1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Schmitz, M.
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
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
RNA
RNARFU
2122
1355-8382
6
1212
1225
10.1017/S1355838200000881
10999599
Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA.
2000
10.2210/pdb1f79/pdb
pdb_00001f79
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
8634.127
RNASE P RNA RIBOZYME, P4 DOMAIN MUTANT
P4 STEM
C70U
1
syn
polymer
161.116
COBALT HEXAMMINE(III)
1
syn
non-polymer
no
no
GGAAGUUCGGUCUUCGGACCGGCUUCC
GGAAGUUCGGUCUUCGGACCGGCUUCC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
46.861
1
19
A
1
A
27
-1.213
A_G1:C27_A
1
8.994
0.009
-0.373
-0.332
5.008
1
19
A
2
A
26
-8.054
A_G2:C26_A
2
-17.504
-0.133
0.530
-0.207
1.431
1
20
A
3
A
25
-4.414
A_A3:U25_A
3
-23.513
0.226
-0.390
-0.191
3.150
1
20
A
4
A
24
-1.916
A_A4:U24_A
4
-11.641
-0.012
-0.769
-0.162
-12.815
1
19
A
5
A
23
-2.275
A_G5:C23_A
5
-30.554
-0.172
-0.226
-0.207
-8.103
28
A
6
A
22
1.317
A_U6:G22_A
6
-1.484
2.409
0.393
-0.415
-16.290
1
19
A
8
A
21
-4.331
A_C8:G21_A
7
8.535
0.015
-1.236
-0.741
16.847
1
19
A
9
A
20
-2.581
A_G9:C20_A
8
5.673
-0.224
1.044
-0.305
-1.307
1
19
A
10
A
19
9.873
A_G10:C19_A
9
-24.101
-0.421
-0.944
-0.524
0.741
1
20
A
11
A
18
-0.041
A_U11:A18_A
10
-17.846
-0.081
-1.269
-0.499
-9.134
1
19
A
12
A
17
-1.763
A_C12:G17_A
11
-10.447
0.473
0.097
-0.238
38.120
2
A
13
A
16
-91.139
A_U13:G16_A
12
-12.862
1.139
-1.432
-5.278
3.899
35.002
A
A
1
2
37.244
A
A
27
26
5.523
20.909
-1.029
-1.117
AA_G1G2:C26C27_AA
1
-4.437
7.903
27.881
-6.950
0.630
3.082
35.548
A
A
2
3
19.204
A
A
26
25
3.600
11.493
0.271
-1.083
AA_G2A3:U25C26_AA
2
4.632
-7.739
33.384
-3.545
0.270
3.945
33.721
A
A
3
4
-7.579
A
A
25
24
3.842
-4.384
0.663
-0.889
AA_A3A4:U24U25_AA
3
1.242
-2.146
33.421
-0.682
-0.902
4.293
31.077
A
A
4
5
7.880
A
A
24
23
4.446
4.209
0.301
-0.874
AA_A4G5:C23U24_AA
4
0.138
-0.258
30.797
-2.714
-0.526
2.324
43.014
A
A
5
6
27.179
A
A
23
22
3.085
19.268
0.585
-0.974
AA_G5U6:G22C23_AA
5
-2.666
3.761
38.552
-3.000
-1.030
1.572
44.959
A
A
6
8
59.983
A
A
22
21
4.422
37.574
0.457
-0.740
AA_U6C8:G21G22_AA
6
14.685
-23.442
20.274
-5.405
1.137
1.859
30.070
A
A
8
9
20.342
A
A
21
20
2.574
10.147
0.178
-1.085
AA_C8G9:C20G21_AA
7
-10.045
20.138
26.533
-3.593
-1.830
3.365
42.345
A
A
9
10
38.500
A
A
20
19
4.236
25.479
1.245
-0.325
AA_G9G10:C19C20_AA
8
13.447
-20.320
31.370
-3.979
0.139
3.001
34.403
A
A
10
11
16.963
A
A
19
18
3.391
9.899
-0.592
-0.944
AA_G10U11:A18C19_AA
9
-0.622
1.066
32.984
-3.139
0.903
2.622
40.737
A
A
11
12
35.576
A
A
18
17
3.657
23.264
-0.663
-0.846
AA_U11C12:G17A18_AA
10
-6.267
9.584
33.095
-3.969
0.210
2.875
104.617
A
A
12
13
-0.392
A
A
17
16
3.000
-0.620
1.573
-0.999
AA_C12U13:G16G17_AA
11
-11.246
7.113
104.187
-0.623
-1.135
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2000-10-09
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
1F6Z shows the structure of the free C70U mutant P4 stem oligoribonucleotide
1F6X shows the structure of the free wildtype P4 stem oligoribonucleotide
RCSB
Y
RCSB
2000-06-23
REL
REL
NCO
COBALT HEXAMMINE(III)
synthesized from DNA ologonucleotide template by T7 RNA polymerase
sample
