0.015423
0.000000
0.004649
0.000000
0.044293
0.000000
0.000000
0.000000
0.027436
0.00000
0.00000
0.00000
Hays, F.A.
Vargason, J.M.
Ho, P.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
106.78
90.00
64.840
22.580
38.070
C9 H12 Br N2 O8 P
387.078
n
5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
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
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
CA
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
P
N
144
N
O
N
145
N
O
N
146
N
O
N
147
N
C
N
148
R
C
N
149
N
O
N
150
S
C
N
151
N
O
N
152
N
C
N
153
R
C
N
154
N
N
N
155
N
C
N
156
N
O
N
157
N
N
N
158
N
C
N
159
N
O
N
160
N
C
N
161
N
C
N
162
N
C
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
O
N
179
N
H
N
180
N
H
N
181
N
NA
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
sing
N
37
N
doub
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
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
Y
58
N
sing
Y
59
N
sing
Y
60
N
doub
N
61
N
sing
Y
62
N
sing
Y
63
N
sing
Y
64
N
doub
N
65
N
sing
Y
66
N
doub
N
67
N
sing
N
68
N
sing
Y
69
N
sing
Y
70
N
doub
N
71
N
sing
Y
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
doub
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
doub
N
99
N
sing
N
100
N
doub
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
N
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
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
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
doub
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
doub
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
42
9586
9597
10.1021/bi0346603
12911300
Effect of Sequence on the Conformation of DNA Holliday Junctions
2003
10.2210/pdb1p54/pdb
pdb_00001p54
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
IMAGE PLATE
2002-12-19
RIGAKU RAXIS IV
NI FILTER
SINGLE WAVELENGTH
M
x-ray
1
1.542
1.0
1.542
ROTATING ANODE
RIGAKU RU300
3109.874
5'-D(*CP*CP*AP*GP*TP*AP*CP*(BRU)P*GP*G)-3'
2
syn
polymer
22.990
SODIUM ION
1
syn
non-polymer
40.078
CALCIUM ION
1
syn
non-polymer
18.015
water
87
nat
water
no
yes
(DC)(DC)(DA)(DG)(DT)(DA)(DC)(BRU)(DG)(DG)
CCAGTACUGG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
1
1.93
35.87
7.50
0.6mM DNA, 5mM Tris-HCL, 120mM calcium acetate, 16% 2-methyl-2,4-pentane diol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.50
298
Tris-HCL
1
calcium acetate
1
2-methyl-2,4-pentane diol
1
H2O
1
calcium acetate
2
Tris-HCL
2
2-methyl-2,4-pentane diol
2
H2O
2
-0.110
1
19
A
1
B
20
0.485
A_DC1:DG20_B
1
-13.775
0.041
0.058
-0.058
-1.830
1
19
A
2
B
19
-0.482
A_DC2:DG19_B
2
-16.662
0.469
0.543
-0.121
-3.669
1
20
A
3
B
18
1.743
A_DA3:BRU18_B
3
-6.015
-0.085
0.417
-0.067
4.459
1
19
A
4
B
17
-6.000
A_DG4:DC17_B
4
-16.673
-0.843
0.221
-0.485
4.364
1
20
A
5
B
16
4.769
A_DT5:DA16_B
5
-0.040
0.106
0.178
-0.055
14.311
1
20
A
6
B
15
3.463
A_DA6:DT15_B
6
-16.557
0.217
0.205
0.159
3.743
45.533
A
A
1
2
3.292
B
B
20
19
3.646
2.540
0.200
2.022
AA_DC1DC2:DG19DG20_BB
1
6.057
-7.850
45.082
2.359
0.346
2.226
45.393
A
A
2
3
-19.845
B
B
19
18
3.276
-15.048
0.263
2.820
AA_DC2DA3:BRU18DG19_BB
2
2.188
-2.885
42.898
4.811
-0.173
3.088
34.629
A
A
3
4
10.690
B
B
18
17
3.132
6.329
0.383
0.066
AA_DA3DG4:DC17BRU18_BB
3
-0.576
0.973
34.058
-0.823
-0.728
3.130
30.588
A
A
4
5
16.024
B
B
17
16
3.204
8.337
0.806
-0.076
AA_DG4DT5:DA16DC17_BB
4
3.047
-5.856
29.301
-1.779
-0.931
3.194
38.435
A
A
5
6
3.777
B
B
16
15
3.175
2.485
-0.797
0.824
AA_DT5DA6:DT15DA16_BB
5
1.202
-1.828
38.339
0.951
1.356
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
2003-09-02
1
1
2008-04-29
1
2
2011-07-13
1
3
2011-11-16
1
4
2023-08-16
_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_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.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
Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions
Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions
RCSB
Y
RCSB
2003-04-25
REL
REL
NA
SODIUM ION
CA
CALCIUM ION
HOH
water
DNA was synthesized on an Applied Biosystems DNA synthesizer using phosphoramidite chemistry, with the trityl-protecting group left intact at the 5-terminal nucleotide, FOR SUBSEQUENT HPLC PURIFICATION, THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN.
