0.027640
0.000000
0.000000
0.000000
0.027488
0.000000
0.000000
0.000000
0.015843
0.00000
0.00000
0.00000
Kondo, J.
Umeda, S.
Sunami, T.
Takenaka, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
36.180
36.380
63.120
C9 H13 I N3 O7 P
433.094
n
5-IODO-2'-DEOXY-CYTIDINE-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
K 1
39.098
POTASSIUM ION
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
I
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
Y
51
N
C
N
52
N
N
Y
53
N
N
Y
54
N
C
Y
55
N
N
Y
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
N
83
N
N
N
84
N
C
N
85
N
O
N
86
N
N
N
87
N
C
N
88
N
N
N
89
N
C
N
90
N
C
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
O
N
106
N
P
N
107
N
O
N
108
N
O
N
109
N
O
N
110
N
C
N
111
R
C
N
112
N
O
N
113
S
C
N
114
N
O
N
115
N
C
N
116
R
C
Y
117
N
N
Y
118
N
C
Y
119
N
N
Y
120
N
C
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
N
N
126
N
N
Y
127
N
C
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
H
N
142
N
O
N
143
N
H
N
144
N
H
N
145
N
K
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
Y
64
N
sing
Y
65
N
doub
N
66
N
sing
Y
67
N
doub
N
68
N
sing
N
69
N
sing
Y
70
N
sing
Y
71
N
doub
N
72
N
sing
Y
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
N
97
N
sing
N
98
N
sing
N
99
N
doub
N
100
N
sing
N
101
N
doub
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
doub
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
doub
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
N
131
N
sing
Y
132
N
sing
Y
133
N
sing
Y
134
N
doub
N
135
N
sing
Y
136
N
sing
N
137
N
sing
Y
138
N
doub
N
139
N
doub
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
32
2541
2549
10.1093/nar/gkh575
15133122
Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats
2004
10.2210/pdb1v3p/pdb
pdb_00001v3p
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
2000-11-11
ADSC QUANTUM 4
SINGLE WAVELENGTH
M
x-ray
1
1.0
1.0
BL-18B
Photon Factory
1.0
SYNCHROTRON
PHOTON FACTORY BEAMLINE BL-18B
2602.540
5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'
2
syn
polymer
39.098
POTASSIUM ION
2
syn
non-polymer
18.015
water
97
nat
water
no
yes
(DG)(C38)(DG)(DA)(DG)(DA)(DG)(DC)
GCGAGAGC
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
1
1.91
35.70
VAPOR DIFFUSION, HANGING DROP
7.0
