0.030343
0.017518
0.000000
0.000000
0.035037
0.000000
0.000000
0.000000
0.011292
0.00000
0.00000
0.00000
Hays, F.A.
Watson, J.
Ho, P.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
32.957
32.957
88.556
C10 H15 N6 O6 P
346.236
n
2,6-DIAMINOPURINE NUCLEOTIDE
DNA linking
Ca 2
40.078
CALCIUM ION
non-polymer
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
H2 O
18.015
WATER
non-polymer
Na 1
22.990
SODIUM ION
non-polymer
Y
1
N
N
Y
2
N
C
Y
3
N
C
Y
4
N
C
Y
5
N
C
Y
6
N
C
N
7
N
N
Y
8
N
N
Y
9
N
N
Y
10
N
N
N
11
N
N
N
12
N
P
N
13
N
O
N
14
N
O
N
15
N
O
N
16
N
C
N
17
R
C
N
18
N
O
N
19
R
C
N
20
N
C
N
21
S
C
N
22
N
O
N
23
N
O
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
H
N
38
N
H
N
39
N
CA
N
40
N
O
N
41
N
P
N
42
N
O
N
43
N
O
N
44
N
O
N
45
N
C
N
46
R
C
N
47
N
O
N
48
S
C
N
49
N
O
N
50
N
C
N
51
R
C
Y
52
N
N
Y
53
N
C
Y
54
N
N
Y
55
N
C
Y
56
N
C
N
57
N
N
Y
58
N
N
Y
59
N
C
Y
60
N
N
Y
61
N
C
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
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
O
N
77
N
P
N
78
N
O
N
79
N
O
N
80
N
O
N
81
N
C
N
82
R
C
N
83
N
O
N
84
S
C
N
85
N
O
N
86
N
C
N
87
R
C
N
88
N
N
N
89
N
C
N
90
N
O
N
91
N
N
N
92
N
C
N
93
N
N
N
94
N
C
N
95
N
C
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
O
N
111
N
P
N
112
N
O
N
113
N
O
N
114
N
O
N
115
N
C
N
116
R
C
N
117
N
O
N
118
S
C
N
119
N
O
N
120
N
C
N
121
R
C
Y
122
N
N
Y
123
N
C
Y
124
N
N
Y
125
N
C
N
126
N
C
N
127
N
O
N
128
N
N
N
129
N
C
N
130
N
N
N
131
N
N
Y
132
N
C
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
H
N
145
N
H
N
146
N
H
N
147
N
O
N
148
N
P
N
149
N
O
N
150
N
O
N
151
N
O
N
152
N
C
N
153
R
C
N
154
N
O
N
155
S
C
N
156
N
O
N
157
N
C
N
158
R
C
N
159
N
N
N
160
N
C
N
161
N
O
N
162
N
N
N
163
N
C
N
164
N
O
N
165
N
C
N
166
N
C
N
167
N
C
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
O
N
184
N
H
N
185
N
H
N
186
N
NA
Y
1
N
sing
Y
2
N
doub
N
3
N
sing
Y
4
N
doub
Y
5
N
doub
Y
6
N
sing
Y
7
N
sing
Y
8
N
sing
Y
9
N
sing
N
10
N
sing
Y
11
N
sing
Y
12
N
doub
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
doub
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
sing
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
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
doub
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
Y
64
N
sing
Y
65
N
sing
Y
66
N
doub
N
67
N
sing
Y
68
N
sing
Y
69
N
sing
Y
70
N
doub
N
71
N
sing
Y
72
N
doub
N
73
N
sing
N
74
N
sing
Y
75
N
sing
Y
76
N
doub
N
77
N
sing
Y
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
doub
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
doub
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
doub
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
Y
137
N
sing
Y
138
N
sing
Y
139
N
doub
N
140
N
sing
Y
141
N
sing
N
142
N
sing
Y
143
N
doub
N
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
doub
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
doub
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
doub
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
doub
N
183
N
sing
N
184
N
sing
N
185
N
doub
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
43
9813
9822
10.1021/bi049461d
15274635
Influence of minor groove substituents on the structure of DNA holliday junctions.
