0.0153
0.0000
0.0056
0.0000
0.0420
0.0000
0.0000
0.0000
0.0284
0.0000
0.0000
0.0000
Naseer, A.
Cardin, C.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.0000
110.0100
90.0000
65.2000
23.8000
37.4100
Ba 2
137.327
BARIUM 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
N
1
N
BA
N
2
N
O
N
3
N
P
N
4
N
O
N
5
N
O
N
6
N
O
N
7
N
C
N
8
R
C
N
9
N
O
N
10
S
C
N
11
N
O
N
12
N
C
N
13
R
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
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
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
N
C
N
49
R
C
N
50
N
N
N
51
N
C
N
52
N
O
N
53
N
N
N
54
N
C
N
55
N
N
N
56
N
C
N
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
P
N
74
N
O
N
75
N
O
N
76
N
O
N
77
N
C
N
78
R
C
N
79
N
O
N
80
S
C
N
81
N
O
N
82
N
C
N
83
R
C
Y
84
N
N
Y
85
N
C
Y
86
N
N
Y
87
N
C
N
88
N
C
N
89
N
O
N
90
N
N
N
91
N
C
N
92
N
N
N
93
N
N
Y
94
N
C
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
H
N
109
N
O
N
110
N
P
N
111
N
O
N
112
N
O
N
113
N
O
N
114
N
C
N
115
R
C
N
116
N
O
N
117
S
C
N
118
N
O
N
119
N
C
N
120
R
C
N
121
N
N
N
122
N
C
N
123
N
O
N
124
N
N
N
125
N
C
N
126
N
O
N
127
N
C
N
128
N
C
N
129
N
C
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
H
N
145
N
O
N
146
N
H
N
147
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
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
108
17610
17614
10.1073/pnas.1108685108
21969542
Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand.
2011
10.2210/pdb3gom/pdb
pdb_00003gom
100
1
multigraded optics
CCD
OXFORD SAPPHIRE CCD
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
SEALED TUBE
OXFORD DIFFRACTION ENHANCE ULTRA
Holliday junction structure
3045.992
5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
2
syn
polymer
137.327
BARIUM ION
5
syn
non-polymer
18.015
water
36
nat
water
no
no
(DT)(DC)(DG)(DG)(DC)(DG)(DC)(DC)(DG)(DA)
TCGGCGCCGA
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
1
2.24
45.05
VAPOR DIFFUSION, SITTING DROP
7
BaCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
290
BaCl2
1
MPD
1
Na Cacodylate
1
BaCl2
2
MPD
2
Na Cacodylate
2
-2.410
A
1
B
20
5.979
A_DT1:DA20_B
1
-15.787
0.413
0.290
0.138
5.381
1
19
A
2
B
19
-0.312
A_DC2:DG19_B
2
-7.201
0.043
0.291
-0.115
-3.311
1
19
A
3
B
18
-2.592
A_DG3:DC18_B
3
-12.242
0.136
0.252
-0.238
12.289
1
19
A
4
B
17
-2.291
A_DG4:DC17_B
4
-8.972
0.142
0.769
-0.389
-2.435
1
19
A
5
B
16
-5.603
A_DC5:DG16_B
5
-15.298
-0.942
0.062
-0.023
-0.288
1
19
A
6
B
15
-5.071
A_DG6:DC15_B
6
-14.743
-0.393
0.182
-0.148
3.568
37.728
A
A
1
2
8.156
B
B
20
19
3.335
5.242
0.102
2.089
AA_DT1DC2:DG19DA20_BB
1
5.301
-8.248
37.010
2.508
0.572
3.493
44.502
A
A
2
3
-3.057
B
B
19
18
3.585
-2.313
-0.714
2.531
AA_DC2DG3:DC18DG19_BB
2
-2.823
3.732
44.359
3.573
0.661
2.879
29.902
A
A
3
4
5.569
B
B
18
17
2.927
2.859
0.425
0.651
AA_DG3DG4:DC17DC18_BB
3
-4.537
8.838
29.428
0.731
-1.666
3.428
37.224
A
A
4
5
-6.901
B
B
17
16
3.592
-4.385
-0.568
0.402
AA_DG4DC5:DG16DC17_BB
4
4.662
-7.337
36.689
1.259
1.560
3.429
37.695
A
A
5
6
8.064
B
B
16
15
3.354
5.194
0.481
0.746
AA_DC5DG6:DC15DG16_BB
5
0.454
-0.704
37.346
0.454
-0.683
software
diffrn_source
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
Database references
Refinement description
Data collection
Data collection
Database references
Derived calculations
Refinement description
1
0
2009-04-07
1
1
2011-07-13
1
2
2011-11-02
1
3
2017-11-01
1
4
2018-04-04
1
5
2023-09-06
_software.name
_diffrn_source.type
_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.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_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.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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Strontium bound to the Holliday junction sequence d(TCGGTACCGA)4
Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions
RCSB
Y
RCSB
2009-03-19