2-methyl-2,4-pentanediol, spermine tetrahydrochloride, sodium chloride, potassium chloride, sodium cacodylate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
277
2-methyl-2,4-pentanediol
1
spermine tetrahydrochloride
1
sodium chloride
1
potassium chloride
1
sodium cacodylate
1
sodium chloride
2
potassium chloride
2
sodium cacodylate
2
-10.542
1
19
A
1
B
16
0.255
A_DG1:DC16_B
1
3.740
-0.473
-0.317
0.035
16.170
1
19
A
2
B
15
3.599
A_C382:DG15_B
2
3.583
0.511
0.050
-0.091
26.533
9
11
A
3
B
14
7.540
A_DG3:DA14_B
3
-22.600
6.418
1.476
-4.642
-25.910
9
11
A
6
B
11
16.130
A_DA6:DG11_B
4
-22.469
-6.137
1.547
-4.029
-16.031
1
19
A
7
B
10
-0.066
A_DG7:C3810_B
5
4.366
-0.298
0.080
-0.212
-0.182
1
19
A
8
B
9
-0.846
A_DC8:DG9_B
6
2.943
0.012
0.045
-0.288
2.771
30.814
A
A
1
2
0.265
B
B
16
15
2.793
0.141
0.568
-0.153
AA_DG1C382:DG15DC16_BB
1
-1.065
2.004
30.796
-0.312
-1.245
3.413
51.753
A
A
2
3
10.698
B
B
15
14
3.217
9.294
0.440
1.409
AA_C382DG3:DA14DG15_BB
2
0.790
-0.909
50.962
0.973
-0.449
3.548
58.087
A
A
6
7
5.958
B
B
11
10
3.379
5.776
-0.645
1.782
AA_DA6DG7:C3810DG11_BB
3
-2.366
2.441
57.779
1.511
0.531
3.078
28.729
A
A
7
8
1.211
B
B
10
9
3.072
0.601
-0.216
0.203
AA_DG7DC8:DG9C3810_BB
4
-0.365
0.736
28.721
0.282
0.357
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2004-06-08
1
1
2008-04-27
1
2
2011-07-13
1
3
2023-10-25
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr1_symmetry
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.ptnr3_symmetry
_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_asym_id
_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.ptnr1_symmetry
_struct_conn.ptnr2_auth_asym_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.ptnr2_symmetry
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
The same structure, Br-derivative
The same structure, I-derivative
PDBJ
Y
PDBJ
2003-11-03
REL
K
POTASSIUM ION
HOH
water
1V3N
PDB ENTRY 1V3N
PDB
experimental model
K
114
2
K
K
114
A
K
115
2
K
K
115
B
HOH
17
3
HOH
HOH
17
A
HOH
19
3
HOH
HOH
19
A
HOH
21
3
HOH
HOH
21
A
HOH
23
3
HOH
HOH
23
A
HOH
24
3
HOH
HOH
24
A
HOH
25
3
HOH
HOH
25
A
HOH
26
3
HOH
HOH
26
A
HOH
28
3
HOH
HOH
28
A
HOH
29
3
HOH
HOH
29
A
HOH
31
3
HOH
HOH
31
A
HOH
33
3
HOH
HOH
33
A
HOH
35
3
HOH
HOH
35
A
HOH
37
3
HOH
HOH
37
A
HOH
38
3
HOH
HOH
38
A
HOH
42
3
HOH
HOH
42
A
HOH
44
3
HOH
HOH
44
A
HOH
46
3
HOH
HOH
46
A
HOH
47
3
HOH
HOH
47
A
HOH
49
3
HOH
HOH
49
A
HOH
51
3
HOH
HOH
51
A
HOH
