1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Colmenarejo, G.
Tinoco Jr., I.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
Co H18 N6 3
161.116
COBALT HEXAMMINE(III)
non-polymer
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
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
CO
N
75
N
N
N
76
N
N
N
77
N
N
N
78
N
N
N
79
N
N
N
80
N
N
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
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
O
N
100
N
P
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
C
N
105
R
C
N
106
N
O
N
107
S
C
N
108
N
O
N
109
R
C
N
110
N
O
N
111
R
C
N
112
N
N
N
113
N
C
N
114
N
O
N
115
N
N
N
116
N
C
N
117
N
O
N
118
N
C
N
119
N
C
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
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
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
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
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
doub
N
104
N
sing
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
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
doub
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
doub
N
132
N
sing
N
133
N
doub
N
134
N
sing
N
135
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
290
119
135
10.1006/jmbi.1999.2867
10388561
Structure and thermodynamics of metal binding in the P5 helix of a group I intron ribozyme.
1999
10.2210/pdb1c0o/pdb
pdb_00001c0o
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
CLOSED BY A UUCG TETRALOOP; COBALT (III) HEXAMMINE BINDS AT THE MAJOR GROOVE OF TWO TANDEM G-U WOBBLE PAIRS IN 5'-GU-3' ORIENTATION
4471.667
RNA (5'-R(*GP*GP*GP*UP*CP*UP*UP*CP*GP*GP*GP*UP*CP*C)-3')
1
man
polymer
161.116
COBALT HEXAMMINE(III)
1
syn
non-polymer
no
no
GGGUCUUCGGGUCC
GGGUCUUCGGGUCC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Tetrahymena
sample
SYNTHESIZED ENZYMATICALLY IN-VITRO USING T7 RNA POLYMERASE
5911
Tetrahymena thermophila
-25.118
1
19
A
1
A
14
-4.366
A_G1:C14_A
1
-12.116
-0.744
-0.240
-0.369
-3.997
1
19
A
2
A
13
-2.522
A_G2:C13_A
2
-14.346
-0.750
-0.133
-0.476
-7.851
28
A
3
A
12
-0.617
A_G3:U12_A
3
-23.421
-2.780
-0.161
-0.944
-7.877
28
A
4
A
11
-2.014
A_U4:G11_A
4
-14.773
2.754
-0.092
-0.881
-2.624
1
19
A
5
A
10
-1.515
A_C5:G10_A
5
-4.836
1.032
-0.839
-0.721
-3.956
2
A
6
A
9
-95.639
A_U6:G9_A
6
-15.485
1.017
-0.272
-5.120
2.874
32.320
A
A
1
2
20.155
A
A
14
13
2.910
10.992
-0.361
0.329
AA_G1G2:C13C14_AA
1
-2.835
5.199
30.311
-1.188
0.189
1.608
34.456
A
A
2
3
35.953
A
A
13
12
3.062
19.854
0.626
-1.243
AA_G2G3:U12C13_AA
2
-7.385
13.374
27.332
-4.578
-1.979
3.142
59.683
A
A
3
4
6.735
A
A
12
11
3.206
6.691
-0.072
-0.472
AA_G3U4:G11U12_AA
3
-1.054
1.061
59.332
-0.801
0.021
1.648
28.560
A
A
4
5
31.017
A
A
11
10
3.060
14.305
-0.547
-1.295
AA_U4C5:G10G11_AA
4
9.422
-20.430
22.939
-5.237
2.829
2.779
90.045
A
A
5
6
9.520
A
A
10
9
2.879
13.392
-0.415
0.067
AA_C5U6:G9G10_AA
5
16.110
-11.452
88.088
-0.191
0.580
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Data collection
1
0
1999-08-31
1
1
2008-04-26
1
2
2011-07-13
1
3
2022-02-16
1
4
2023-12-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
1999-03-16
REL
NCO
COBALT HEXAMMINE(III)
THE STRUCTURE WAS DETERMINED USING A NON-ISOTOPICALLY LABELLED RNA SAMPLE. ALL
13C EXPERIMENTS WERE DONE USING NATURAL ABUNDANCE. COBALT (III) HEXAMMINE WAS
LOCATED USING DOCKING WITH 7 INTERMOLECULAR NOES OBSERVED IN 2D WATER NOESY
EXPERIMENTS.
