0.023568
0.000000
0.000000
0.000000
0.023568
0.000000
0.000000
0.000000
0.040404
0.00000
0.00000
0.00000
Jain, S.C.
Zon, G.
Sundaralingam, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
42.430
42.430
24.750
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
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
Y
13
N
N
Y
14
N
C
Y
15
N
N
Y
16
N
C
Y
17
N
C
N
18
N
N
Y
19
N
N
Y
20
N
C
Y
21
N
N
Y
22
N
C
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
H
N
36
N
H
N
37
N
O
N
38
N
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
N
C
N
48
R
C
N
49
N
N
N
50
N
C
N
51
N
O
N
52
N
N
N
53
N
C
N
54
N
N
N
55
N
C
N
56
N
C
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
H
N
71
N
O
N
72
N
P
N
73
N
O
N
74
N
O
N
75
N
O
N
76
N
C
N
77
R
C
N
78
N
O
N
79
S
C
N
80
N
O
N
81
N
C
N
82
R
C
Y
83
N
N
Y
84
N
C
Y
85
N
N
Y
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
N
N
92
N
N
Y
93
N
C
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
O
N
109
N
P
N
110
N
O
N
111
N
O
N
112
N
O
N
113
N
C
N
114
R
C
N
115
N
O
N
116
S
C
N
117
N
O
N
118
N
C
N
119
R
C
N
120
N
N
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
C
N
128
N
C
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
H
N
142
N
H
N
143
N
H
N
144
N
N
N
145
N
C
N
146
N
C
N
147
N
C
N
148
N
N
N
149
N
C
N
150
N
C
N
151
N
C
N
152
N
C
N
153
N
N
N
154
N
C
N
155
N
C
N
156
N
C
N
157
N
N
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
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
Y
24
N
sing
Y
25
N
sing
Y
26
N
doub
N
27
N
sing
Y
28
N
sing
Y
29
N
sing
Y
30
N
doub
N
31
N
sing
Y
32
N
doub
N
33
N
sing
N
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
doub
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
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
doub
N
65
N
sing
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
doub
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
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
sing
N
102
N
sing
Y
103
N
doub
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
doub
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
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
doub
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
28
2360
2364
10.1021/bi00432a002
2730868
Base only binding of spermine in the deep groove of the A-DNA octamer d(GTGTACAC).
1989
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
197
141
145
The Potentially Z-DNA-Forming Sequence d(GTGTACAC) Crystallizes as A-DNA
1987
10.2210/pdb1dns/pdb
pdb_00001dns
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
277.00
1
OSCILLATION CAMERA
x-ray
1
1.0
ROTATING ANODE
ELLIOTT GX-6
2426.617
DNA (5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3')
1
syn
polymer
202.340
SPERMINE
1
syn
non-polymer
no
no
(DG)(DT)(DG)(DT)(DA)(DC)(DA)(DC)
GTGTACAC
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
2.30
46.41
VAPOR DIFFUSION
VAPOR DIFFUSION
WATER
1
MPD
1
MGCL2
1
SPERMINE
1
WATER
2
MPD
2
-11.161
1
19
A
1
A
8
-1.866
A_DG1:DC8_A
1
-11.808