53
3
HOH
HOH
53
A
HOH
55
3
HOH
HOH
55
A
HOH
58
3
HOH
HOH
58
A
HOH
61
3
HOH
HOH
61
A
HOH
63
3
HOH
HOH
63
A
HOH
64
3
HOH
HOH
64
A
HOH
66
3
HOH
HOH
66
A
HOH
67
3
HOH
HOH
67
A
HOH
71
3
HOH
HOH
71
A
HOH
76
3
HOH
HOH
76
A
HOH
81
3
HOH
HOH
81
A
HOH
85
3
HOH
HOH
85
A
HOH
86
3
HOH
HOH
86
A
HOH
87
3
HOH
HOH
87
A
HOH
90
3
HOH
HOH
90
A
HOH
92
3
HOH
HOH
92
A
HOH
93
3
HOH
HOH
93
A
HOH
94
3
HOH
HOH
94
A
HOH
97
3
HOH
HOH
97
A
HOH
98
3
HOH
HOH
98
A
HOH
99
3
HOH
HOH
99
A
HOH
100
3
HOH
HOH
100
A
HOH
102
3
HOH
HOH
102
A
HOH
103
3
HOH
HOH
103
A
HOH
105
3
HOH
HOH
105
A
HOH
106
3
HOH
HOH
106
A
HOH
109
3
HOH
HOH
109
A
HOH
110
3
HOH
HOH
110
A
HOH
112
3
HOH
HOH
112
A
HOH
113
3
HOH
HOH
113
A
HOH
18
3
HOH
HOH
18
B
HOH
20
3
HOH
HOH
20
B
HOH
22
3
HOH
HOH
22
B
HOH
27
3
HOH
HOH
27
B
HOH
30
3
HOH
HOH
30
B
HOH
32
3
HOH
HOH
32
B
HOH
34
3
HOH
HOH
34
B
HOH
36
3
HOH
HOH
36
B
HOH
39
3
HOH
HOH
39
B
HOH
40
3
HOH
HOH
40
B
HOH
41
3
HOH
HOH
41
B
HOH
43
3
HOH
HOH
43
B
HOH
45
3
HOH
HOH
45
B
HOH
48
3
HOH
HOH
48
B
HOH
50
3
HOH
HOH
50
B
HOH
52
3
HOH
HOH
52
B
HOH
54
3
HOH
HOH
54
B
HOH
56
3
HOH
HOH
56
B
HOH
57
3
HOH
HOH
57
B
HOH
59
3
HOH
HOH
59
B
HOH
60
3
HOH
HOH
60
B
HOH
62
3
HOH
HOH
62
B
HOH
65
3
HOH
HOH
65
B
HOH
68
3
HOH
HOH
68
B
HOH
69
3
HOH
HOH
69
B
HOH
70
3
HOH
HOH
70
B
HOH
72
3
HOH
HOH
72
B
HOH
73
3
HOH
HOH
73
B
HOH
74
3
HOH
HOH
74
B
HOH
75
3
HOH
HOH
75
B
HOH
77
3
HOH
HOH
77
B
HOH
78
3
HOH
HOH
78
B
HOH
79
3
HOH
HOH
79
B
HOH
80
3
HOH
HOH
80
B
HOH
82
3
HOH
HOH
82
B
HOH
83
3
HOH
HOH
83
B
HOH
84
3
HOH
HOH
84
B
HOH
88
3
HOH
HOH
88
B
HOH
89
3
HOH
HOH
89
B
HOH
91
3
HOH
HOH
91
B
HOH
95
3
HOH
HOH
95
B
HOH
96
3
HOH
HOH
96
B
HOH
101
3
HOH
HOH
101
B
HOH
104
3
HOH
HOH
104
B
HOH
107
3
HOH
HOH
107
B
HOH
108
3
HOH
HOH
108
B
HOH
111
3
HOH
HOH
111
B
G
1
n
1
DG
1
A
CID
2
n
2
C38
2
A
G
3
n
3
DG
3
A
A
4
n
4
DA
4
A
G
5
n
5
DG
5
A
A
6
n
6
DA
6
A
G
7
n
7
DG
7
A
C
8
n
8
DC
8
A
G
9
n
1
DG
9
B
CID
10
n
2
C38
10
B
G
11
n
3
DG
11
B
A
12
n
4
DA
12
B
G
13
n
5
DG
13
B
A
14
n
6
DA
14
B
G
15
n
7
DG
15
B
C
16
n
8
DC
16
B
author_defined_assembly
8
octameric
A
DG
5
A
O6
DG
5
1_555
A
K
114
C
K
K
1_555
A
DG
5
A
O6
DG
5
3_655
122.2
A
DG
5
A
O6
DG
5
1_555
A
K
114
C
K
K
1_555
A
DG
5
A
O6
DG
5
2_665
111.0
A
DG
5
A
O6
DG
5
3_655
A
K
114
C
K
K
1_555
A
DG
5
A
O6
DG
5
2_665
96.3
A
DG
5
A
O6
DG
5
1_555
A
K
114
C
K
K
1_555
A
DG
5
A
O6
DG
5
4_565
96.3
A
DG
5
A
O6
DG
5
3_655
A