2004
10.2210/pdb1s1k/pdb
pdb_00001s1k
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
103.0
1
BENT CONICAL SI-MIRROR (RH COATING)
CCD
2002-01-08
ADSC QUANTUM 4
BENT GE(111) MONOCHROMATOR
SINGLE WAVELENGTH
M
x-ray
1
0.9
1.0
14-BM-C
APS
0.9
SYNCHROTRON
APS BEAMLINE 14-BM-C
3060.019
5'-D(*CP*CP*(1AP)P*GP*TP*AP*CP*TP*GP*G)-3'
1
syn
polymer
40.078
CALCIUM ION
2
syn
non-polymer
22.990
SODIUM ION
1
syn
non-polymer
18.015
water
40
nat
water
no
yes
(DC)(DC)(1AP)(DG)(DT)(DA)(DC)(DT)(DG)(DG)
CCAGTACTGG
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
1
2.02
38.5
VAPOR DIFFUSION, SITTING DROP
7.50
5mM TRIS(HCl), 23mM CaAcetate, 16% MPD, .6mM DNA against 28% MPD at RT, pH 7.50, VAPOR DIFFUSION, SITTING DROP
TRIS(HCl)
1
CaAcetate
1
16% MPD
1
DNA
1
water
28% MPD
TRIS(HCl)
0.319
1
19
A
1
A
10
-3.917
A_DC1:DG10_A
1
-0.481
0.772
-0.044
-0.507
-3.987
1
19
A
2
A
9
-5.656
A_DC2:DG9_A
2
-8.813
0.286
0.246
-0.077
-4.157
A
3
A
8
-2.518
A_1AP3:DT8_A
3
-5.707
0.131
-0.239
0.006
-1.850
1
19
A
4
A
7
-3.866
A_DG4:DC7_A
4
-11.463
-0.331
0.212
-0.017
-1.504
1
20
A
5
A
6
-2.231
A_DT5:DA6_A
5
-11.056
-0.171
0.330
-0.178
1.504
1
20
A
6
A
5
-2.231
A_DA6:DT5_A
6
-11.056
0.171
0.330
-0.178
1.850
1
19
A
7
A
4
-3.866
A_DC7:DG4_A
7
-11.463
0.331
0.212
-0.017
4.157
A
8
A
3
-2.518
A_DT8:1AP3_A
8
-5.707
-0.131
-0.239
0.006
3.987
1
19
A
9
A
2
-5.656
A_DG9:DC2_A
9
-8.813
-0.286
0.246
-0.077
-0.319
1
19
A
10
A
1
-3.917
A_DG10:DC1_A
10
-0.481
-0.772
-0.044
-0.507
3.317
34.087
A
A
1
2
13.012
A
A
10
9
3.403
7.566
-0.392
0.060
AA_DC1DC2:DG9DG10_AA
1
1.394
-2.398
33.233
-1.148
0.900
3.491
40.064
A
A
2
3
12.005
A
A
9
8
3.398
8.156
0.231
0.780
AA_DC21AP3:DT8DG9_AA
2
4.349
-6.402
39.026
0.143
0.193
3.126
32.028
A
A
3
4
5.242
A
A
8
7
3.243
2.881
0.533
-0.116
AA_1AP3DG4:DC7DT8_AA
3
-4.180
7.607
31.633
-0.719
-1.705
3.248
29.298
A
A
4
5
6.090
A
A
7
6
3.351
3.072
-0.021
-0.755
AA_DG4DT5:DA6DC7_AA
4
-2.195
4.350
29.059
-2.164
-0.439
3.262
45.713
A
A
5
6
3.650
A
A
6
5
3.246
2.834
0.000
0.368
AA_DT5DA6:DT5DA6_AA
5
0.000
0.000
45.629
0.228
0.000
3.248
29.298
A
A
6
7
6.090
A
A
5
4
3.351
3.072
0.021
-0.755
AA_DA6DC7:DG4DT5_AA
6
2.195
-4.350
29.059
-2.164
0.439
3.126
32.028
A
A
7
8
5.242
A
A
4
3
3.243
2.881
-0.533
-0.116
AA_DC7DT8:1AP3DG4_AA
7
4.180
-7.607
31.633
-0.719
1.705
3.491
40.064
A
A
8
9
12.005
A
A
3
2
3.398
8.156
-0.231
0.780
AA_DT8DG9:DC21AP3_AA
8
-4.349
6.402
39.026
0.143
-0.193
3.317
34.087
A
A
9
10
13.012
A
A
2
1
3.403
7.566
0.392
0.060
AA_DG9DG10:DC1DC2_AA
9
-1.394
2.398
33.233
-1.148
-0.900
atom_site
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
Atomic model
Data collection
Database references
Derived calculations
Refinement description
1
0
2004-08-31
1
1
2008-04-29
1
2
2011-07-13
2
0
2023-08-23
_atom_site.occupancy
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_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.ptnr2_auth_comp_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr2_label_atom_id
_pdbx_struct_conn_angle.ptnr2_label_comp_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.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.ptnr1_symmetry
_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
Unmodified ACT strand
BIOMOLECULE: 1
THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
WHICH CONSISTS OF 1 CHAIN(S). THE FULL BIOLOGICAL UNIT
CONSISTS OF TWO STRANDS FORMING A B-DNA DUPLEX STRUCTURE.
SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL
MOLECULE(S).
RCSB
Y
RCSB
2004-01-06
REL
REL
CA
CALCIUM ION
NA
SODIUM ION
HOH
water
1P4Z
PDB
experimental model
CA
11
2
CA
CA
11
A
CA
14
2
CA
CA
14
A
NA
15
3
NA
NA
15
A
WAT
12
4
HOH
HOH
12
A
WAT
13
4
HOH
HOH
13
A
WAT
16
4
HOH
HOH
16
A
WAT
17
4
HOH
HOH
17
A
WAT
18
4
HOH
HOH
18
A
WAT
19
4
HOH
HOH
19
A
WAT
20
4
HOH
HOH
20
A
WAT
21
4
HOH
HOH
21
A
WAT
22
4
HOH
HOH
22
A
WAT
23
4
HOH
HOH
23
A
WAT
24
4
HOH
HOH
24
A
WAT
25
4
HOH
HOH
25
A
WAT
26
4
HOH
HOH
26
A
WAT
27
4
HOH
HOH
27
A
WAT
28
4
HOH
HOH
28
A
WAT
29
4
HOH
HOH
29
A
WAT
30
4
HOH
HOH
30
A
WAT
31
4
HOH
HOH
31
A
WAT
32
4
HOH
HOH
32
A
WAT
33
4
HOH
HOH
33
A
WAT
34
4
HOH
HOH
34
A
WAT
35
4
HOH
HOH
35
A
WAT
36
4
HOH
HOH
36
A
WAT
37
4
HOH
HOH
37
A
WAT
38
4
HOH
HOH
38
A
WAT
41
4
HOH
HOH
41
A
WAT
42
4
HOH
HOH
42
A
WAT
43
4
HOH
HOH
43
A
WAT
44
4
HOH
HOH
44
A
WAT
45
4
HOH
HOH
45
A
WAT
46
4
HOH
HOH
46
A
WAT
47
4
HOH
HOH
47
A
WAT
48
4
HOH
HOH
48
A
WAT
49
4
HOH
HOH
49
A
WAT
50
4
HOH
HOH
50
A
WAT
51
4
HOH
HOH
51
A
WAT
52
4
HOH
HOH
52
A
WAT
53
4
HOH
HOH
53
A
WAT
54
4
HOH
HOH
54
A
WAT
55
4
HOH
HOH
55
A
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
DAP
3
n
3
1AP
3
A
G
4
n
4
DG
4
A
T
5
n
5
DT
5
A
A
6
n
6
DA
6
A
C
7
n
7
DC
7
A
T
8
n
8
DT
8
A
G
9
n
9
DG
9
A
G
10
n
10
DG
10
A
author_defined_assembly
2
dimeric
A
DT
5
A
OP1
DT
5
1_555
A
NA
15
D
NA
NA
1_555
A
HOH
31
E
O
HOH
1_555
101.0
A
DT
5
A
OP1
DT
5
1_555
A
NA
15
D
NA
NA
1_555
A
HOH
36
E
O
HOH
1_555
57.7
A
HOH
31
E
O
HOH
1_555
A
NA
15
D
NA
NA
1_555
A
HOH
36
E
O
HOH
1_555
145.2
A
DC
7
A
OP2
DC
7
1_555
A
CA
14
C
CA
CA
1_555
A
DC
7
A
OP2
DC
7
8_555
169.6
A
DC
7
A
OP2
DC
7
1_555
A
CA
14
C
CA
CA
1_555
A
HOH
23
E
O
HOH
8_555
105.6
A
DC
7
A
OP2
DC
7
8_555
A
CA
14
C
CA
CA
1_555
A
HOH
23
E
O
HOH
8_555
72.0
A
DC
7
A
OP2
DC
7
1_555
A
CA
14
C
CA
CA
1_555
A
HOH
28
E
O
HOH
1_555
81.5
A
DC
7
A
OP2
DC
7
8_555
A
CA
14
C
CA
CA
1_555
A
HOH
28
E
O
HOH
1_555
104.3
A
HOH
23
E
O
HOH
8_555
A
CA
14
C
CA
CA
1_555
A
HOH
28
E
O
HOH
1_555
159.0
A
DC
7
A
OP2
DC
7
1_555
A
CA
14
C
CA
CA
1_555
A
HOH
28
E
O
HOH
8_555
102.5
A
DC
7
A
OP2
DC
7
8_555
A
CA
14
C
CA
CA
1_555
A
HOH
28
E
O
HOH
8_555
84.2
A
HOH
23
E
O
HOH
8_555
A
CA
14
C
CA
CA
1_555
A
HOH
28
E
O
HOH
8_555
52.3
A
HOH
28
E
O
HOH
1_555
A
CA
14
