0.023800
0.000000
0.000000
0.000000
0.023800
0.000000
0.000000
0.000000
0.012246
0.00000
0.00000
0.00000
Kiliszek, A.
Kierzek, R.
Krzyzosiak, W.J.
Rypniewski, R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
24
90.00
90.00
90.00
42.016
42.016
81.656
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
C11 H14 N5 O8 P
375.231
n
[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE
RNA linking
O4 S -2
96.063
SULFATE 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
R
C
N
12
N
O
N
13
R
C
N
14
N
N
N
15
N
C
N
16
N
O
N
17
N
N
N
18
N
C
N
19
N
N
N
20
N
C
N
21
N
C
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
H
N
36
N
O
N
37
N
P
N
38
N
O
N
39
N
O
N
40
N
O
N
41
N
C
N
42
R
C
N
43
N
O
N
44
S
C
N
45
N
O
N
46
R
C
N
47
N
O
N
48
R
C
Y
49
N
N
Y
50
N
C
Y
51
N
N
Y
52
N
C
N
53
N
C
N
54
N
O
N
55
N
N
N
56
N
C
N
57
N
N
N
58
N
N
Y
59
N
C
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
H
N
73
N
H
N
74
N
O
N
75
N
H
N
76
N
H
N
77
N
P
N
78
N
O
N
79
N
O
N
80
N
C
N
81
S
C
N
82
N
C
Y
83
N
N
Y
84
N
C
Y
85
N
C
Y
86
N
N
Y
87
N
C
N
88
N
C
N
89
R
C
N
90
N
O
N
91
R
C
N
92
R
C
N
93
N
C
N
94
N
N
N
95
N
O
N
96
N
O
N
97
N
N
N
98
N
N
N
99
N
O
N
100
N
O
N
101
N
O
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
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
S
N
117
N
O
N
118
N
O
N
119
N
O
N
120
N
O
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
sing
N
27
N
doub
N
28
N
sing
N
29
N
doub
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
doub
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
doub
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
N
59
N
sing
N
60
N
sing
Y
61
N
sing
Y
62
N
sing
Y
63
N
doub
N
64
N
sing
Y
65
N
sing
N
66
N
sing
Y
67
N
doub
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
doub
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
Y
95
N
sing
Y
96
N
sing
N
97
N
sing
Y
98
N
doub
N
99
N
sing
Y
100
N
doub
N
101
N
sing
Y
102
N
sing
N
103
N
sing
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
doub
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
doub
N
122
N
doub
N
123
N
sing
N
124
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
40
8155
8162
10.1093/nar/gks557
22718980
Crystallographic characterization of CCG repeats.
2012
10.2210/pdb4e58/pdb
pdb_00004e58
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2011-03-19
MARMOSAIC 225 mm CCD
Si
SINGLE WAVELENGTH
M
x-ray
1
0.9148
1.0
14.1
BESSY
0.9148
SYNCHROTRON
BESSY BEAMLINE 14.1
2528.579
RNA duplex containing CCG repeats
3
syn
polymer
96.063
SULFATE ION
2
syn
non-polymer
18.015
water
14
nat
water
no
yes
GCC(LCG)CCGC
GCCGCCGC
C,E,D
polyribonucleotide
n
n
n
n
n
n
n
n
1
2.38
48.22
VAPOR DIFFUSION, SITTING DROP
5.6
MES, MgCl2 and Li2SO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 292.0K
292.0
-16.776
1
19
C
3
D
7
-5.868
C_C3:G7_D
1
-1.190
0.060
0.234
-0.100
0.000
1
19
C
4
D
6
-1.510
C_LCG4:C6_D
2
-14.025
-0.304
0.389
-0.286
-13.016
C
5
D
5
-22.282
C_C5:C5_D
3
-20.467
2.379
0.252
