0.054597
-0.000000
0.000000
0.000000
0.032595
0.000000
0.000000
0.000000
0.023534
0.00000
0.00000
0.00000
Tereshko, V.
Wilds, C.J.
Minasov, G.
Prakash, T.P.
Maier, M.A.
Howard, A.
Wawrzak, Z.
Manoharan, M.
Egli, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90
90
90
18.316
30.680
42.491
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
C10 H26 N4
202.340
SPERMINE
non-polymer
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
N
C
N
12
R
C
N
13
N
N
N
14
N
C
N
15
N
O
N
16
N
N
N
17
N
C
N
18
N
N
N
19
N
C
N
20
N
C
N
21
N
H
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
H
N
35
N
O
N
36
N
P
N
37
N
O
N
38
N
O
N
39
N
O
N
40
N
C
N
41
R
C
N
42
N
O
N
43
S
C
N
44
N
O
N
45
N
C
N
46
R
C
Y
47
N
N
Y
48
N
C
Y
49
N
N
Y
50
N
C
N
51
N
C
N
52
N
O
N
53
N
N
N
54
N
C
N
55
N
N
N
56
N
N
Y
57
N
C
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
H
N
71
N
H
N
72
N
O
N
73
N
H
N
74
N
H
N
75
N
N
N
76
N
C
N
77
N
C
N
78
N
C
N
79
N
N
N
80
N
C
N
81
N
C
N
82
N
C
N
83
N
C
N
84
N
N
N
85
N
C
N
86
N
C
N
87
N
C
N
88
N
N
N
89
N
H
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
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
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
doub
N
27
N
sing
N
28
N
doub
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
doub
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
N
58
N
sing
Y
59
N
sing
Y
60
N
sing
Y
61
N
doub
N
62
N
sing
Y
63
N
sing
N
64
N
sing
Y
65
N
doub
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
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
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
29
1208
1215
10.1093/nar/29.5.1208
11222771
Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments.
2001
10.2210/pdb1i0t/pdb
pdb_00001i0t
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
1999-11-01
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
0.6630
1.0
17-ID
APS
0.6630
SYNCHROTRON
APS BEAMLINE 17-ID
1810.205
5'-D(*CP*GP*CP*GP*CP*G)-3'
2
syn
polymer
202.340
SPERMINE
1
syn
non-polymer
18.015
water
40
nat
water
no
no
(DC)(DG)(DC)(DG)(DC)(DG)
CGCGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
1
1.65
25.40
VAPOR DIFFUSION, SITTING DROP
6.0
spermine, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298 K, VAPOR DIFFUSION, SITTING DROP
298
1.810
1
19
A
1
B
12
2.764
A_DC1:DG12_B
1
-3.201
-0.200
0.058
-0.133
-2.760
1
19
A
2
B
11
1.806
A_DG2:DC11_B
2
3.834
0.259
0.128
-0.168
2.807
1
19
A
3
B
10
2.776
A_DC3:DG10_B
3
6.271
-0.295
0.030
-0.154
-4.966
1
19
A
4
B
9
2.402
A_DG4:DC9_B
4
3.459
0.292
0.043
-0.179
5.492
1
19
A
5
B
8
1.095
A_DC5:DG8_B
5
-7.915
-0.178
-0.052
-0.178
-3.906
1
19
A
6
B
7
1.747
A_DG6:DC7_B
6
2.661
0.217
0.065
-0.157
4.222
-9.631
A
A
1
2
9.516
B
B
12
11
3.553
-1.574
0.266
5.459
AA_DC1DG2:DC11DG12_BB
1
2.353
14.221
-9.207
-28.654
7.356
3.114
-55.039
A
A
2
3
7.292
B
B
11
10
3.183
-6.724
0.655
-0.300
AA_DG2DC3:DG10DC11_BB
2
1.332
1.445
-54.643
0.710
0.785
2.585
-7.399
A
A
3
4
-8.467
B
B
10
9
3.613
1.080
-0.433
5.578
AA_DC3DG4:DC9DG10_BB
3
-1.579
-12.375
-7.148
-46.785
-8.566
3.271
-51.549
A
A
4
5
0.871
B
B
9
8
3.278
-0.757
-0.704
-1.054
AA_DG4DC5:DG8DC9_BB
4
0.610
0.701
-51.540
1.264
-0.769
3.566
-7.162
A
A
5
6
1.047
B
B
8
7
3.702
-0.128
0.097
5.520
AA_DC5DG6:DC7DG8_BB
5
2.341
19.089
-6.768
-43.650
10.543
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-04-04
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2001-01-29
REL
SPM
SPERMINE
HOH
water
SPM
13
2
SPM
SPM
13
A
HOH
100
3
HOH
HOH
100
A
HOH
101
3
HOH
HOH