C
CA
CA
1_555
A
HOH
28
E
O
HOH
8_555
107.2
A
HOH
20
E
O
HOH
1_555
A
CA
11
B
CA
CA
1_555
A
HOH
20
E
O
HOH
8_555
107.8
A
HOH
20
E
O
HOH
1_555
A
CA
11
B
CA
CA
1_555
A
HOH
45
E
O
HOH
1_555
125.9
A
HOH
20
E
O
HOH
8_555
A
CA
11
B
CA
CA
1_555
A
HOH
45
E
O
HOH
1_555
107.2
A
HOH
20
E
O
HOH
1_555
A
CA
11
B
CA
CA
1_555
A
HOH
45
E
O
HOH
8_555
107.6
A
HOH
20
E
O
HOH
8_555
A
CA
11
B
CA
CA
1_555
A
HOH
45
E
O
HOH
8_555
124.7
A
HOH
45
E
O
HOH
1_555
A
CA
11
B
CA
CA
1_555
A
HOH
45
E
O
HOH
8_555
83.8
A
1AP
3
2,6-DIAMINOPURINE NUCLEOTIDE
A
1AP
3
DA
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
0.5000000000
0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
12_545
x,x-y-1,-z+1/6
crystal symmetry operation
16.4785000000
-28.5415992325
14.7593333333
1
A
CA
11
B
CA
1
A
CA
14
C
CA
1
A
HOH
32
E
HOH
1
A
A
O4'
O
DC
HOH
2
48
2.03
1
A
A
OP2
O
DA
HOH
6
37
2.04
1
A
A
O2
O
DT
HOH
5
49
2.10
1
A
A
OP1
O
DG
HOH
9
16
2.11
1
A
A
O
O
HOH
HOH
35
41
2.11
1
A
DA
6
0.086
SIDE CHAIN
1
A
DC
7
0.128
SIDE CHAIN
1
A
DG
9
0.083
SIDE CHAIN
1
A
DG
10
0.120
SIDE CHAIN
1
3.87
0.30
108.30
112.17
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
5.57
0.70
119.20
124.77
A
A
A
N1
C2
N3
DC
DC
DC
1
1
1
N
1
-3.19
0.40
121.90
118.71
A
A
A
N3
C4
C5
DC
DC
DC
1
1
1
N
1
-4.88
0.60
118.90
114.02
A
A
A
N1
C2
O2
DC
DC
DC
1
1
1
N
1
15.42
1.10
110.50
125.92
A
A
A
O3'
P
OP2
DC
DC
DC
1
2
2
Y
1
-8.26
0.90
105.70
97.44
A
A
A
O5'
P
OP2
DC
DC
DC
2
2
2
N
1
-11.85
1.80
114.10
102.25
A
A
A
C5'
C4'
C3'
DC
DC
DC
2
2
2
N
1
-7.99
1.00
110.10
102.11
A
A
A
C1'
O4'
C4'
DC
DC
DC
2
2
2
N
1
7.38
0.30
108.30
115.68
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
26.39
1.10
110.50
136.89
A
A
A
O3'
P
OP2
1AP
DG
DG
3
4
4
Y
1
-28.68
2.20
105.20
76.52
A
A
A
O3'
P
OP1
1AP
DG
DG
3
4
4
Y
1
3.70
0.60
106.00
109.70
A
A
A
O4'
C4'
C3'
DG
DG
DG
4
4
4
N
1
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
-3.91
0.60
123.90
119.99
A
A
A
N1
C2
N3
DG
DG
DG
4
4
4
N
1
3.28
0.50
111.90
115.18
A
A
A
C2
N3
C4
DG
DG
DG
4
4
4
N
1
-3.16
0.40
110.80
107.64
A
A
A
C4
C5
N7
DG
DG
DG
4
4
4
N
1
3.19
0.50
104.30
107.49
A
A
A
C5
N7
C8
DG
DG
DG
4
4
4
N
1
7.76
1.10
110.50
118.26
A
A
A
O3'
P
OP2
DG
DT
DT
4
5
5
Y
1
4.85
0.60
106.00
110.85
A
A
A
O4'
C4'
C3'
DT
DT
DT
5
5
5
N
1
-26.83
2.50
109.40
82.57
A
A
A