-0.959
-11.228
1
19
C
6
D
4
-0.632
C_C6:LCG4_D
4
-13.816
-0.228
0.871
-0.227
23.169
1
19
C
7
D
3
-0.042
C_G7:C3_D
5
2.798
-0.315
0.313
-0.089
13.131
1
19
E
1
D
2
-0.643
E_G1:C2_D
6
-9.890
-0.174
0.582
-0.239
0.797
1
19
E
2
D
1
-1.178
E_C2:G1_D
7
-13.851
0.422
0.208
-0.207
1.708
32.281
C
C
3
4
28.098
D
D
7
6
2.683
15.046
0.854
-1.455
CC_C3LCG4:C6G7_DD
1
-0.600
1.120
28.637
-4.524
-1.612
3.402
44.880
C
C
4
5
8.310
D
D
6
5
3.647
6.325
-0.863
-1.628
CC_LCG4C5:C5C6_DD
2
-0.337
0.443
44.454
-2.753
1.098
2.556
25.370
C
C
5
6
12.237
D
D
5
4
2.945
5.329
1.070
-1.963
CC_C5C6:LCG4C5_DD
3
2.217
-5.091
24.715
-5.781
-1.891
1.022
17.493
C
C
6
7
36.074
D
D
4
3
2.329
10.259
-0.761
-1.356
CC_C6G7:C3LCG4_DD
4
1.547
-5.440
14.104
-8.015
3.040
3.575
48.133
C
E
7
1
7.747
D
D
3
2
3.456
6.276
-1.423
-0.276
CE_G7G1:C2C3_DD
5
-7.934
9.793
47.120
-0.874
1.068
3.357
43.165
E
E
1
2
1.486
D
D
2
1
3.403
1.092
0.141
-1.943
EE_G1C2:G1C2_DD
6
2.926
-3.980
43.057
-2.752
0.105
pdbx_entity_src_syn
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_site
repository
Initial release
Refinement description
Source and taxonomy
Data collection
Database references
Derived calculations
Refinement description
1
0
2012-12-12
1
1
2017-11-15
1
2
2023-09-13
_pdbx_entity_src_syn.ncbi_taxonomy_id
_pdbx_entity_src_syn.organism_scientific
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2012-03-14
REL
REL
SO4
SULFATE ION
HOH
water
Similar sequences occur in mRNA in humans
9606
Homo sapiens
sample
3GLP
PDB ENTRY 3GLP
PDB
experimental model
SO4
1
2
SO4
SO4
101
C
SO4
2
2
SO4
SO4
101
D
HOH
3
3
HOH
HOH
201
C
HOH
6
3
HOH
HOH
202
C
HOH
11
3
HOH
HOH
203
C
HOH
13
3
HOH
HOH
204
C
HOH
2
3
HOH
HOH
101
E
HOH
7
3
HOH
HOH
102
E
HOH
10
3
HOH
HOH
103
E
HOH
16
3
HOH
HOH
104
E
HOH
17
3
HOH
HOH
105
E
HOH
18
3
HOH
HOH
106
E
HOH
19
3
HOH
HOH
107
E
HOH
8
3
HOH
HOH
201
D
HOH
9
3
HOH
HOH
202
D
HOH
15
3
HOH
HOH
203
D
G
1
n
1
G
1
C
C
2
n
2
C
2
C
C
3
n
3
C
3
C
LCG
4
n
4
LCG
4
C
C
5
n
5
C
5
C
C
6
n
6
C
6
C
G
7
n
7
G
7
C
C
8
n
8
C
8
C
G
1
n
1
G
1
E
C
2
n
2
C
2
E
C
3
n
3
C
3
E
LCG
4
n
4
LCG
4
E
C
5
n
5
C
5
E
C
6
n
6
C
6
E
G
7
n
7
G
7
E
C
8
n
8
C
8
E
G
1
n
1
G
1
D
C
2
n
2
C
2
D
C
3
n
3
C
3
D
LCG
4
n
4
LCG
4
D
C
5
n
5
C
5
D
C
6
n
6
C
6
D
G
7
n
7
G
7
D
C
8
n
8
C
8
D
author_and_software_defined_assembly
PISA
2
dimeric
author_and_software_defined_assembly
PISA
2
dimeric
2380
-27
2840
1750
6
2820
C
LCG
4
A
LCG
4
DG
E
LCG
4
B
LCG
4
DG
D
LCG
4
C
LCG
4
DG
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
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
7_555
y,x,-z+1/4
crystal symmetry operation
0.0000000000
0.0000000000
20.4140000000
1
D
HOH
203
H
HOH
1
E
C4'
C
8
B
C4'
C
8
1
Y
1
E
O4'
C
8
B
O4'
C
8
1
Y
1
E
C3'
C
8
B
C3'
C
8
1
Y
1
E
O3'
C
8
B
O3'
C
8
1
Y
1
E
C2'
C
8
B
C2'
C
8
1
Y
1
E
O2'
C
8
B
O2'
C
8
1
Y
1
E
C1'
C
8
B
C1'
C
8
1
Y
1
E
N1
C
8
B
N1
C
8
1
Y
1
E
C2
C
8
B
C2
C
8
1
Y
1
E
O2
C
8
B
O2
C
8
1
Y
1
E
N3
C
8
B
N3
C
8
1
Y
1
E
C4
C
8
B
C4
C
8
1
Y
1
E
N4
C
8
B
N4
