0.015035
0.000000
0.005475
0.000000
0.041358
0.000000
0.000000
0.000000
0.028760
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
90.0
110.010
90.0
66.513
24.179
37.004
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
Na 1
22.990
SODIUM 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
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
NA
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
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/pdb1p4y/pdb
pdb_00001p4y
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
2003-01-24
RIGAKU RAXIS IV
NI FILTER
SINGLE WAVELENGTH
M
x-ray
1
1.542
1.0
1.542
ROTATING ANODE
RIGAKU RU300
3046.980
5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3'
2
syn
polymer
22.990
SODIUM ION
4
syn
non-polymer
18.015
water
108
nat
water
no
no
(DC)(DC)(DG)(DG)(DC)(DG)(DC)(DC)(DG)(DG)
CCGGCGCCGG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
1
1.94
35.95
7.00
0.5mM DNA, 25mM sodium cacodylate, 7.5mM CaCl2, 0.1mM SPERMINE TETRAHYDROCHLORIDE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00
298
sodium cacodylate
1
CaCl2
1
SPERMINE TETRAHYDROCHLORIDE
1
H2O
1
sodium cacodylate
2
CaCl2
2
SPERMINE TETRAHYDROCHLORIDE
2
H2O
2
-4.913
1
19
A
1
B
20
0.007
A_DC1:DG20_B
1
-7.931
0.293
-0.028
-0.111
1.298
1
19
A
2
B
19
5.301
A_DC2:DG19_B
2
-1.726
0.116
-0.281
0.100
2.223
1
19
A
3
B
18
-0.414
A_DG3:DC18_B
3
5.867
-0.399
0.153
-0.179
-2.849
1
19
A
4
B
17
-0.780
A_DG4:DC17_B
4
-25.438
-0.077
0.368
-0.140
-21.163
1
19
A
5
B
16
-6.733
A_DC5:DG16_B
5
6.011
-0.436
0.938
0.049
-0.618
1
19
A
6
B
15
-2.019
A_DG6:DC15_B
6
-11.453
-0.172
0.100
-0.138
3.794
38.136
A
A
1
2
9.619
B
B
20
19
3.431
6.244
0.397
2.433
AA_DC1DC2:DG19DG20_BB
1
4.588
-7.068
37.369
2.842
0.039
3.389
35.095
A
A
2
3
-0.491
B
B
19
18
3.402
-0.295
-0.264
2.728
AA_DC2DG3:DC18DG19_BB
2
-3.669
6.096
34.907
4.570
-0.135
3.759
40.534
A
A
3
4
0.499
B
B
18
17
3.664
0.345
-1.195
1.809
AA_DG3DG4:DC17DC18_BB
3
-3.205
4.631
40.411
2.567
1.319
3.742
38.783
A
A
4
5
-2.682
B
B
17
16
3.863
-1.775
0.458
0.520
AA_DG4DC5:DG16DC17_BB
4
-5.310
8.022
38.393
1.036
-1.447
3.045
30.035
A
A
5
6
9.296
B
B
16
15
3.035
4.789
0.017
0.408
AA_DC5DG6:DC15DG16_BB
5
3.273
-6.354
29.483
-0.136
0.598
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_site
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
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
2024-02-14
1
4
2024-04-03
_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.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_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.value
_struct_conn.pdbx_dist_value
_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_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
2003-04-24
REL
REL
NA
SODIUM 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
1DCW
UD0008
PDB
experimental model
N
21
2
NA
NA
21
A
N
36
2
NA
NA
36
A
N
49
2
NA
NA
49
A
N
55
2
NA
NA
55
B
W
22
3
HOH