C2'
C3'
O3'
DT
DT
DT
5
5
5
N
1
2.35
0.30
108.30
110.65
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
1
4.81
0.60
127.20
132.01
A
A
A
C2
N3
C4
DT
DT
DT
5
5
5
N
1
-14.91
2.20
105.20
90.29
A
A
A
O3'
P
OP1
DT
DA
DA
5
6
6
Y
1
-7.44
0.90
105.70
98.26
A
A
A
O5'
P
OP1
DA
DA
DA
6
6
6
N
1
11.52
1.20
110.70
122.22
A
A
A
O5'
P
OP2
DA
DA
DA
6
6
6
N
1
7.38
0.70
110.30
117.68
A
A
A
C1'
O4'
C4'
DA
DA
DA
6
6
6
N
1
-4.97
0.60
118.60
113.63
A
A
A
C6
N1
C2
DA
DA
DA
6
6
6
N
1
4.36
0.50
129.30
133.66
A
A
A
N1
C2
N3
DA
DA
DA
6
6
6
N
1
4.89
0.50
110.60
115.49
A
A
A
C2
N3
C4
DA
DA
DA
6
6
6
N
1
-4.49
0.70
126.80
122.31
A
A
A
N3
C4
C5
DA
DA
DA
6
6
6
N
1
3.09
0.50
113.80
116.89
A
A
A
N7
C8
N9
DA
DA
DA
6
6
6
N
1
13.59
1.10
110.50
124.09
A
A
A
O3'
P
OP2
DA
DC
DC
6
7
7
Y
1
-26.91
2.20
105.20
78.29
A
A
A
O3'
P
OP1
DA
DC
DC
6
7
7
Y
1
18.58
1.20
110.70
129.28
A
A
A
O5'
P
OP1
DC
DC
DC
7
7
7
N
1
-7.37
0.90
105.70
98.33
A
A
A
O5'
P
OP2
DC
DC
DC
7
7
7
N
1
-22.57
1.90
109.30
86.73
A
A
A
C5'
C4'
O4'
DC
DC
DC
7
7
7
N
1
-5.64
0.50
119.90
114.26
A
A
A
C2
N3
C4
DC
DC
DC
7
7
7
N
1
5.21
0.70
110.30
115.51
A
A
A
C1'
O4'
C4'
DT
DT
DT
8
8
8
N
1
19.19
1.90
104.00
123.19
A
A
A
O3'
P
O5'
DT
DG
DG
8
9
9
Y
1
12.99
1.10
110.50
123.49
A
A
A
O3'
P
OP2
DT
DG
DG
8
9
9
Y
1
-22.13
2.20
105.20
83.07
A
A
A
O3'
P
OP1
DT
DG
DG
8
9
9
Y
1
-8.59
0.90
105.70
97.11
A
A
A
O5'
P
OP2
DG
DG
DG
9
9
9
N
1
-4.34
0.40
104.50
100.16
A
A
A
O4'
C4'
C3'
DG
DG
DG
9
9
9
N
1
-12.39
1.90
109.30
96.91
A
A
A
C5'
C4'
O4'
DG
DG
DG
9
9
9
N
1
-8.16
0.80
102.40
94.24
A
A
A
C3'
C2'
C1'
DG
DG
DG
9
9
9
N
1
5.51
0.50
106.80
112.31
A
A
A
O4'
C1'
C2'
DG
DG
DG
9
9
9
N
1
-4.30
0.60
130.40
126.10
A
A
A
C6
C5
N7
DG
DG
DG
9
9
9
N
1
13.97
1.90
104.00
117.97
A
A
A
O3'
P
O5'
DG
DG
DG
9
10
10
Y
1
-14.14
0.90
105.70
91.56
A
A
A
O5'
P
OP1
DG
DG
DG
10
10
10
N
1
12.00
1.10
109.80
121.80
A
A
A
C5'
C4'
O4'
DG
DG
DG
10
10
10
N
1
-6.07
1.00
110.10
104.03
A
A
A
C1'
O4'
C4'
DG
DG
DG
10
10
10
N
1
-24.32
2.50
109.70
85.38
A
A
A
C4'
C3'
O3'
DG
DG
DG
10
10
10
N
1
2.02
0.30
108.30
110.32
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
7.01
0.60
125.10
132.11
A
A
A
C6
N1
C2
DG
DG
DG
10
10
10
N
1
-3.28
0.50
111.90
108.62
A
A
A
C2
N3
C4
DG
DG
DG
10
10
10
N
1
A
A
C3'
C2'
DC
DC
1
1
-0.053
0.008
1.516
1.463
N
1
A
A
