0.045192
0.000000
0.000000
0.000000
0.016888
0.000000
0.000000
0.000000
0.021842
0.00000
0.00000
0.00000
Thorpe, J.H.
Teixeira, S.C.M.
Gale, B.C.
Cardin, C.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
22.128
59.215
45.784
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
Co H18 N6 3
161.116
COBALT HEXAMMINE(III)
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
Y
13
N
N
Y
14
N
C
Y
15
N
N
Y
16
N
C
Y
17
N
C
N
18
N
N
Y
19
N
N
Y
20
N
C
Y
21
N
N
Y
22
N
C
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
H
N
36
N
H
N
37
N
O
N
38
N
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
N
C
N
48
R
C
N
49
N
N
N
50
N
C
N
51
N
O
N
52
N
N
N
53
N
C
N
54
N
N
N
55
N
C
N
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
Y
83
N
N
Y
84
N
C
Y
85
N
N
Y
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
N
N
92
N
N
Y
93
N
C
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
H
N
106
N
H
N
107
N
H
N
108
N
O
N
109
N
P
N
110
N
O
N
111
N
O
N
112
N
O
N
113
N
C
N
114
R
C
N
115
N
O
N
116
S
C
N
117
N
O
N
118
N
C
N
119
R
C
N
120
N
N
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
C
N
128
N
C
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
H
N
143
N
H
N
144
N
O
N
145
N
H
N
146
N
H
N
147
N
CO
N
148
N
N
N
149
N
N
N
150
N
N
N
151
N
N
N
152
N
N
N
153
N
N
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
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
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
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
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
31
844
849
10.1093/nar/gkg168
12560479
Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic
resolution
2003
10.2210/pdb1mf5/pdb
pdb_00001mf5
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
100
1
CCD
2002-05-19
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
0.811
1.0
X11
EMBL/DESY, HAMBURG
0.811
0.811
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE X11
2113.410
5'-D(*GP*CP*AP*TP*GP*CP*T)-3'
2
syn
polymer
161.116
COBALT HEXAMMINE(III)
1
syn
non-polymer
18.015
water
38
nat
water
no
no
(DG)(DC)(DA)(DT)(DG)(DC)(DT)
GCATGCT
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
1
1.77
30.67
VAPOR DIFFUSION, SITTING DROP
6.6
Cobalt Hexammine, Cacodylate, MPD, NaCl, KCl, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
Cobalt Hexammine
1
Cacodylate
1
MPD
1
NaCl
1
KCl
1
-2.155
A
1
A
6
176.744
A_DG1:DC6_A
1
40.830
-3.252
-0.379
8.800
11.055
A
2
A
5
176.174
A_DC2:DG5_A
2
36.495
3.258
-0.286
8.403
-11.727
B
8
B
13
173.995
B_DG8:DC13_B
3
32.550
-2.907
-0.458
8.518
9.392
B
9