K
114
C
K
K
1_555
A
DG
5
A
O6
DG
5
4_565
111.0
A
DG
5
A
O6
DG
5
2_665
A
K
114
C
K
K
1_555
A
DG
5
A
O6
DG
5
4_565
122.2
A
DG
5
A
O6
DG
5
1_555
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
1_555
73.8
A
DG
5
A
O6
DG
5
3_655
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
1_555
67.6
A
DG
5
A
O6
DG
5
2_665
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
1_555
162.1
A
DG
5
A
O6
DG
5
4_565
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
1_555
73.0
A
DG
5
A
O6
DG
5
1_555
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
3_655
67.6
A
DG
5
A
O6
DG
5
3_655
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
3_655
73.8
A
DG
5
A
O6
DG
5
2_665
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
3_655
73.0
A
DG
5
A
O6
DG
5
4_565
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
3_655
162.1
B
DG
13
B
O6
DG
5
1_555
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
3_655
94.1
A
DG
5
A
O6
DG
5
1_555
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
4_565
73.0
A
DG
5
A
O6
DG
5
3_655
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
4_565
162.1
A
DG
5
A
O6
DG
5
2_665
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
4_565
67.6
A
DG
5
A
O6
DG
5
4_565
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
4_565
73.8
B
DG
13
B
O6
DG
5
1_555
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
4_565
129.3
B
DG
13
B
O6
DG
5
3_655
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
4_565
107.2
A
DG
5
A
O6
DG
5
1_555
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
2_665
162.1
A
DG
5
A
O6
DG
5
3_655
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
2_665
73.0
A
DG
5
A
O6
DG
5
2_665
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
2_665
73.8
A
DG
5
A
O6
DG
5
4_565
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
2_665
67.6
B
DG
13
B
O6
DG
5
1_555
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
2_665
107.2
B
DG
13
B
O6
DG
5
3_655
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
2_665
129.3
B
DG
13
B
O6
DG
5
4_565
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
2_665
94.1
A
DG
5
A
O6
DG
5
1_555
A
K
114
C
K
K
1_555
B
K
115
D
K
K
1_555
124.5
A
DG
5
A
O6
DG
5
3_655
A
K
114
C
K
K
1_555
B
K
115
D
K
K
1_555
55.5
A
DG
5
A
O6
DG
5
2_665
A
K
114
C
K
K
1_555
B
K
115
D
K
K
1_555
124.5
A
DG
5
A
O6
DG
5
4_565
A
K
114
C
K
K
1_555
B
K
115
D