C2'
C1'
DC
DC
1
1
0.087
0.010
1.519
1.606
N
1
A
A
C4
C5
DC
DC
1
1
0.053
0.008
1.425
1.478
N
1
A
A
C5
C6
DC
DC
1
1
0.125
0.008
1.339
1.464
N
1
A
A
P
OP2
DC
DC
2
2
0.115
0.017
1.485
1.600
N
1
A
A
C3'
C2'
DC
DC
2
2
-0.048
0.008
1.516
1.468
N
1
A
A
C4
N4
DC
DC
2
2
0.106
0.009
1.335
1.441
N
1
A
A
N1
C2
DC
DC
2
2
0.083
0.010
1.397
1.480
N
1
A
A
C5
C6
DC
DC
2
2
-0.051
0.008
1.339
1.288
N
1
A
A
P
O5'
DG
DG
4
4
0.070
0.010
1.593
1.663
N
1
A
A
O3'
C3'
DG
DG
4
4
-0.121
0.006
1.419
1.298
N
1
A
A
C2
N3
DG
DG
4
4
0.059
0.008
1.323
1.382
N
1
A
A
C4
C5
DG
DG
4
4
-0.083
0.007
1.379
1.296
N
1
A
A
C8
N9
DG
DG
4
4
-0.095
0.007
1.374
1.279
N
1
A
A
O3'
P
DG
DT
4
5
-0.081
0.012
1.607
1.526
Y
1
A
A
C2'
C1'
DT
DT
5
5
0.115
0.010
1.519
1.634
N
1
A
A
O3'
C3'
DT
DT
5
5
-0.164
0.006
1.419
1.255
N
1
A
A
C1'
N1
DT
DT
5
5
0.106
0.013
1.488
1.594
N
1
A
A
C2
N3
DT
DT
5
5
-0.077
0.008
1.373
1.296
N
1
A
A
C4
C5
DT
DT
5
5
-0.102
0.009
1.445
1.343
N
1
A
A
C6
N1
DT
DT
5
5
0.051
0.007
1.378
1.429
N
1
A
A
C2
O2
DT
DT
5
5
0.090
0.008
1.220
1.310
N
1
A
A
C4
O4
DT
DT
5
5
-0.074
0.009
1.228
1.154
N
1
A
A
C5
C7
DT
DT
5
5
-0.043
0.006
1.496
1.453
N
1
A
A
P
OP1
DA
DA
6
6
-0.199
0.017
1.485
1.286
N
1
A
A
P
OP2
DA
DA
6
6
0.135
0.017
1.485
1.620
N
1
A
A
P
O5'
DA
DA
6
6
-0.061
0.010
1.593
1.532
N
1
A
A
C2
N3
DA
DA
6
6
-0.080
0.009
1.331
1.251
N
1
A
A
N3
C4
DA
DA
6
6
-0.038
0.006
1.344
1.306
N
1
A
A
C5
C6
DA
DA
6
6
0.124
0.009
1.406
1.530
N
1
A
A
C6
N6
DA
DA
6
6
-0.162
0.008
1.335
1.173
N
1
A
A
P
O5'
DC
DC
7
7
-0.109
0.010
1.593
1.484
N
1
A
A
C2
O2
DC
DC
7
7
-0.060
0.009
1.240
1.180
N
1
A
A
C4
N4
DC
DC
7
7
-0.088
0.009
1.335
1.247
N
1
A
A
N1
C6
DC
DC
7
7
-0.073
0.006
1.367
1.294
N
1
A
A
O3'
P
DC
DT
7
8
0.132
0.012
1.607
1.739
Y
1
A
A
P
OP2
DT
DT
8
8
0.176
0.017
1.485
1.661
N
1
A
A
C2'
C1'
DT
DT
8
8
-0.110
0.010
1.518
1.408
N
1
A
A
O4'
C4'
DT
DT
8
8
-0.115
0.010
1.446
1.331
N
1
A
A
O3'
C3'
DT
DT
8
8
-0.040
0.006
1.419
1.379
N
1
A
A
C5
C6
DT
DT
8
8
-0.079
0.007
1.339
1.260
N
1
A
A
C2
O2
DT
DT
8
8
-0.119
0.008
1.220
1.101
N
1
A
A
C5
C7
DT
DT
8
8
-0.092
0.006
1.496
1.404
N
1
A
A
P
OP1
DG
DG
9
9
-0.128
0.017
1.485
1.357
N
1
A
A
P
OP2
DG
DG
9
9
-0.143
0.017
1.485
1.342
N
1
A
A
C2
N3
DG
DG
9
9
0.091
0.008
1.323
1.414
N
1
A
A
N3
C4
DG
DG
9
9
-0.068
0.007
1.350