sample
1L6B
1L6B USED FOR INITIAL SOLUTION VIA MOLECULAR REPLACEMENT
PDB
experimental model
NA
37
2
NA
NA
37
A
CA
67
3
CA
CA
67
A
HOH
21
4
HOH
HOH
21
A
HOH
23
4
HOH
HOH
23
A
HOH
24
4
HOH
HOH
24
A
HOH
25
4
HOH
HOH
25
A
HOH
26
4
HOH
HOH
26
A
HOH
27
4
HOH
HOH
27
A
HOH
29
4
HOH
HOH
29
A
HOH
30
4
HOH
HOH
30
A
HOH
32
4
HOH
HOH
32
A
HOH
33
4
HOH
HOH
33
A
HOH
34
4
HOH
HOH
34
A
HOH
36
4
HOH
HOH
36
A
HOH
38
4
HOH
HOH
38
A
HOH
39
4
HOH
HOH
39
A
HOH
40
4
HOH
HOH
40
A
HOH
42
4
HOH
HOH
42
A
HOH
43
4
HOH
HOH
43
A
HOH
44
4
HOH
HOH
44
A
HOH
46
4
HOH
HOH
46
A
HOH
50
4
HOH
HOH
50
A
HOH
52
4
HOH
HOH
52
A
HOH
53
4
HOH
HOH
53
A
HOH
54
4
HOH
HOH
54
A
HOH
55
4
HOH
HOH
55
A
HOH
57
4
HOH
HOH
57
A
HOH
61
4
HOH
HOH
61
A
HOH
62
4
HOH
HOH
62
A
HOH
64
4
HOH
HOH
64
A
HOH
65
4
HOH
HOH
65
A
HOH
66
4
HOH
HOH
66
A
HOH
68
4
HOH
HOH
68
A
HOH
70
4
HOH
HOH
70
A
HOH
72
4
HOH
HOH
72
A
HOH
73
4
HOH
HOH
73
A
HOH
76
4
HOH
HOH
76
A
HOH
77
4
HOH
HOH
77
A
HOH
79
4
HOH
HOH
79
A
HOH
80
4
HOH
HOH
80
A
HOH
81
4
HOH
HOH
81
A
HOH
82
4
HOH
HOH
82
A
HOH
85
4
HOH
HOH
85
A
HOH
86
4
HOH
HOH
86
A
HOH
87
4
HOH
HOH
87
A
HOH
88
4
HOH
HOH
88
A
HOH
90
4
HOH
HOH
90
A
HOH
96
4
HOH
HOH
96
A
HOH
100
4
HOH
HOH
100
A
HOH
101
4
HOH
HOH
101
A
HOH
103
4
HOH
HOH
103
A
HOH
107
4
HOH
HOH
107
A
HOH
22
4
HOH
HOH
22
B
HOH
28
4
HOH
HOH
28
B
HOH
31
4
HOH
HOH
31
B
HOH
35
4
HOH
HOH
35
B
HOH
41
4
HOH
HOH
41
B
HOH
45
4
HOH
HOH
45
B
HOH
47
4
HOH
HOH
47
B
HOH
48
4
HOH
HOH
48
B
HOH
49
4
HOH
HOH
49
B
HOH
51
4
HOH
HOH
51
B
HOH
56
4
HOH
HOH
56
B
HOH
58
4
HOH
HOH
58
B
HOH
59
4
HOH
HOH
59
B
HOH
60
4
HOH
HOH
60
B
HOH
63
4
HOH
HOH
63
B
HOH
69
4
HOH
HOH
69
B
HOH
71
4
HOH
HOH
71
B
HOH
74
4
HOH
HOH
74
B
HOH
75
4
HOH
HOH
75
B
HOH
78
4
HOH
HOH
78
B
HOH
83
4
HOH
HOH
83
B
HOH
84
4
HOH
HOH
84
B
HOH
89
4
HOH
HOH
89
B
HOH
91
4
HOH
HOH
91
B
HOH
92
4
HOH
HOH
92
B
HOH
93
4
HOH
HOH
93
B
HOH
94
4
HOH
HOH
94
B
HOH
95
4
HOH
HOH
95
B
HOH
97
4
HOH
HOH
97
B
HOH
98
4
HOH
HOH
98
B
HOH
99
4
HOH
HOH
99
B
HOH
102
4
HOH
HOH
102
B
HOH
104
4
HOH
HOH
104
B
HOH
105
4
HOH
HOH
105
B
HOH
106
4
HOH
HOH
106
B
HOH
108
4
HOH
HOH
108
B
HOH
109
4
HOH
HOH
109
B
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
A
3
n
3
DA
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
+U
8
n
8
BRU
8
A
G
9
n
9
DG
9
A
G
10
n
10
DG
10
A
C
11
n
1
DC
11
B
C
12
n
2
DC
12
B
A
13
n
3
DA
13
B
G
14
n
4
DG
14
B
T
15
n
5
DT
15
B
A
16
n
6
DA
16
B
C
17
n
7
DC
17
B
+U
18
n
8
BRU
18
B
G
19
n
9
DG
19
B
G
20
n
10
DG
20
B
author_defined_assembly
4
tetrameric
A
HOH
27
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