K
K
1_555
55.5
B
DG
13
B
O6
DG
5
1_555
A
K
114
C
K
K
1_555
B
K
115
D
K
K
1_555
53.6
B
DG
13
B
O6
DG
5
3_655
A
K
114
C
K
K
1_555
B
K
115
D
K
K
1_555
126.4
B
DG
13
B
O6
DG
5
4_565
A
K
114
C
K
K
1_555
B
K
115
D
K
K
1_555
126.4
B
DG
13
B
O6
DG
5
2_665
A
K
114
C
K
K
1_555
B
K
115
D
K
K
1_555
53.6
A
DG
5
A
O6
DG
5
1_555
A
K
114
C
K
K
1_555
B
K
115
D
K
K
3_655
55.5
A
DG
5
A
O6
DG
5
3_655
A
K
114
C
K
K
1_555
B
K
115
D
K
K
3_655
124.5
A
DG
5
A
O6
DG
5
2_665
A
K
114
C
K
K
1_555
B
K
115
D
K
K
3_655
55.5
A
DG
5
A
O6
DG
5
4_565
A
K
114
C
K
K
1_555
B
K
115
D
K
K
3_655
124.5
B
DG
13
B
O6
DG
5
1_555
A
K
114
C
K
K
1_555
B
K
115
D
K
K
3_655
126.4
B
DG
13
B
O6
DG
5
3_655
A
K
114
C
K
K
1_555
B
K
115
D
K
K
3_655
53.6
B
DG
13
B
O6
DG
5
4_565
A
K
114
C
K
K
1_555
B
K
115
D
K
K
3_655
53.6
B
DG
13
B
O6
DG
5
2_665
A
K
114
C
K
K
1_555
B
K
115
D
K
K
3_655
126.4
B
K
115
D
K
K
1_555
A
K
114
C
K
K
1_555
B
K
115
D
K
K
3_655
180.0
A
DG
5
A
O6
DG
5
1_555
A
K
114
C
K
K
1_555
B
K
115
D
K
K
4_565
55.5
A
DG
5
A
O6
DG
5
3_655
A
K
114
C
K
K
1_555
B
K
115
D
K
K
4_565
124.5
A
DG
5
A
O6
DG
5
2_665
A
K
114
C
K
K
1_555
B
K
115
D
K
K
4_565
55.5
A
DG
5
A
O6
DG
5
4_565
A
K
114
C
K
K
1_555
B
K
115
D
K
K
4_565
124.5
B
DG
13
B
O6
DG
5
1_555
A
K
114
C
K
K
1_555
B
K
115
D
K
K
4_565
126.4
B
DG
13
B
O6
DG
5
3_655
A
K
114
C
K
K
1_555
B
K
115
D
K
K
4_565
53.6
B
DG
13
B
O6
DG
5
4_565
A
K
114
C
K
K
1_555
B
K
115
D
K
K
4_565
53.6
B
DG
13
B
O6
DG
5
2_665
A
K
114
C
K
K
1_555
B
K
115
D
K
K
4_565
126.4
B
K
115
D
K
K
1_555
A
K
114
C
K
K
1_555
B
K
115
D
K
K
4_565
180.0
B
K
115
D
K
K
3_655
A
K
114
C
K
K
1_555
B
K
115
D
K
K
4_565
0.0
A
DG
5
A
O6
DG
5
1_555
A
K
114
C
K
K
1_555
B
K
115
D
K
K
2_665
124.5
A
DG
5
A
O6
DG
5
3_655
A
K
114
C
K
K
1_555
B
K
115
D
K
K
2_665
55.5
A
DG
5
A
O6
DG
5
2_665
A
K
114
C
K
K
1_555
B
K
115
D
K
K
2_665
124.5
A
DG
5
A
O6
DG
5
4_565
A
K
114
C
K
K
1_555
B
K
115
D
K
K
2_665
55.5
B
DG
13
B
O6
DG
5
1_555
A
K
114
C
K
K
1_555
B
K
115
D
K
K
2_665
53.6
B
DG
13
B
O6
DG
5
3_655
A
K
114
C
K
K
1_555
B
K
115
D
K
K
2_665
126.4
B
DG
13
B
O6
DG
5
4_565
A
K
114
C
K
K
1_555
B
K
115
D
K
K
2_665
126.4
B
DG
13
B
O6
DG
5
2_665
A
K
114
C
K
K
1_555
B
K
115
D
K
K
2_665
53.6
B
K
115
D
K
K
1_555
A
K
114
C
K
K
1_555
B
K
115
D
K
K
2_665
0.0
B
K
115
D
K
K
3_655
A
K
114
C
K
K
1_555
B
K
115
D
K
K
2_665
180.0
B
K
115
D
K
K
4_565
A
K
114
C
K
K
1_555
B
K
115
D
K