REL
REL
BA
BARIUM ION
HOH
water
1NVY
PDB entry 1NVY
PDB
experimental model
BA
21
2
BA
BA
21
A
BA
23
2
BA
BA
23
A
BA
22
2
BA
BA
22
B
BA
25
2
BA
BA
25
B
BA
49
2
BA
BA
49
B
HOH
28
3
HOH
HOH
28
A
HOH
29
3
HOH
HOH
29
A
HOH
30
3
HOH
HOH
30
A
HOH
31
3
HOH
HOH
31
A
HOH
32
3
HOH
HOH
32
A
HOH
33
3
HOH
HOH
33
A
HOH
40
3
HOH
HOH
40
A
HOH
41
3
HOH
HOH
41
A
HOH
43
3
HOH
HOH
43
A
HOH
44
3
HOH
HOH
44
A
HOH
52
3
HOH
HOH
52
A
HOH
53
3
HOH
HOH
53
A
HOH
55
3
HOH
HOH
55
A
HOH
56
3
HOH
HOH
56
A
HOH
58
3
HOH
HOH
58
A
HOH
60
3
HOH
HOH
60
A
HOH
24
3
HOH
HOH
24
B
HOH
34
3
HOH
HOH
34
B
HOH
35
3
HOH
HOH
35
B
HOH
36
3
HOH
HOH
36
B
HOH
37
3
HOH
HOH
37
B
HOH
38
3
HOH
HOH
38
B
HOH
39
3
HOH
HOH
39
B
HOH
45
3
HOH
HOH
45
B
HOH
46
3
HOH
HOH
46
B
HOH
47
3
HOH
HOH
47
B
HOH
48
3
HOH
HOH
48
B
HOH
50
3
HOH
HOH
50
B
HOH
51
3
HOH
HOH
51
B
HOH
57
3
HOH
HOH
57
B
HOH
59
3
HOH
HOH
59
B
HOH
61
3
HOH
HOH
61
B
HOH
62
3
HOH
HOH
62
B
HOH
63
3
HOH
HOH
63
B
HOH
64
3
HOH
HOH
64
B
HOH
65
3
HOH
HOH
65
B
T
1
n
1
DT
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
A
10
n
10
DA
10
A
T
11
n
1
DT
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
A
20
n
10
DA
20
B
author_and_software_defined_assembly
PISA
4
tetrameric
5740
-98
6090
A
DG
4
A
O6
DG
4
1_555
A
BA
21
C
BA
BA
1_555
B
HOH
48
I
O
HOH
1_555
101.5
B
HOH
24
I
O
HOH
1_555
A
BA
23
D
BA
BA
1_555
B
HOH
65
I
O
HOH
1_555
47.7
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
B
B
OP2
O
DG
HOH
16
51
1.94
1
A
B
O
O
HOH
HOH
28
48
2.06
1
-5.18
0.80
102.40
97.22
A
A
A
C3'
C2'
C1'
DG
DG
DG
4
4
4
N
1
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
2.50
0.30
108.30
110.80
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
1
-5.95
0.70
108.00
102.05
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
1
1.82
0.30
108.30
110.12
B
B
B
O4'
C1'
N1
DC
DC
DC
18
18
18
N
31.247
-2.250
0.000
-0.970
3.160
0.000
-1.570
0.918
0.860
0.349
0.260
0.264
0.264
2.300
19.956
101
2351
2351
4.300
93.220
13.500
0.291
0.604
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.371
0.800
0.800
1.200
PDB entry 1NVY
MASK
2.300
19.956
36
445
5
404
0
0.008
452
0.021
1.822
694
3.000
0.066
78
0.200
0.006
208
0.020
0.193
121
0.200
0.316
259
0.200
0.325
28
0.200
31.247
2.300
19.956
3GOM
26
-28
10
0
16
0
2518
2351
1.00
1.00
0.052
1
2.7
93.220
0.21
2.300
2.360
3.21
461
1
2.6
93.220
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran
http://www.ccp4.ac.uk/main.html
REFMAC
program
data extraction
H.Yang
sw-help@rcsb.rutgers.edu
March 3, 2004
C/C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
program
1.401
data collection
CrysalisPro
Red
data reduction
CrysalisPro
Red
data scaling
CrysalisPro
Red
phasing
MOLREP
Barium bound to the Holliday junction sequence d(TCGGCGCCGA)4
1
N
N
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
3
N
N
metalc
2.562
A
DG
4
A
O6
DG
4
1_555
A
BA
21
C
BA
BA
1_555
metalc
2.550
A
BA
21
C
BA
BA
1_555
B
HOH
48
I
O
HOH
1_555
metalc
3.124
A
BA
23
D
BA
BA
1_555
B
HOH
24
I
O
HOH
1_555
metalc
2.508
A
BA
23
D
BA
BA
1_555
B
HOH
65
I
O
HOH
1_555
metalc
2.642
B
BA
25
F
BA
BA
1_555
B
HOH
57
I
O
HOH
1_555
hydrog
DT-DA PAIR
A
DT
1
A
N3
DT
1
1_555
B
DA
20
B
N1
DA
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
DG-DC PAIR
A
DG
3
A
O6
DG
3
1_555
B
DC
17
B
N4
DC
7
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 structure, DNA
3GOM
PDB
1
1
3GOM
TCGGCGCCGA
1
10
3GOM
1
10
3GOM
A
1
1
10
11
20
3GOM
11
20
3GOM
B
1
1
10
BINDING SITE FOR RESIDUE BA A 21
A
BA
21
Software
6
BINDING SITE FOR RESIDUE BA A 23
A
BA
23
Software
1
BINDING SITE FOR RESIDUE BA B 25
B
BA
25
Software
2
BINDING SITE FOR RESIDUE BA B 49
B
BA
49
Software
1
A
DG
3
A
DG
3
6
1_555
A
DG
4
A
DG
4
6
1_555
A
HOH
28
H
HOH
6
1_555
A
HOH
29
H
HOH
6
1_555
A
HOH
53
H
HOH
6
1_555
B
HOH
48
I
HOH
6
1_555
B
HOH
65
I
HOH
1
1_555
B
HOH
57
I
HOH
2
1_555
B
HOH
62
I
HOH
2
1_555
B
HOH
50
I
HOH
1
1_555
5
C 1 2 1