C
8
1
Y
1
E
C5
C
8
B
C5
C
8
1
Y
1
E
C6
C
8
B
C6
C
8
1
Y
49.43
6.3525
-0.0000
0.0000
6.3525
-0.0000
-12.7050
0.3008
0.2580
0.2580
0.2580
1.952
18.790
562
5717
5717
100.00
99.46
0.36
RANDOM
1
Isotropic
THROUGHOUT
0.00
MOLECULAR REPLACEMENT
31.83
0.49
0.80
PDB ENTRY 3GLP
ML
FLAT BULK SOLVENT MODEL
36.220
0.348
1.952
18.790
14
510
10
486
0
0.010
549
1.230
856
16.246
252
0.066
110
0.012
23
0.4417
0.3766
2.1486
129
179
1238
97.00
50.7
1.95
20.00
4E58
5762
5762
0
0
0.067
1
23.7
28.3
99.8
1.95
1.98
2.175
273
0.673
1
15.6
97.5
data collection
MAR345
phasing
PHASER
refinement
PHENIX
(phenix.refine: 1.7_650)
data reduction
DENZO
data scaling
SCALEPACK
Crystal structure of GCC(LCG)CCGC duplex containing LNA residue
1
N
N
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
3
N
N
covale
1.597
both
C
C
3
A
O3'
C
3
1_555
C
LCG
4
A
P
LCG
4
1_555
covale
1.591
both
C
LCG
4
A
O3'
LCG
4
1_555
C
C
5
A
P
C
5
1_555
covale
1.610
both
E
C
3
B
O3'
C
3
1_555
E
LCG
4
B
P
LCG
4
1_555
covale
1.604
both
E
LCG
4
B
O3'
LCG
4
1_555
E
C
5
B
P
C
5
1_555
covale
1.595
both
D
C
3
C
O3'
C
3
1_555
D
LCG
4
C
P
LCG
4
1_555
covale
1.607
both
D
LCG
4
C
O3'
LCG
4
1_555
D
C
5
C
P
C
5
1_555
hydrog
WATSON-CRICK
C
C
3
A
N3
C
3
1_555
D
G
7
C
N1
G
7
1_555
hydrog
WATSON-CRICK
C
C
3
A
N4
C
3
1_555
D
G
7
C
O6
G
7
1_555
hydrog
WATSON-CRICK
C
C
3
A
O2
C
3
1_555
D
G
7
C
N2
G
7
1_555
hydrog
WATSON-CRICK
C
LCG
4
A
N1
LCG
4
1_555
D
C
6
C
N3
C
6
1_555
hydrog
WATSON-CRICK
C
LCG
4
A
N2
LCG
4
1_555
D
C
6
C
O2
C
6
1_555
hydrog
WATSON-CRICK
C
LCG
4
A
O6
LCG
4
1_555
D
C
6
C
N4
C
6
1_555
hydrog
C-LCG PAIR
C
C
5
A
N4
C
5
1_555
D
LCG
4
C
O6
LCG
4
1_555
hydrog
C-C MISPAIR
C
C
5
A
N3
C
5
1_555
D
C
5
C
N4
C
5
1_555
hydrog
WATSON-CRICK
C
C
6
A
N3
C
6
1_555
D
LCG
4
C
N1
LCG
4
1_555
hydrog
WATSON-CRICK
C
C
6
A
N4
C
6
1_555
D
LCG
4
C
O6
LCG
4
1_555
hydrog
WATSON-CRICK
C
C
6
A
O2
C
6
1_555
D
LCG
4
C
N2
LCG
4
1_555
hydrog
WATSON-CRICK
C
G
7
A
N1
G
7
1_555
D
C
3
C
N3
C
3
1_555
hydrog
WATSON-CRICK
C
G
7
A
N2
G
7
1_555
D
C
3
C
O2
C
3
1_555
hydrog
WATSON-CRICK
C
G
7
A
O6
G
7
1_555
D
C
3
C
N4
C
3
1_555
hydrog
WATSON-CRICK
E
G
1
B
N1
G
1
1_555
D
C
2
C
N3
C
2
1_555
hydrog
WATSON-CRICK
E
G
1
B
N2
G
1
1_555
D
C
2
C
O2
C
2
1_555
hydrog
WATSON-CRICK
E
G
1
B
O6
G
1
1_555
D
C
2
C
N4
C
2
1_555
hydrog
WATSON-CRICK
E
C
2
B
N3
C
2
1_555
D
G
1
C
N1
G
1
1_555
hydrog
WATSON-CRICK
E
C
2
B
N4
C
2
1_555
D
G
1
C
O6
G
1
1_555
hydrog
WATSON-CRICK
E
C
2
B
O2
C
2
1_555
D
G
1
C
N2
G
1
1_555
RNA
CCG repeats, 5' slippery duplexes, X-linked mental retardation, Huntington's disease, myotonic dystrophy type 1, LNA Guanosine, RNA
4E58
PDB
1
1
4E58
GCCGCCGC
1
8
4E58
1
8
4E58
C
1
1
8
1
8
4E58
1
8
4E58
E
1
1
8
1
8
4E58
1
8
4E58
D
1
1
8
BINDING SITE FOR RESIDUE SO4 C 101
C
SO4
101
Software
3
BINDING SITE FOR RESIDUE SO4 D 101
D
SO4
101
Software
4
C
C
2
A
C
2
3
1_555
C
C
3
A
C
3
3
1_555
C
HOH
202
F
HOH
3
1_555
C
G
7
A
G
7
4
1_555
C
C
8
A
C
8
4
1_555
D
LCG
4
C
LCG
4
4
1_555
D
C
5
C
C
5
4
1_555
95
P 43 2 2