B
12
176.510
B_DC9:DG12_B
4
34.642
3.791
-0.003
8.222
2.837
29.282
A
A
1
2
14.254
A
A
6
5
2.822
7.136
0.268
0.421
AA_DG1DC2:DG5DC6_AA
1
-0.363
0.726
28.416
-0.522
-0.598
3.045
32.521
B
B
8
9
9.059
B
B
13
12
3.028
5.050
0.149
0.453
BB_DG8DC9:DG12DC13_BB
2
-2.237
4.014
32.061
-0.017
-0.631
chem_comp_atom
chem_comp_bond
database_2
diffrn_source
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
2003-02-11
1
1
2008-04-28
1
2
2011-07-13
1
3
2024-02-14
1
4
2024-04-03
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_diffrn_source.pdbx_synchrotron_site
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
GCATGCT With Different Ion Content
RCSB
Y
RCSB
2002-08-09
REL
REL
NCO
COBALT HEXAMMINE(III)
HOH
water
184D
UDG028
PDB
experimental model
NCO
15
2
NCO
NCO
15
B
HOH
101
3
HOH
HOH
101
A
HOH
102
3
HOH
HOH
102
A
HOH
106
3
HOH
HOH
106
A
HOH
107
3
HOH
HOH
107
A
HOH
110
3
HOH
HOH
110
A
HOH
116
3
HOH
HOH
116
A
HOH
119
3
HOH
HOH
119
A
HOH
126
3
HOH
HOH
126
A
HOH
127
3
HOH
HOH
127
A
HOH
129
3
HOH
HOH
129
A
HOH
130
3
HOH
HOH
130
A
HOH
131
3
HOH
HOH
131
A
HOH
132
3
HOH
HOH
132
A
HOH
134
3
HOH
HOH
134
A
HOH
135
3
HOH
HOH
135
A
HOH
137
3
HOH
HOH
137
A
HOH
100
3
HOH
HOH
100
B
HOH
103
3
HOH
HOH
103
B
HOH
104
3
HOH
HOH
104
B
HOH
105
3
HOH
HOH
105
B
HOH
108
3
HOH
HOH
108
B
HOH
109
3
HOH
HOH
109
B
HOH
111
3
HOH
HOH
111
B
HOH
112
3
HOH
HOH
112
B
HOH
113
3
HOH
HOH
113
B
HOH
114
3
HOH
HOH
114
B
HOH
115
3
HOH
HOH
115
B
HOH
117
3
HOH
HOH
117
B
HOH
118
3
HOH
HOH
118
B
HOH
120
3
HOH
HOH
120
B
HOH
121
3
HOH
HOH
121
B
HOH
122
3
HOH
HOH
122
B
HOH
123
3
HOH
HOH
123
B
HOH
124
3
HOH
HOH
124
B
HOH
125
3
HOH
HOH
125
B
HOH
128
3
HOH
HOH
128
B
HOH
133
3
HOH
HOH
133
B
HOH
136
3
HOH
HOH
136
B
G
1
n
1
DG
1
A
C
2
n
2
DC
2
A
A
3
n
3
DA
3
A
T
4
n
4
DT
4
A
G
5
n
5
DG
5
A
C
6
n
6
DC
6
A
T
7
n
7
DT
7
A
G
8
n
1
DG
8
B
C
9
n
2
DC
9
B
A
10
n
3
DA
10
B
T
11
n
4
DT
11
B
G
12
n
5
DG
12
B
C
13
n
6
DC
13
B
T
14
n
7
DT
14
B
0.2164
0.2163
0.2126
0.2126
0.2295
0.224
563
625
4.49
4.99
11296
author_defined_assembly
4
tetrameric
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
3_654
-x+1,y,-z-1/2
crystal symmetry operation
22.1280000000
0.0000000000
-22.8920000000
1
A
HOH
126
D
HOH
1
B
HOH
128
E
HOH
1
-4.96
0.70
108.00
103.04
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
4.04
0.60
118.90
122.94
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
1
3.68
0.60
106.00
109.68
A
A
A
O4'
C4'
C3'
DA
DA
DA
3
3
3
N
1
-3.35
0.50
129.30
125.95
A
A
A
N1
C2
N3
DA
DA
DA
3
3
3
N
1
3.45
0.50
110.60
114.05
A
A
A
C2
N3
C4
DA
DA
DA
3
3
3
N
1
-5.20
0.80
102.40
97.20
A