A
HOH
80
E
O
HOH
1_555
83.5
A
HOH
27
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
A
HOH
81
E
O
HOH
1_555
106.8
A
HOH
80
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
A
HOH
81
E
O
HOH
1_555
76.9
A
HOH
27
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
A
HOH
82
E
O
HOH
1_555
71.0
A
HOH
80
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
A
HOH
82
E
O
HOH
1_555
152.0
A
HOH
81
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
A
HOH
82
E
O
HOH
1_555
121.1
A
HOH
27
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
B
HOH
69
F
O
HOH
2_555
136.1
A
HOH
80
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
B
HOH
69
F
O
HOH
2_555
140.0
A
HOH
81
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
B
HOH
69
F
O
HOH
2_555
84.5
A
HOH
82
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
B
HOH
69
F
O
HOH
2_555
67.1
A
HOH
27
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
B
HOH
75
F
O
HOH
2_555
90.3
A
HOH
80
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
B
HOH
75
F
O
HOH
2_555
97.6
A
HOH
81
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
B
HOH
75
F
O
HOH
2_555
161.0
A
HOH
82
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
B
HOH
75
F
O
HOH
2_555
71.7
B
HOH
69
F
O
HOH
2_555
A
CA
67
D
CA
CA
1_555
B
HOH
75
F
O
HOH
2_555
88.8
A
HOH
27
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
B
HOH
93
F
O
HOH
2_555
150.1
A
HOH
80
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
B
HOH
93
F
O
HOH
2_555
89.4
A
HOH
81
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
B
HOH
93
F
O
HOH
2_555
99.7
A
HOH
82
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
B
HOH
93
F
O
HOH
2_555
106.7
B
HOH
69
F
O
HOH
2_555
A
CA
67
D
CA
CA
1_555
B
HOH
93
F
O
HOH
2_555
59.1
B
HOH
75
F
O
HOH
2_555
A
CA
67
D
CA
CA
1_555
B
HOH
93
F
O
HOH
2_555
61.8
A
BRU
8
A
BRU
8
DU
B
BRU
18
B
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
2_555
-x,y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1
A
NA
37
C
NA
1
A
HOH
68
E
HOH
1
A
HOH
86
E
HOH
1
B
DG
19
0.054
SIDE CHAIN
9.50
0.242
0.012
0.215
0.215
1.90
19.18
388
4011
3745
10.4
86.7
RANDOM
1
RESTRAINED
THROUGHOUT
0.000
MOLECULAR REPLACEMENT
1L6B USED FOR INITIAL SOLUTION VIA MOLECULAR REPLACEMENT
0.26
0.22
5.00
0.18
0.14
1.90
19.18
87
493
2
404
0
0.005
0.9
18.30
1.37
0.248
0.041
0.259
2.02
37
385
6
8.8
60.10
4.3
1.800
19.180
1P54
4177
0.000
0.041
1
4.05
82.0
0.189
1.80
1.86
34.9
data reduction
DENZO
data scaling
SCALEPACK
phasing
EPMR
refinement
CNS
