1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kieft, J.S.
Tinoco Junior, I.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
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
UK
Structure
STRUE6
2005
0969-2126
5
713
721
10.1016/S0969-2126(97)00225-6
9195889
Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine.
1997
10.2210/pdb1ajf/pdb
pdb_00001ajf
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
5812.515
RNA (5'-R(*GP*AP*CP*AP*GP*GP*GP*GP*AP*AP*AP*CP*UP*UP*UP*GP*UP*C)-3')
TETRALOOP OF TETRALOOP-TETRALOOP RECEPTOR TERTIARY INTERACTION
C1G, U2A
1
syn
polymer
161.116
COBALT HEXAMMINE(III)
1
syn
non-polymer
GAAA TETRALOOP OF A GROUP I INTRON
no
no
GACAGGGGAAACUUUGUC
GACAGGGGAAACUUUGUC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-27.726
1
19
A
1
A
18
-4.319
A_G1:C18_A
1
-17.123
-0.476
-0.438
-0.288
5.557
1
20
A
2
A
17
-11.070
A_A2:U17_A
2
-2.361
0.410
0.507
-0.063
10.152
1
19
A
3
A
16
-1.708
A_C3:G16_A
3
-10.140
0.461
-0.250
-0.272
-7.828
1
20
A
4
A
15
2.116
A_A4:U15_A
4
-25.907
-0.002
-0.787
-0.313
-17.834
28
A
5
A
14
0.037
A_G5:U14_A
5
-9.893
-2.479
-1.171
-0.660
3.955
28
A
6
A
13
1.629
A_G6:U13_A
6
-0.086
-2.568
0.547
-0.498
-5.324
1
19
A
7
A
12
-4.273
A_G7:C12_A
7
0.653
-0.435
0.020
-0.365
19.040
10
A
8
A
11
-24.735
A_G8:A11_A
8
-1.049
6.955
0.263
-5.370
2.570
34.825
A
A
1
2
-10.027
A
A
18
17
2.354
-5.950
-0.749
-0.981
AA_G1A2:U17C18_AA
1
-5.377
9.061
33.917
-0.949
0.627
3.220
36.065
A
A
2
3
4.478
A
A
17
16
3.019
2.743
1.619
-1.220
AA_A2C3:G16U17_AA
2
8.879
-14.495
34.886
-2.349
-1.394
2.276
35.280
A
A
3
4
34.427
A
A
16
15
3.693
19.647
-0.040
-1.407
AA_C3A4:U15G16_AA
3
5.311
-9.307
28.971
-5.261
0.860
2.061
31.715
A
A
4
5
35.022
A
A
15
14
3.429
17.867
-0.465
-1.430
AA_A4G5:U14U15_AA
4
-7.216
14.145
25.310
-5.707
-0.397
2.985
32.972
A
A
5
6
-22.528
A
A
14
13
3.020
-12.192
0.107
-1.166
AA_G5G6:U13U14_AA
5
-12.002
22.177
28.292
0.004
-2.216
2.566
47.177
A
A
6
7
23.895
A
A
13
12
3.434
18.652
-0.349
-1.666
AA_G6G7:C12U13_AA
6
-1.993
2.553
43.485
-3.547
0.280
2.455
60.828
A
A
7
8
2.706
A
A
12
11
2.459
2.738
-1.130
-0.956
AA_G7G8:A11C12_AA
7
-2.319
2.291
60.732
-1.043
1.032
database_2
pdbx_database_status
pdbx_entity_src_syn
pdbx_nmr_representative
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Other
Source and taxonomy
1
0
1997-07-07
1
1
2008-03-24
1
2
2011-07-13
1
3
2021-10-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_pdbx_entity_src_syn.ncbi_taxonomy_id
_pdbx_entity_src_syn.organism_scientific
_pdbx_nmr_software.authors
_pdbx_nmr_software.classification
_pdbx_nmr_software.name
_pdbx_nmr_software.version
_pdbx_nmr_spectrometer.manufacturer
_pdbx_nmr_spectrometer.model
_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_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
Y
BNL
1997-05-02
REL
REL
NCO
COBALT HEXAMMINE(III)
SYNTHESIZED ENZYMATICALLY IN-VITRO USING T7 RNA POLYMERASE
32630
synthetic construct
sample
NOE ENERGY (LEAST RESTRAINT VIOLATIONS), TOTAL ENERGY
32
1
DQF-COSY
D2O NOESY
H2O NOESY
13C-1H HMQC
6.4
283
K
REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
RESTRAINED MOLECULAR DYNAMICS
1
BRUNGER
refinement
X-PLOR
3.1
Accelrys Software Inc.
structure calculation
Felix
95
BRUNGER
structure calculation
X-PLOR
3.1
Accelrys Software Inc.