A
A
C3'
C2'
C1'
DT
DT
DT
4
4
4
N
1
3.66
0.60
119.00
122.66
A
A
A
C4
C5
C7
DT
DT
DT
4
4
4
N
1
-5.21
0.80
109.40
104.19
A
A
A
O5'
C5'
C4'
DG
DG
DG
5
5
5
N
1
-5.05
0.70
108.00
102.95
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
1
4.39
0.30
108.30
112.69
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
1
-5.15
0.80
123.10
117.95
A
A
A
N1
C2
O2
DT
DT
DT
7
7
7
N
1
-5.70
0.70
108.00
102.30
B
B
B
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
-3.37
0.50
117.40
114.03
B
B
B
C4
C5
C6
DC
DC
DC
9
9
9
N
1
4.10
0.50
121.00
125.10
B
B
B
C5
C6
N1
DC
DC
DC
9
9
9
N
1
-3.46
0.50
129.30
125.84
B
B
B
N1
C2
N3
DA
DA
DA
10
10
10
N
1
3.17
0.50
110.60
113.77
B
B
B
C2
N3
C4
DA
DA
DA
10
10
10
N
1
4.86
0.30
108.30
113.16
B
B
B
O4'
C1'
N1
DT
DT
DT
11
11
11
N
1
-4.13
0.60
127.20
123.07
B
B
B
C2
N3
C4
DT
DT
DT
11
11
11
N
1
-8.98
0.80
109.40
100.42
B
B
B
O5'
C5'
C4'
DC
DC
DC
13
13
13
N
1
2.08
0.30
108.30
110.38
B
B
B
O4'
C1'
N1
DC
DC
DC
13
13
13
N
1
-5.45
0.60
127.20
121.75
B
B
B
C2
N3
C4
DT
DT
DT
14
14
14
N
1
4.70
0.60
115.20
119.90
B
B
B
N3
C4
C5
DT
DT
DT
14
14
14
N
1
-5.29
0.60
122.30
117.01
B
B
B
N3
C2
O2
DT
DT
DT
14
14
14
N
1
-4.24
0.60
119.90
115.66
B
B
B
N3
C4
O4
DT
DT
DT
14
14
14
N
1
A
A
O3'
P
DA
DT
3
4
0.098
0.012
1.607
1.705
Y
1
A
A
O4'
C4'
DT
DT
7
7
-0.060
0.010
1.446
1.386
N
ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
0.224
0.2126
0.216
0.216
1.10
20
2924
625
12514
12514
2847
4.99
97.5
RANDOM
1
FREE R
0.0
MOLECULAR REPLACEMENT
UDG028
ENGH AND HUBER
0
175.00
322.00
1.10
20
38
325
7
280
0
0.018
0.035
0.000
0.0018
0.000
0.000
0.013
0.000
0.034
0.000
18.213
1.10
29.62
1MF5
12514
0.11
1
10.96
7.7
99.3
0.37
1.10
1.20
5.24
2803
6.59
99.4
data scaling
XDS
data scaling
XSCALE
model building
SHELX
refinement
SHELXL-97
data reduction
XDS
phasing
SHELX
GCATGCT Quadruplex
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
hydrog
DG-DC PAIR
A
DG
1
A
N2
DG
1
1_555
A
DC
6
A
O2
DC
6
1_555
hydrog
DC-DG PAIR
A
DC
2
A
O2
DC
2
1_555
A
DG
5
A
N2
DG
5
1_555
hydrog
DG-DC PAIR
B
DG
8
B
N2
DG
1
1_555
B
DC
13
B
O2
DC
6
1_555
hydrog
DC-DG PAIR
B
DC
9
B
O2
DC
2
1_555
B
DG
12
B
N2
DG
5
1_555
DNA
QUADRUPLEX, ATOMIC RESOLUTION, DNA
1MF5
PDB
1
1MF5
1
7
1MF5
1
7
1MF5
A
1
1
7
8
14
1MF5
8
14
1MF5
B
1
1
7
BINDING SITE FOR RESIDUE NCO B 15
B
NCO
15
Software
11
A
DA
3
A
DA
3
11
2_655
B
DG
8
B
DG
1
11
1_555
B
DC
9
B
DC
2
11
1_555
B
DC
9
B
DC
2
11
4_555
B
DA
10
B
DA
3
11
4_555
B
DG
12
B
DG
5
11
1_555
B
DC
13
B
DC
6
11
1_555
B
HOH
103
E
HOH
11
4_555
B
HOH
104
E
HOH
11
4_555
B
HOH
111
E
HOH
11
1_555
B
HOH
112
E
HOH
11
4_555
20
C 2 2 21