1.0
Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
This entry contains the crystallographic asymmetric unit which consists of two chains A and B. The full four stranded Holliday junction structure can be generated by the following:
matrix =
(-1.00000 0.00001 0.00000)
(0.00001 1.00000 -0.00002)
(0.00000 -0.00002 -1.00000)
translation =
(0.00022 0.00018 -0.00034)
covale
1.613
both
A
DC
7
A
O3'
DC
7
1_555
A
BRU
8
A
P
BRU
8
1_555
covale
1.609
both
A
BRU
8
A
O3'
BRU
8
1_555
A
DG
9
A
P
DG
9
1_555
covale
1.609
both
B
DC
17
B
O3'
DC
7
1_555
B
BRU
18
B
P
BRU
8
1_555
covale
1.612
both
B
BRU
18
B
O3'
BRU
8
1_555
B
DG
19
B
P
DG
9
1_555
metalc
2.777
A
DA
6
A
OP2
DA
6
1_555
A
NA
37
C
NA
NA
1_555
metalc
2.303
A
HOH
27
E
O
HOH
1_555
A
CA
67
D
CA
CA
1_555
metalc
2.278
A
CA
67
D
CA
CA
1_555
A
HOH
80
E
O
HOH
1_555
metalc
2.242
A
CA
67
D
CA
CA
1_555
A
HOH
81
E
O
HOH
1_555
metalc
2.948
A
CA
67
D
CA
CA
1_555
A
HOH
82
E
O
HOH
1_555
metalc
3.119
A
CA
67
D
CA
CA
1_555
B
HOH
69
F
O
HOH
2_555
metalc
3.011
A
CA
67
D
CA
CA
1_555
B
HOH
75
F
O
HOH
2_555
metalc
3.261
A
CA
67
D
CA
CA
1_555
B
HOH
93
F
O
HOH
2_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
20
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
20
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
20
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
19
B
N1
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
19
B
O6
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
19
B
N2
DG
9
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
BRU
18
B
N3
BRU
8
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
BRU
18
B
O4
BRU
8
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
17
B
N3
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
17
B
O2
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
17
B
N4
DC
7
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
DA
16
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
DA
16
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
15
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
15
B
O4
DT
5
1_555
DNA
DNA Holliday Junction, Four-Way Junction, stacked-X junction, brominated uracil, DNA
1P54
PDB
1
1P54
1
10
1P54
1
10
1P54
A
1
1
10
11
20
1P54
11
20
1P54
B
1
1
10
BINDING SITE FOR RESIDUE NA A 37
A
NA
37
Software
2
BINDING SITE FOR RESIDUE CA A 67
A
CA
67
Software
5
A
DA
6
A
DA
6
2
1_555
A
DA
6
A
DA
6
2
2_555
A
HOH
27
E
HOH
5
1_555
A
HOH
80
E
HOH
5
1_555
A
HOH
81
E
HOH
5
1_555
A
HOH
82
E
HOH
5
1_555
B
HOH
75
F
HOH
5
2_555
5
C 1 2 1