-0.378
-0.048
-0.175
-0.764
1
20
A
2
A
7
1.125
A_DT2:DA7_A
2
-10.255
-0.040
0.173
-0.047
-4.570
1
19
A
3
A
6
-0.799
A_DG3:DC6_A
3
-13.832
-0.334
0.171
-0.201
-5.135
1
20
A
4
A
5
-4.193
A_DT4:DA5_A
4
-7.670
-0.176
0.342
-0.181
5.135
1
20
A
5
A
4
-4.193
A_DA5:DT4_A
5
-7.669
0.176
0.342
-0.181
4.570
1
19
A
6
A
3
-0.799
A_DC6:DG3_A
6
-13.832
0.334
0.171
-0.201
0.764
1
20
A
7
A
2
1.125
A_DA7:DT2_A
7
-10.255
0.040
0.173
-0.047
11.161
1
19
A
8
A
1
-1.866
A_DC8:DG1_A
8
-11.808
0.378
-0.048
-0.175
2.846
33.114
A
A
1
2
12.685
A
A
8
7
3.190
7.175
0.359
-1.248
AA_DG1DT2:DA7DC8_AA
1
-0.764
1.350
32.340
-3.319
-0.750
2.739
30.453
A
A
2
3
18.325
A
A
7
6
3.329
9.468
0.376
-1.471
AA_DT2DG3:DC6DA7_AA
2
1.729
-3.347
28.926
-4.601
-0.387
3.007
37.130
A
A
3
4
9.175
A
A
6
5
3.272
5.820
-0.214
-1.524
AA_DG3DT4:DA5DC6_AA
3
-0.626
0.987
36.681
-3.144
0.255
2.821
30.128
A
A
4
5
5.820
A
A
5
4
2.974
3.020
0.000
-1.421
AA_DT4DA5:DT4DA5_AA
4
0.000
0.000
29.980
-3.280
0.000
3.007
37.130
A
A
5
6
9.175
A
A
4
3
3.272
5.820
0.214
-1.524
AA_DA5DC6:DG3DT4_AA
5
0.626
-0.987
36.681
-3.144
-0.255
2.739
30.453
A
A
6
7
18.325
A
A
3
2
3.329
9.468
-0.376
-1.471
AA_DC6DA7:DT2DG3_AA
6
-1.729
3.347
28.926
-4.601
0.387
2.846
33.114
A
A
7
8
12.685
A
A
2
1
3.190
7.175
-0.359
-1.248
AA_DA7DC8:DG1DT2_AA
7
0.764
-1.350
32.340
-3.319
0.750
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
1990-04-15
1
1
2008-05-22
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
BNL
Y
BNL
1989-02-22
REL
SPM
SPERMINE
SPM
9
2
SPM
SPM
9
A
G
1
n
1
DG
1
A
T
2
n
2
DT
2
A
G
3
n
3
DG
3
A
T
4
n
4
DT
4
A
A
5
n
5
DA
5
A
C
6
n
6
DC
6
A
A
7
n
7
DA
7
A
C
8
n
8
DC
8
A
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
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
7_555
y,x,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1
A
C8
SPM
9
B
C8
SPM
1
1
N
1
A
C9
SPM
9
B
C9
SPM
1
1
N
1
A
N10
SPM
9
B
N10
SPM
1
1
N
1
A
C11
SPM
9
B
C11
SPM
1
1
N
1
A
C12
SPM
9
B
C12
SPM
1
1
N
1
A
C13
SPM
9
B
C13
SPM
1
1
N
1
A
N14
SPM
9
B
N14
SPM
1
1
N
1
3.28
0.50
111.50
114.78
A
A
A
C5
C6
N1
DG
DG
DG
1
1
1
N
1
-4.41
0.60
128.60
124.19
A
A
A
C5
C6
O6
DG
DG
DG
1
1
1
N
1
7.56
1.20
119.70
127.26
A
A
A
C3'
O3'
P
DG
DG
DT
1
1
2
Y
1
-13.25
1.50
119.60
106.35
A
A
A
OP1
P
OP2
DT
DT
DT
2
2
2
N
1
12.53
1.20
110.70
123.23
A
A
A
O5'
P
OP1
DT
DT
DT
2
2
2
N
1
3.14
0.30
108.30
111.44
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
1
3.64
0.60
114.60
118.24
A
A
A
N1
C2
N3
DT
DT
DT
2
2
2
N
1
-5.49
0.60
127.20
121.71
A
A
A
C2
N3
C4
DT
DT
DT
2
2
2
N
1
3.80
0.60
115.20
119.00
A
A
A
N3
C4
C5
DT
DT
DT
2
2
2
N
1
3.95
0.30
108.30
112.25
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
-6.52
0.70
119.90
113.38
A
A
A
N3
C2
N2
DG
DG
DG
3
3
3
N
1
9.64
1.20
119.70
129.34
A
A
A
C3'
O3'
P
DG
DG
DT
3
3
4
Y
1
-7.25
0.90
105.70
98.45
A
A
A
O5'
P
OP1
DT
DT
DT
4
4
4
N
1
15.54
1.20
110.70
126.24
A
A
A
O5'
P
OP2
DT
DT
DT
4
4
4
N
1
-5.63
0.80
109.40
103.77
A
A
A
O5'
C5'
C4'
DT
DT
DT
4
4
4
N
1
4.46
0.60
114.60
119.06
A
A
A
N1
C2
N3
DT
DT
DT
4
4
4
N
1
-6.12