NOE ENERGY (LEAST RESTRAINT VIOLATIONS), DIHEDRAL ENERGY (LEAST RESTRAINT
VIOLATIONS), TOTAL ENERGY
40
19
DQF-COSY
D2O NOESY
H2O NOESY
TOCSY
13C-1H HMQC
31P-1H HETCOR
31P-1H TOCSY
31P-1H TOCSY-NOESY
100 mM NACL
6.4
1
atm
298
K
REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
RESTRAINED MOLECULAR DYNAMICS
PHOSPHATE BUFFER, EDTA
BRUNGER
refinement
X-PLOR
3.1
structure solution
FELIX95
structure solution
X-PLOR
3.1
500
Bruker
AMX600
600
Bruker
DRX500
NCO
15
2
NCO
NCO
15
A
G
1
n
1
G
1
A
G
2
n
2
G
2
A
G
3
n
3
G
3
A
U
4
n
4
U
4
A
C
5
n
5
C
5
A
U
6
n
6
U
6
A
U
7
n
7
U
7
A
C
8
n
8
C
8
A
G
9
n
9
G
9
A
G
10
n
10
G
10
A
G
11
n
11
G
11
A
U
12
n
12
U
12
A
C
13
n
13
C
13
A
C
14
n
14
C
14
A
author_defined_assembly
1
monomeric
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
A
A
HO2'
O6
U
G
6
9
1.57
3
A
A
HO2'
O6
U
G
6
9
1.59
5
A
A
HO2'
O6
U
G
6
9
1.59
6
A
A
O2
H1
U
G
6
9
1.59
6
A
A
HO2'
O6
U
G
6
9
1.60
6
A
A
O6
H41
G
C
1
14
1.60
7
A
A
HO2'
O6
U
G
6
9
1.53
7
A
A
O2
H1
U
G
6
9
1.59
8
A
A
HO2'
O6
U
G
6
9
1.55
8
A
A
O2
H1
U
G
6
9
1.57
9
A
A
HO2'
O6
U
G
6
9
1.53
10
A
A
HO2'
O6
U
G
6
9
1.55
13
A
A
HO2'
O6
U
G
6
9
1.57
13
A
A
O2
H1
U
G
6
9
1.58
14
A
A
HO2'
O6
U
G
6
9
1.56
15
A
A
HO2'
O6
U
G
6
9
1.59
17
A
A
HO2'
O6
U
G
6
9
1.60
17
A
A
O6
H41
G
C
2
13
1.60
19
A
A
HO2'
O6
U
G
6
9
1.57
19
A
A
O2
H1
U
G
6
9
1.60
SOLUTION STRUCTURE OF THE P5 HAIRPIN FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, 19 CONVERGED STRUCTURES
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
14
A
N3
C
14
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
14
A
O2
C
14
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
14
A
N4
C
14
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
13
A
N3
C
13
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
13
A
O2
C
13
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
13
A
N4
C
13
1_555
hydrog
TYPE_28_PAIR
A
G
3
A
N1
G
3
1_555
A
U
12
A
O2
U
12
1_555
hydrog
TYPE_28_PAIR
A
G
3
A
O6
G
3
1_555
A
U
12
A
N3
U
12
1_555
hydrog
TYPE_28_PAIR
A
U
4
A
N3
U
4
1_555
A
G
11
A
O6
G
11
1_555
hydrog
TYPE_28_PAIR
A
U
4
A
O2
U
4
1_555
A
G
11
A
N1
G
11
1_555
hydrog
WATSON-CRICK
A
C
5
A
N3
C
5
1_555
A
G
10
A
N1
G
10
1_555
hydrog
WATSON-CRICK
A
C
5
A
N4
C
5
1_555
A
G
10
A
O6
G
10
1_555
hydrog
WATSON-CRICK
A
C
5
A
O2
C
5
1_555
A
G
10
A
N2
G
10
1_555
hydrog
U-G MISPAIR
A
U
6
A
O2
U
6
1_555
A
G
9
A
N1
G
9
1_555
hydrog
TYPE_28_PAIR
A
U
6
A
N3
U
6
1_555
A
G
10
A
O6
G
10
1_555
hydrog
TYPE_28_PAIR
A
U
6
A
O2
U
6
1_555
A
G
10
A
N1
G
10
1_555
RNA
RIBONUCLEIC ACID, COBALT (III) HEXAMMINE, METAL BINDING, RNA STRUCTURE, RNA
1C0O
PDB
1
1C0O
1
14
1C0O
1
14
1C0O
A
1
1
14
BINDING SITE FOR RESIDUE NCO A 15
A
NCO
15
Software
5
A
G
2
A
G
2
5
1_555
A
G
3
A
G
3
5
1_555
A
U
4
A
U
4
5
1_555
A
G
11
A
G
11
5
1_555
A
U
12
A
U
12
5
1_555
1
P 1