HOH
22
A
W
24
3
HOH
HOH
24
A
W
25
3
HOH
HOH
25
A
W
26
3
HOH
HOH
26
A
W
27
3
HOH
HOH
27
A
W
32
3
HOH
HOH
32
A
W
33
3
HOH
HOH
33
A
W
34
3
HOH
HOH
34
A
W
37
3
HOH
HOH
37
A
W
38
3
HOH
HOH
38
A
W
39
3
HOH
HOH
39
A
W
41
3
HOH
HOH
41
A
W
43
3
HOH
HOH
43
A
W
46
3
HOH
HOH
46
A
W
47
3
HOH
HOH
47
A
W
48
3
HOH
HOH
48
A
W
51
3
HOH
HOH
51
A
W
54
3
HOH
HOH
54
A
W
56
3
HOH
HOH
56
A
W
58
3
HOH
HOH
58
A
W
59
3
HOH
HOH
59
A
W
62
3
HOH
HOH
62
A
W
67
3
HOH
HOH
67
A
W
70
3
HOH
HOH
70
A
W
71
3
HOH
HOH
71
A
W
72
3
HOH
HOH
72
A
W
78
3
HOH
HOH
78
A
W
80
3
HOH
HOH
80
A
W
81
3
HOH
HOH
81
A
W
82
3
HOH
HOH
82
A
W
84
3
HOH
HOH
84
A
W
85
3
HOH
HOH
85
A
W
86
3
HOH
HOH
86
A
W
87
3
HOH
HOH
87
A
W
88
3
HOH
HOH
88
A
W
90
3
HOH
HOH
90
A
W
95
3
HOH
HOH
95
A
W
97
3
HOH
HOH
97
A
W
98
3
HOH
HOH
98
A
W
101
3
HOH
HOH
101
A
W
103
3
HOH
HOH
103
A
W
105
3
HOH
HOH
105
A
W
107
3
HOH
HOH
107
A
W
109
3
HOH
HOH
109
A
W
110
3
HOH
HOH
110
A
W
115
3
HOH
HOH
115
A
W
116
3
HOH
HOH
116
A
W
119
3
HOH
HOH
119
A
W
120
3
HOH
HOH
120
A
W
121
3
HOH
HOH
121
A
W
122
3
HOH
HOH
122
A
W
123
3
HOH
HOH
123
A
W
125
3
HOH
HOH
125
A
W
127
3
HOH
HOH
127
A
W
130
3
HOH
HOH
130
A
W
131
3
HOH
HOH
131
A
W
132
3
HOH
HOH
132
A
W
23
3
HOH
HOH
23
B
W
28
3
HOH
HOH
28
B
W
29
3
HOH
HOH
29
B
W
30
3
HOH
HOH
30
B
W
31
3
HOH
HOH
31
B
W
35
3
HOH
HOH
35
B
W
40
3
HOH
HOH
40
B
W
42
3
HOH
HOH
42
B
W
44
3
HOH
HOH
44
B
W
45
3
HOH
HOH
45
B
W
50
3
HOH
HOH
50
B
W
52
3
HOH
HOH
52
B
W
53
3
HOH
HOH
53
B
W
57
3
HOH
HOH
57
B
W
60
3
HOH
HOH
60
B
W
61
3
HOH
HOH
61
B
W
63
3
HOH
HOH
63
B
W
64
3
HOH
HOH
64
B
W
65
3
HOH
HOH
65
B
W
66
3
HOH
HOH
66
B
W
68
3
HOH
HOH
68
B
W
69
3
HOH
HOH
69
B
W
73
3
HOH
HOH
73
B
W
74
3
HOH
HOH
74
B
W
75
3
HOH
HOH
75
B
W
76
3
HOH
HOH
76
B
W
77
3
HOH
HOH
77
B
W
79
3
HOH
HOH
79
B
W
83
3
HOH
HOH
83
B
W
89
3
HOH
HOH
89
B
W
91
3
HOH
HOH
91
B
W
92
3
HOH
HOH
92
B
W
93
3
HOH
HOH
93
B
W
94
3
HOH
HOH
94
B
W
96
3
HOH
HOH
96
B
W
99
3
HOH
HOH
99
B
W
100
3
HOH
HOH
100
B
W
102
3
HOH
HOH
102
B
W
104
3
HOH
HOH
104
B
W
106
3
HOH
HOH
106
B
W
108
3
HOH
HOH
108
B
W
111
3
HOH
HOH
111
B
W
112
3
HOH
HOH
112
B
W
113
3
HOH
HOH
113
B
W
114
3
HOH
HOH
114
B
W
117
3
HOH
HOH
117
B
W
118
3
HOH
HOH
118
B
W
124
3
HOH
HOH
124
B
W
126
3
HOH
HOH
126
B
W
128
3
HOH
HOH
128
B
W
129
3
HOH
HOH
129
B
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
G
3
n
3
DG
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
7
DC
7
A
C
8
n
8
DC
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
G
13
n
3
DG
13
B
G
14
n
4
DG
14
B
C
15
n
5
DC
15
B
G
16
n
6
DG
16
B
C
17
n
7
DC
17
B
C
18
n
8
DC
18
B
G
19
n
9
DG
19
B
G
20
n
10
DG
20
B
author_defined_assembly
4
tetrameric
A
DC
1
A
O5'
DC
1
1_555
A
NA
36
D
NA
NA
1_555
A
HOH
82
G
O
HOH
1_555
121.7
A
DG
10
A
N3
DG
10
1_555
A
NA
49
E
NA
NA
1_555
A
HOH
56
G
O
HOH
1_555
101.5
A
HOH
24
G
O
HOH
1_555
A
NA
21
C
NA
NA
1_555
A
HOH
25
G
O
HOH
1_555
77.2
A
HOH
24
G
O
HOH
1_555
A
NA
21
C
NA
NA
1_555
A
HOH
56
G
O
HOH
1_555
83.5
A
HOH
25
G
O
HOH
1_555
A