K
2_665
180.0
A
DG
5
A
O6
DG
5
4_565
B
K
115
D
K
K
1_555
A
DG
5
A
O6
DG
5
3_655
100.2
A
DG
5
A
O6
DG
5
4_565
B
K
115
D
K
K
1_555
A
HOH
49
E
O
HOH
1_555
80.8
A
DG
5
A
O6
DG
5
3_655
B
K
115
D
K
K
1_555
A
HOH
49
E
O
HOH
1_555
173.7
A
DG
5
A
O6
DG
5
4_565
B
K
115
D
K
K
1_555
A
HOH
49
E
O
HOH
2_665
173.7
A
DG
5
A
O6
DG
5
3_655
B
K
115
D
K
K
1_555
A
HOH
49
E
O
HOH
2_665
80.8
A
HOH
49
E
O
HOH
1_555
B
K
115
D
K
K
1_555
A
HOH
49
E
O
HOH
2_665
98.8
A
DG
5
A
O6
DG
5
4_565
B
K
115
D
K
K
1_555
B
DG
13
B
O6
DG
5
1_555
68.3
A
DG
5
A
O6
DG
5
3_655
B
K
115
D
K
K
1_555
B
DG
13
B
O6
DG
5
1_555
63.4
A
HOH
49
E
O
HOH
1_555
B
K
115
D
K
K
1_555
B
DG
13
B
O6
DG
5
1_555
111.7
A
HOH
49
E
O
HOH
2_665
B
K
115
D
K
K
1_555
B
DG
13
B
O6
DG
5
1_555
117.4
A
DG
5
A
O6
DG
5
4_565
B
K
115
D
K
K
1_555
B
DG
13
B
O6
DG
5
2_665
63.4
A
DG
5
A
O6
DG
5
3_655
B
K
115
D
K
K
1_555
B
DG
13
B
O6
DG
5
2_665
68.3
A
HOH
49
E
O
HOH
1_555
B
K
115
D
K
K
1_555
B
DG
13
B
O6
DG
5
2_665
117.4
A
HOH
49
E
O
HOH
2_665
B
K
115
D
K
K
1_555
B
DG
13
B
O6
DG
5
2_665
111.7
B
DG
13
B
O6
DG
5
1_555
B
K
115
D
K
K
1_555
B
DG
13
B
O6
DG
5
2_665
100.8
A
C38
2
A
C38
2
DC
B
C38
10
B
C38
2
DC
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
2_665
-x+1,-y+1,z
crystal symmetry operation
36.1800000000
36.3800000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
3_655
-x+1,y,-z
crystal symmetry operation
36.1800000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_565
x,-y+1,-z
crystal symmetry operation
0.0000000000
36.3800000000
0.0000000000
1
A
K
114
C
K
1
B
K
115
D
K
1
A
HOH
17
E
HOH
1
A
HOH
64
E
HOH
1
B
HOH
75
F
HOH
0.265
0.234
2.3
9.0
174
1972
1903
RANDOM
1
3.0
MOLECULAR REPLACEMENT
PDB ENTRY 1V3N
G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64
0.31
5.0
0.29
2.3
9.0
97
431
2
332
0
0.005
0.9
20.8
0.8
0.368
0.37
2.38
14
87.1
2.3
20
1V3P
2014
1980
0.0
0.0
0.084
1
7.1
98.4
0.24
2.3
2.38
2.4
199
99.0
data collection
CrystalClear
data scaling
SCALA
phasing
AMoRE
refinement
CNS
1.0
data reduction
CrystalClear
(MSC/RIGAKU)
data scaling
CCP4
(SCALA)
Crystal structure of d(GCGAGAGC): the DNA octaplex structure with I-motif of G-quartet
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
The biological assembly is an octaplex generated from the duplex in the asymmetric unit by the operations: (x, y, z), (1-x, 1-y, z), (x,1-y,2-z) and (1-x, y, 2-z).
