d(GGACAGATGGGAG)
1
N
N
2
N
N
3
N
N
covale
1.595
both
X
DA
3
A
O3'
DA
3
1_555
X
CBR
4
A
P
CBR
4
1_555
covale
1.593
both
X
CBR
4
A
O3'
CBR
4
1_555
X
DA
5
A
P
DA
5
1_555
covale
1.574
both
X
DA
7
A
O3'
DA
7
1_555
X
BRU
8
A
P
BRU
8
1_555
covale
1.565
both
X
BRU
8
A
O3'
BRU
8
1_555
X
DG
9
A
P
DG
9
1_555
metalc
2.159
X
MG
51
B
MG
MG
1_555
X
HOH
71
C
O
HOH
1_555
metalc
2.168
X
MG
51
B
MG
MG
1_555
X
HOH
72
C
O
HOH
1_555
metalc
2.167
X
MG
51
B
MG
MG
1_555
X
HOH
73
C
O
HOH
1_555
metalc
2.164
X
MG
51
B
MG
MG
1_555
X
HOH
74
C
O
HOH
1_555
hydrog
TYPE_7_PAIR
X
DG
1
A
N7
DG
1
1_555
X
DG
10
A
N1
DG
10
6_454
hydrog
TYPE_7_PAIR
X
DG
1
A
O6
DG
1
1_555
X
DG
10
A
N2
DG
10
6_454
hydrog
TYPE_4_PAIR
X
DG
2
A
N2
DG
2
1_555
X
DG
11
A
N3
DG
11
6_454
hydrog
TYPE_4_PAIR
X
DG
2
A
N3
DG
2
1_555
X
DG
11
A
N2
DG
11
6_454
hydrog
TYPE_2_PAIR
X
DA
3
A
N6
DA
3
1_555
X
DA
12
A
N7
DA
12
6_454
hydrog
TYPE_2_PAIR
X
DA
3
A
N7
DA
3
1_555
X
DA
12
A
N6
DA
12
6_454
DNA
continuous three-dimensional dna lattice, parallel-stranded base pairs, DNA
1P1Y
PDB
1
1P1Y
1
13
1P1Y
1
13
1P1Y
X
1
1
13
BINDING SITE FOR RESIDUE MG X 51
X
MG
51
Software
4
X
HOH
71
C
HOH
4
1_555
X
HOH
72
C
HOH
4
1_555
X
HOH
73
C
HOH
4
1_555
X
HOH
74
C
HOH
4
1_555
172
P 64