NA
21
C
NA
NA
1_555
A
HOH
56
G
O
HOH
1_555
147.8
A
HOH
24
G
O
HOH
1_555
A
NA
21
C
NA
NA
1_555
A
HOH
109
G
O
HOH
1_555
134.8
A
HOH
25
G
O
HOH
1_555
A
NA
21
C
NA
NA
1_555
A
HOH
109
G
O
HOH
1_555
143.1
A
HOH
56
G
O
HOH
1_555
A
NA
21
C
NA
NA
1_555
A
HOH
109
G
O
HOH
1_555
66.6
B
DG
19
B
O4'
DG
9
1_555
B
NA
55
F
NA
NA
1_555
B
HOH
75
H
O
HOH
1_555
57.0
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_556
-x,y,-z+1
crystal symmetry operation
-12.6621821170
0.0000000000
34.7701763015
8.7
0.26
0.012
0.229
0.229
1.70
22.50
490
4940
4436
10
77.1
RANDOM
1
THROUGHOUT
2.000
MOLECULAR REPLACEMENT
UD0008
0.26
0.21
5.00
0.10
0.03
1.70
22.50
108
516
4
404
0
0.007
1.2
18.5
1.57
0.285
0.046
0.209
1.81
39
374
6
9.4
40.8
1.6
1.650
22.550
1P4Y
4940
0.000
0.048
1
74.0
0.279
1.65
1.71
2.140
21.7
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
2
N
N
2
N
N
2
N
N
3
N
N
3
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 -0.00046 -0.00015 )
( -0.00046 1.00000 0.00072 )
( 0.00015 0.00072 -1.00000 )
translation=
(-12.65734 -0.02663 34.77174)
metalc
2.475
A
DC
1
A
O5'
DC
1
1_555
A
NA
36
D
NA
NA
1_555
metalc
2.945
A
DG
10
A
N3
DG
10
1_555
A
NA
49
E
NA
NA
1_555
metalc
2.810
A
NA
21
C
NA
NA
1_555
A
HOH
24
G
O
HOH
1_555
metalc
2.470
A
NA
21
C
NA
NA
1_555
A
HOH
25
G
O
HOH
1_555
metalc
2.716
A
NA
21
C
NA
NA
1_555
A
HOH
56
G
O
HOH
1_555
metalc
2.476
A
NA
21
C
NA
NA
1_555
A
HOH
109
G
O
HOH
1_555
metalc
2.638
A
NA
36
D
NA
NA
1_555
A
HOH
82
G
O
HOH
1_555
metalc
2.560
A
NA
49
E
NA
NA
1_555
A
HOH
56
G
O
HOH
1_555
metalc
2.634
B
DG
19
B
O4'
DG
9
1_555
B
NA
55
F
NA
NA
1_555
metalc
2.806
B
NA
55
F
NA
NA
1_555
B
HOH
75
H
O
HOH
1_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
DG
3
A
N1
DG
3
1_555
B
DC
18
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
DC
18
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
DC
18
B
N4
DC
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
DC
5
A
N3
DC
5
1_555
B
DG
16
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
16
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
16
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
DC
15
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
15
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
15
B
N4
DC
5
1_555
DNA
Holliday Junction, DNA Four-Way Junction, DNA
1P4Y
PDB
1
1P4Y
1
10
1P4Y
1
10
1P4Y
A
1
1
10
11
20
1P4Y
11
20
1P4Y
B
1
1
10
BINDING SITE FOR RESIDUE NA A 21
A
NA
21
Software
6
BINDING SITE FOR RESIDUE NA A 36
A
NA
36
Software
4
BINDING SITE FOR RESIDUE NA A 49
A
NA
49
Software
3
BINDING SITE FOR RESIDUE NA B 55
B
NA
55
Software
2
A
HOH
24
G
HOH
6
1_555
A
HOH
25
G
HOH
6
1_555
A
NA
49
E
NA
6
1_555
A
HOH
56
G
HOH
6
1_555
A
HOH
109
G
HOH
6
1_555
B
HOH
76
H
HOH
6
2_556
A
DC
1
A
DC
1
4
1_555
A
DC
2
A
DC
2
4
1_555
A
HOH
82
G
HOH
4
1_555
B
DG
14
B
DG
4
4
2_557
A
DG
10
A
DG
10
3
1_555
A
NA
21
C
NA
3
1_555
A
HOH
56
G
HOH
3
1_555
B
DG
19
B
DG
9
2
1_555
B
HOH
75
H
HOH
2
1_555
5
C 1 2 1