1.282
N
1
A
A
C6
N1
DG
DG
9
9
-0.056
0.007
1.391
1.335
N
1
A
A
C2
N2
DG
DG
9
9
0.149
0.010
1.341
1.490
N
1
A
A
C6
O6
DG
DG
9
9
-0.091
0.009
1.237
1.146
N
1
A
A
P
O5'
DG
DG
10
10
-0.094
0.010
1.593
1.499
N
1
A
A
O4'
C1'
DG
DG
10
10
0.076
0.011
1.420
1.496
N
1
A
A
O3'
C3'
DG
DG
10
10
-0.112
0.006
1.419
1.307
N
1
A
A
N3
C4
DG
DG
10
10
0.144
0.007
1.350
1.494
N
1
A
A
C5
C6
DG
DG
10
10
-0.072
0.010
1.419
1.347
N
1
A
A
C6
N1
DG
DG
10
10
-0.060
0.007
1.391
1.331
N
1
A
A
C5
N7
DG
DG
10
10
-0.045
0.006
1.388
1.343
N
1
A
A
N9
C4
DG
DG
10
10
0.049
0.008
1.375
1.424
N
1
A
A
C2
N2
DG
DG
10
10
0.084
0.010
1.341
1.425
N
1
A
A
O
O
HOH
HOH
37
37
1.34
1_555
8_555
14.0
3.22
3.51
0.00
3.22
0.00
-6.45
0.258
0.017
0.232
0.253
0.232
1.90
17.49
228
2528
2413
9.400
93.9
RANDOM
29235.77
29235.77
0.0
1
RESTRAINED
THROUGHOUT
0.000
0
MOLECULAR REPLACEMENT
1P4Z
CNS
0.26
0.25
5.00
0.33
0.26
1.90
17.49
40
246
3
203
0
0.067
6.20
21.60
5.46
0.4
0.069
0.308
2.02
34
287
6
10.60
80.70
8.80
1.850
17.50
1S1K
2528
2528
0.000
0.056
1
96.3
0.245
1.85
1.92
4.980
72.2
data reduction
DENZO
data scaling
SCALEPACK
phasing
EPMR
refinement
CNS
1.0
INFLUENCE OF GROOVE INTERACTIONS ON DNA HOLLIDAY JUNCTION FORMATION
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
covale
1.626
both
A
DC
2
A
O3'
DC
2
1_555
A
1AP
3
A
P
1AP
3
1_555
covale
1.634
one
A
1AP
3
A
O3'
1AP
3
1_555
A
DG
4
A
P
DG
4
1_555
covale
1.935
none
A
1AP
3
A
O3'
1AP
3
1_555
A
DG
4
A
OP1
DG
4
1_555
metalc
2.502
A
DT
5
A
OP1
DT
5
1_555
A
NA
15
D
NA
NA
1_555
metalc
2.539
A
DC
7
A
OP2
DC
7
1_555
A
CA
14
C
CA
CA
1_555
metalc
2.448
A
DC
7
A
OP2
DC
7
8_555
A
CA
14
C
CA
CA
1_555
metalc
3.150
A
CA
11
B
CA
CA
1_555
A
HOH
20
E
O
HOH
1_555
metalc
3.173
A
CA
11
B
CA
CA
1_555
A
HOH
20
E
O
HOH
8_555
metalc
2.830
A
CA
11
B
CA
CA
1_555
A
HOH
45
E
O
HOH
1_555
metalc
2.840
A
CA
11
B
CA
CA
1_555
A
HOH
45
E
O
HOH
8_555
metalc
3.355
A
CA
14
C
CA
CA
1_555
A
HOH
23
E
O
HOH
8_555
metalc
2.375
A
CA
14
C
CA
CA
1_555
A
HOH
28
E
O
HOH
1_555
metalc
2.342
A
CA
14
C
CA
CA
1_555
A
HOH
28
E
O
HOH
8_555
metalc
1.795
A
NA
15
D
NA
NA
1_555
A
HOH
31
E
O
HOH
1_555
metalc
2.731
A
NA
15
D
NA
NA
1_555
A
HOH
36
E
O
HOH
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
A
DG
10
A
N1
DG
10
12_545
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