covale
1.605
both
A
DG
1
A
O3'
DG
1
1_555
A
C38
2
A
P
C38
2
1_555
covale
1.603
one
A
C38
2
A
O3'
C38
2
1_555
A
DG
3
A
P
DG
3
1_555
covale
1.604
both
B
DG
9
B
O3'
DG
1
1_555
B
C38
10
B
P
C38
2
1_555
covale
1.602
one
B
C38
10
B
O3'
C38
2
1_555
B
DG
11
B
P
DG
3
1_555
metalc
2.689
A
DG
5
A
O6
DG
5
1_555
A
K
114
C
K
K
1_555
metalc
2.689
A
DG
5
A
O6
DG
5
3_655
A
K
114
C
K
K
1_555
metalc
2.689
A
DG
5
A
O6
DG
5
2_665
A
K
114
C
K
K
1_555
metalc
2.689
A
DG
5
A
O6
DG
5
4_565
A
K
114
C
K
K
1_555
metalc
2.887
A
DG
5
A
O6
DG
5
4_565
B
K
115
D
K
K
1_555
metalc
2.887
A
DG
5
A
O6
DG
5
3_655
B
K
115
D
K
K
1_555
metalc
2.675
A
HOH
49
E
O
HOH
1_555
B
K
115
D
K
K
1_555
metalc
2.675
A
HOH
49
E
O
HOH
2_665
B
K
115
D
K
K
1_555
metalc
2.680
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
1_555
metalc
2.680
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
3_655
metalc
2.680
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
4_565
metalc
2.680
A
K
114
C
K
K
1_555
B
DG
13
B
O6
DG
5
2_665
metalc
3.375
A
K
114
C
K
K
1_555
B
K
115
D
K
K
1_555
metalc
3.375
A
K
114
C
K
K
1_555
B
K
115
D
K
K
3_655
metalc
3.375
A
K
114
C
K
K
1_555
B
K
115
D
K
K
4_565
metalc
3.375
A
K
114
C
K
K
1_555
B
K
115
D
K
K
2_665
metalc
2.799
B
DG
13
B
O6
DG
5
1_555
B
K
115
D
K
K
1_555
metalc
2.799
B
DG
13
B
O6
DG
5
2_665
B
K
115
D
K
K
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
C38
2
A
N3
C38
2
1_555
B
DG
15
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
C38
2
A
N4
C38
2
1_555
B
DG
15
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
C38
2
A
O2
C38
2
1_555
B
DG
15
B
N2
DG
7
1_555
hydrog
TYPE_11_PAIR
A
DG
3
A
N2
DG
3
1_555
B
DA
14
B
N7
DA
6
1_555
hydrog
TYPE_11_PAIR
A
DG
3
A
N3
DG
3
1_555
B
DA
14
B
N6
DA
6
1_555
hydrog
TYPE_11_PAIR
A
DA
6
A
N6
DA
6
1_555
B
DG
11
B
N3
DG
3
1_555
hydrog
TYPE_11_PAIR
A
DA
6
A
N7
DA
6
1_555
B
DG
11
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
B
C38
10
B
N3
C38
2
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
B
C38
10
B
O2
C38
2
1_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
B
C38
10
B
N4
C38
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
octaplex, quadruplex, G-quartet, I-motif, I-motif of G-quartet, base-intercalated duplex, base-intercalated motif, sheared G:A pair, DNA, deoxyribonucleic acid, X-ray analysis
1V3P
PDB
1
1V3P
1
8
1V3P
1
8
1V3P
A
1
1
8
9
16
1V3P
9
16
1V3P
B
1
1
8
BINDING SITE FOR RESIDUE K A 114
A
K
114
Software
12
BINDING SITE FOR RESIDUE K B 115
B
K
115
Software
10
A
DG
5
A
DG
5
12
3_655
A
DG
5
A
DG
5
12
2_665
A
DG
5
A
DG
5
12
4_565
A
DG
5
A
DG
5
12
1_555
B
DG
13
B
DG
5
12
4_565
B
DG
13
B
DG
5
12
3_655
B
DG
13
B
DG
5
12
2_665
B
DG
13
B
DG
5
12
1_555
B
K
115
D
K
12
2_665
B
K
115
D
K
12
1_555
B
K
115
D
K
12
4_565
B
K
115
D
K
12
3_655
A
DG
5
A
DG
5
10
3_655
A
DG
5
A
DG
5
10
4_565
A
HOH
49
E
HOH
10
1_555
A
HOH
49
E
HOH
10
2_665
A
K
114
C
K
10
3_655
A
K
114
C
K
10
2_665
A
K
114
C
K
10
4_565
A
K
114
C
K
10
1_555
B
DG
13
B
DG
5
10
1_555
B
DG
13
B
DG
5
10
2_665
23
I 2 2 2