0.60
127.20
121.08
A
A
A
C2
N3
C4
DT
DT
DT
4
4
4
N
1
4.49
0.60
115.20
119.69
A
A
A
N3
C4
C5
DT
DT
DT
4
4
4
N
1
-5.16
0.80
123.10
117.94
A
A
A
N1
C2
O2
DT
DT
DT
4
4
4
N
1
-6.63
0.70
124.90
118.27
A
A
A
C5
C4
O4
DT
DT
DT
4
4
4
N
1
11.34
1.10
110.50
121.84
A
A
A
O3'
P
OP2
DT
DA
DA
4
5
5
Y
1
-3.34
0.50
129.30
125.96
A
A
A
N1
C2
N3
DA
DA
DA
5
5
5
N
1
7.44
1.10
110.50
117.94
A
A
A
O3'
P
OP2
DC
DA
DA
6
7
7
Y
1
-5.92
0.90
105.70
99.78
A
A
A
O5'
P
OP2
DA
DA
DA
7
7
7
N
1
-5.94
0.80
109.40
103.46
A
A
A
O5'
C5'
C4'
DA
DA
DA
7
7
7
N
1
4.08
0.60
118.60
122.68
A
A
A
C6
N1
C2
DA
DA
DA
7
7
7
N
1
-3.73
0.50
129.30
125.57
A
A
A
N1
C2
N3
DA
DA
DA
7
7
7
N
1
-3.42
0.50
117.70
114.28
A
A
A
C5
C6
N1
DA
DA
DA
7
7
7
N
1
10.04
1.20
110.70
120.74
A
A
A
O5'
P
OP2
DC
DC
DC
8
8
8
N
1
3.81
0.30
108.30
112.11
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
-3.19
0.40
121.90
118.71
A
A
A
N3
C4
C5
DC
DC
DC
8
8
8
N
1
A
A
P
OP2
DT
DT
4
4
-0.105
0.017
1.485
1.380
N
1
A
A
P
O5'
DA
DA
7
7
0.112
0.010
1.593
1.705
N
1
A
A
P
O5'
DC
DC
8
8
-0.071
0.010
1.593
1.522
N
1
A
A
C7
C7
SPM
SPM
9
9
1.55
1_555
7_555
0.1150000
2.000
5.000
1214
1
TR
isotropic
TR
isotropic
2.000
5.000
0
168
7
161
0
0.010
fix
fix
2.000
1DNS
1365
3.000
1
refinement
NUCLSQ
BASE ONLY BINDING OF SPERMINE IN THE DEEP GROOVE OF THE A-DNA OCTAMER D(GTGTACAC)
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
A
DC
8
A
N3
DC
8
7_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
A
DC
8
A
O2
DC
8
7_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
A
DC
8
A
N4
DC
8
7_555
hydrog
WATSON-CRICK
A
DT
2
A
N3
DT
2
1_555
A
DA
7
A
N1
DA
7
7_555
hydrog
WATSON-CRICK
A
DT
2
A
O4
DT
2
1_555
A
DA
7
A
N6
DA
7
7_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
A
DC
6
A
N3
DC
6
7_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
A
DC
6
A
O2
DC
6
7_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
A
DC
6
A
N4
DC
6
7_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
A
DA
5
A
N1
DA
5
7_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
A
DA
5
A
N6
DA
5
7_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
A
DT
4
A
N3
DT
4
7_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
A
DT
4
A
O4
DT
4
7_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
A
DG
3
A
N1
DG
3
7_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
A
DG
3
A
O6
DG
3
7_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
A
DG
3
A
N2
DG
3
7_555
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
A
DT
2
A
N3
DT
2
7_555
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
A
DT
2
A
O4
DT
2
7_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
A
DG
1
A
N1
DG
1
7_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
A
DG
1
A
O6
DG
1
7_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
A
DG
1
A
N2
DG
1
7_555
DNA
A-DNA, DOUBLE HELIX, DNA
1DNS
PDB
1
1DNS
1
8
1DNS
1
8
1DNS
A
1
1
8
BINDING SITE FOR RESIDUE SPM A 9
A
SPM
9
Software
4
A
DT
2
A
DT
2
4
1_555
A
DG
3
A
DG
3
4
1_555
A
DT
4
A
DT
4
4
1_555
A
DC
6
A
DC
6
4
7_555
96
P 43 21 2