structure calculation
Discover
BIOSYM
500
Bruker
AMX
600
GE
GN
NCO
1
2
NCO
NCO
19
A
G
1
n
1
G
1
A
A
2
n
2
A
2
A
C
3
n
3
C
3
A
A
4
n
4
A
4
A
G
5
n
5
G
5
A
G
6
n
6
G
6
A
G
7
n
7
G
7
A
G
8
n
8
G
8
A
A
9
n
9
A
9
A
A
10
n
10
A
10
A
A
11
n
11
A
11
A
C
12
n
12
C
12
A
U
13
n
13
U
13
A
U
14
n
14
U
14
A
U
15
n
15
U
15
A
G
16
n
16
G
16
A
U
17
n
17
U
17
A
C
18
n
18
C
18
A
author_defined_assembly
1
monomeric
A
G
6
A
N7
G
6
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N1
NCO
1_555
106.5
A
G
6
A
N7
G
6
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N2
NCO
1_555
75.8
A
NCO
19
B
N1
NCO
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N2
NCO
1_555
177.5
A
G
6
A
N7
G
6
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N3
NCO
1_555
131.4
A
NCO
19
B
N1
NCO
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N3
NCO
1_555
92.7
A
NCO
19
B
N2
NCO
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N3
NCO
1_555
85.0
A
G
6
A
N7
G
6
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N4
NCO
1_555
53.6
A
NCO
19
B
N1
NCO
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N4
NCO
1_555
81.9
A
NCO
19
B
N2
NCO
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N4
NCO
1_555
100.3
A
NCO
19
B
N3
NCO
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N4
NCO
1_555
173.9
A
G
6
A
N7
G
6
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N5
NCO
1_555
121.9
A
NCO
19
B
N1
NCO
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N5
NCO
1_555
100.2
A
NCO
19
B
N2
NCO
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N5
NCO
1_555
79.1
A
NCO
19
B
N3
NCO
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N5
NCO
1_555
96.8
A
NCO
19
B
N4
NCO
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N5
NCO
1_555
81.4
A
G
6
A
N7
G
6
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N6
NCO
1_555
55.0
A
NCO
19
B
N1
NCO
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N6
NCO
1_555
80.5
A
NCO
19
B
N2
NCO
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N6
NCO
1_555
100.4
A
NCO
19
B
N3
NCO
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N6
NCO
1_555
86.4
A
NCO
19
B
N4
NCO
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N6
NCO
1_555
95.5
A
NCO
19
B
N5
NCO
1_555
A
NCO
19
B
CO
NCO
1_555
A
NCO
19
B
N6
NCO
1_555
176.8
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
A
O6
H41
G
C
7
12
1.60
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
X-PLOR
3.1
SOLUTION STRUCTURE OF THE P5B STEM LOOP FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE
1
N
N
2
N
N
metalc
3.112
A
G
6
A
N7
G
6
1_555
A
NCO
19
B
CO
NCO
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
18
A
N3
C
18
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
18
A
O2
C
18
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
18
A
N4
C
18
1_555
hydrog
WATSON-CRICK
A
A
2
A
N1
A
2
1_555
A
U
17
A
N3
U
17
1_555
hydrog
WATSON-CRICK
A
A
2
A
N6
A
2
1_555
A
U
17
A
O4
U
17
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
A
G
16
A
N1
G
16
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
A
G
16
A
O6
G
16
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
A
G
16
A
N2
G
16
1_555
hydrog
WATSON-CRICK
A
A
4
A
N1
A
4
1_555
A
U
15
A
N3
U
15
1_555
hydrog
WATSON-CRICK
A
A
4
A
N6
A
4
1_555
A
U
15
A
O4
U
15
1_555
hydrog
TYPE_28_PAIR
A
G
5
A
N1
G
5
1_555
A
U
14
A
O2
U
14
1_555
hydrog
TYPE_28_PAIR
A
G
5
A
O6
G
5
1_555
A
U
14
A
N3
U
14
1_555
hydrog
TYPE_28_PAIR
A
G
6
A
N1
G
6
1_555
A
U
13
A
O2
U
13
1_555
hydrog
TYPE_28_PAIR
A
G
6
A
O6
G
6
1_555
A
U
13
A
N3
U
13
1_555
hydrog
WATSON-CRICK
A
G
7
A
N1
G
7
1_555
A
C
12
A
N3
C
12
1_555
hydrog
WATSON-CRICK
A
G
7
A
N2
G
7
1_555
A
C
12
A
O2
C
12
1_555
hydrog
WATSON-CRICK
A
G
7
A
O6
G
7
1_555
A
C
12
A
N4
C
12
1_555
hydrog
G-A MISPAIR
A
G
8
A
N2
G
8
1_555
A
A
11
A
N7
A
11
1_555
RNA
RIBONUCLEIC ACID, COBALT (III) HEXAMMINE, METAL BINDING, RNA STRUCTURE, RNA
1AJF
PDB
1
1AJF
1
18
1AJF
1
18
1AJF
A
1
1
18
BINDING SITE FOR RESIDUE NCO A 19
A
NCO
19
Software
6
A
G
5
A
G
5
6
1_555
A
G
6
A
G
6
6
1_555
A
G
7
A
G
7
6
1_555
A
G
8
A
G
8
6
1_555
A
C
12
A
C
12
6
1_555
A
U
13
A
U
13
6
1_555
1
P 1