101
A
HOH
103
3
HOH
HOH
103
A
HOH
104
3
HOH
HOH
104
A
HOH
105
3
HOH
HOH
105
A
HOH
110
3
HOH
HOH
110
A
HOH
111
3
HOH
HOH
111
A
HOH
112
3
HOH
HOH
112
A
HOH
115
3
HOH
HOH
115
A
HOH
116
3
HOH
HOH
116
A
HOH
117
3
HOH
HOH
117
A
HOH
118
3
HOH
HOH
118
A
HOH
119
3
HOH
HOH
119
A
HOH
120
3
HOH
HOH
120
A
HOH
121
3
HOH
HOH
121
A
HOH
122
3
HOH
HOH
122
A
HOH
124
3
HOH
HOH
124
A
HOH
128
3
HOH
HOH
128
A
HOH
131
3
HOH
HOH
131
A
HOH
132
3
HOH
HOH
132
A
HOH
145
3
HOH
HOH
145
A
HOH
147
3
HOH
HOH
147
A
HOH
102
3
HOH
HOH
102
B
HOH
106
3
HOH
HOH
106
B
HOH
107
3
HOH
HOH
107
B
HOH
109
3
HOH
HOH
109
B
HOH
113
3
HOH
HOH
113
B
HOH
114
3
HOH
HOH
114
B
HOH
123
3
HOH
HOH
123
B
HOH
125
3
HOH
HOH
125
B
HOH
129
3
HOH
HOH
129
B
HOH
133
3
HOH
HOH
133
B
HOH
134
3
HOH
HOH
134
B
HOH
135
3
HOH
HOH
135
B
HOH
136
3
HOH
HOH
136
B
HOH
149
3
HOH
HOH
149
B
HOH
157
3
HOH
HOH
157
B
HOH
165
3
HOH
HOH
165
B
HOH
173
3
HOH
HOH
173
B
HOH
191
3
HOH
HOH
191
B
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
G
4
n
4
DG
4
A
C
5
n
5
DC
5
A
G
6
n
6
DG
6
A
C
7
n
1
DC
7
B
G
8
n
2
DG
8
B
C
9
n
3
DC
9
B
G
10
n
4
DG
10
B
C
11
n
5
DC
11
B
G
12
n
6
DG
12
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
DG
2
0.054
SIDE CHAIN
1
B
DG
10
0.056
SIDE CHAIN
1
7.81
1.20
119.70
127.51
A
A
A
C3'
O3'
P
DG
DG
DC
4
4
5
Y
1
2.48
0.40
120.30
122.78
A
A
A
C6
N1
C2
DC
DC
DC
5
5
5
N
1
-3.62
0.50
117.40
113.78
A
A
A
C4
C5
C6
DC
DC
DC
5
5
5
N
1
-3.80
0.60
128.60
124.80
B
B
B
C5
C6
O6
DG
DG
DG
12
12
12
N
1
A
A
C3'
C2'
DG
DG
4
4
-0.054
0.008
1.516
1.462
N
1
A
A
C5
C6
DC
DC
5
5
0.054
0.008
1.339
1.393
N
1
B
B
O
O
HOH
HOH
157
191
2.19
1_555
2_664
0.1850000
0.1600000
0.1600000
0.60
20
57623
57623
RANDOM
1
THROUGHOUT
0
MOLECULAR REPLACEMENT
0.60
20
40
294
14
240
0
0.60
20
1I0T
57623
57623
-3
0.0620000
1
96.0
phasing
AMoRE
refinement
SHELXL-97
data reduction
DENZO
data scaling
SCALEPACK
0.6 A STRUCTURE OF Z-DNA CGCGCG
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
12
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
12
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
12
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
11
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
11
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
11
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
10
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
10
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
10
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
9
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
9
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
9
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
8
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
8
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
8
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
DC
7
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
7
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
7
B
N4
DC
1
1_555
DNA
Z-form double helix, DNA
1I0T
PDB
1
1I0T
1
6
1I0T
1
6
1I0T
A
1
1
6
7
12
1I0T
7
12
1I0T
B
1
1
6
BINDING SITE FOR RESIDUE SPM A 13
A
SPM
13
Software
16
A
DG
2
A
DG
2
16
1_555
A
DG
2
A
DG
2
16
4_556
A
DC
3
A
DC
3
16
1_555
A
DG
4
A
DG
4
16
1_555
A
HOH
101
D
HOH
16
4_566
A
HOH
103
D
HOH
16
1_555
A
HOH
112
D
HOH
16
1_555
A
HOH
119
D
HOH
16
1_555
B
DG
8
B
DG
2
16
1_555
B
DC
9
B
DC
3
16
4_556
B
DC
9
B
DC
3
16
1_555
B
DG
10
B
DG
4
16
4_556
B
DG
10
B
DG
4
16
1_655
B
DC
11
B
DC
5
16
1_655
B
DG
12
B
DG
6
16
1_655
B
HOH
173
E
HOH
16
4_556
19
orthorhombic
P 21 21 21