A
DG
10
A
O6
DG
10
12_545
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
A
DG
10
A
N2
DG
10
12_545
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
A
DG
9
A
N1
DG
9
12_545
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
A
DG
9
A
O6
DG
9
12_545
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
A
DG
9
A
N2
DG
9
12_545
hydrog
1AP-DT MISPAIR
A
1AP
3
A
N2
1AP
3
1_555
A
DT
8
A
O2
DT
8
12_545
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
A
DC
7
A
N3
DC
7
12_545
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
A
DC
7
A
O2
DC
7
12_545
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
A
DC
7
A
N4
DC
7
12_545
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
A
DA
6
A
N1
DA
6
12_545
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
A
DA
6
A
N6
DA
6
12_545
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
A
DT
5
A
N3
DT
5
12_545
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
A
DT
5
A
O4
DT
5
12_545
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
A
DG
4
A
N1
DG
4
12_545
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
A
DG
4
A
O6
DG
4
12_545
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
A
DG
4
A
N2
DG
4
12_545
hydrog
DT-1AP MISPAIR
A
DT
8
A
O2
DT
8
1_555
A
1AP
3
A
N2
1AP
3
12_545
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
A
DC
2
A
N3
DC
2
12_545
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
A
DC
2
A
O2
DC
2
12_545
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
A
DC
2
A
N4
DC
2
12_545
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
A
DC
1
A
N3
DC
1
12_545
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
A
DC
1
A
O2
DC
1
12_545
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
A
DC
1
A
N4
DC
1
12_545
DNA
B-DNA, DOUBLE HELIX, 2, 6-Diaminopurine, Minor groove interactions, DNA
1S1K
PDB
1
1S1K
1
10
1S1K
1
10
1S1K
A
1
1
10
BINDING SITE FOR RESIDUE CA A 11
A
CA
11
Software
2
BINDING SITE FOR RESIDUE CA A 14
A
CA
14
Software
4
BINDING SITE FOR RESIDUE NA A 15
A
NA
15
Software
3
A
HOH
45
E
HOH
2
1_555
A
HOH
45
E
HOH
2
8_555
A
DC
7
A
DC
7
4
1_555
A
DC
7
A
DC
7
4
8_555
A
HOH
28
E
HOH
4
1_555
A
HOH
28
E
HOH
4
8_555
A
DT
5
A
DT
5
3
1_555
A
HOH
31
E
HOH
3
1_555
A
HOH
36
E
HOH
3
1_555
178
P 61 2 2