This structure was determined using standard 2D homonuclear techniques and 13C and 31P heteronuclear techniques at natural abundance. Intermolecular NOE crosspeaks between RNA protons and cobalt (III) hexammine protons and derived intermolecular distance constraints were used to determine the site of cobalt (III) hexammine binding in the complex structure
1
2D NOESY
2D NOESY
2D NOESY
2D NOESY
DQF-COSY
31P-1H-COSY
13C-1H-HMQC
100 mM Na
6.5
ambient
288
K
100 mM Na
6.5
ambient
288
K
100 mM Na, 10 mM Mg
6.5
ambient
288
K
100 mM Na, 3 mM Co(NH3)6
6.5
ambient
288
K
The average structure is based on superposition of 12 converged structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.5 Angstrom. A total of 268 NOE-derived intramolecular distance constraints, 171 dihedral restraint and 49 distance restraints from hydrogen bonds were used in the refinement. 12 NOE derived intermolecular distance constraints were used to localize the bound cobalt (III) hexammine
restrained molecular dynamics and simulated annealing
minimized average structure
2 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O
90% H2O/10% D2O
2 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 99.96% D2O
99.96% D2O
2 mM P4m RNA; 100 mM sodium chloride; 10 mM magnesium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O
90% H2O/10% D2O
2 mM P4m RNA; 100 mM sodium chloride; 3 mM hexammine cobalt chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O
90% H2O/10% D2O
Bruker
collection
XwinNMR
3.1
MSI
processing
Felix
95
Brunger
structure solution
X-PLOR
3.841
Brunger
refinement
X-PLOR
3.841
600
Bruker
AMX
500
Bruker
DRX
NCO
28
2
NCO
NCO
28
A
G
1
n
1
G
1
A
G
2
n
2
G
2
A
A
3
n
3
A
3
A
A
4
n
4
A
4
A
G
5
n
5
G
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
U
11
n
11
U
11
A
C
12
n
12
C
12
A
U
13
n
13
U
13
A
U
14
n
14
U
14
A
C
15
n
15
C
15
A
G
16
n
16
G
16
A
G
17
n
17
G
17
A
A
18
n
18
A
18
A
C
19
n
19
C
19
A
C
20
n
20
C
20
A
G
21
n
21
G
21
A
G
22
n
22
G
22
A
C
23
n
23
C
23
A
U
24
n
24
U
24
A
U
25
n
25
U
25
A
C
26
n
26
C
26
A
C
27
n
27
C
27
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
O6
H41
G
C
1
27
1.59
minimized average
SOLUTION STRUCTURE OF RNASE P RNA (M1 RNA) P4 STEM C70U MUTANT OLIGORIBONUCLEOTIDE COMPLEXED WITH COBALT(III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
27
A
N3
C
27
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
27
A
O2
C
27
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
27
A
N4
C
27
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
26
A
N3
C
26
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
26
A
O2
C
26
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
26
A
N4
C
26
1_555
hydrog
WATSON-CRICK
A
A
3
A
N1
A
3
1_555
A
U
25
A
N3
U
25
1_555
hydrog
WATSON-CRICK
A
A
3
A
N6
A
3
1_555
A
U
25
A
O4
U
25
1_555
hydrog
WATSON-CRICK
A
A
4
A
N1
A
4
1_555
A
U
24
A
N3
U
24
1_555
hydrog
WATSON-CRICK
A
A
4
A
N6
A
4
1_555
A
U
24
A
O4
U
24
1_555
hydrog
WATSON-CRICK
A
G
5
A
N1
G
5
1_555
A
C
23
A
N3
C
23
1_555
hydrog
WATSON-CRICK
A
G
5
A
N2
G
5
1_555
A
C
23
A
O2
C
23
1_555
hydrog
WATSON-CRICK
A
G
5
A
O6
G
5
1_555
A
C
23
A
N4
C
23
1_555
hydrog
TYPE_28_PAIR
A
U
6
A
N3
U
6
1_555
A
G
22
A
O6
G
22
1_555
hydrog
TYPE_28_PAIR
A
U
6
A
O2
U
6
1_555
A
G
22
A
N1
G
22
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
A
G
21
A
N1
G
21
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
A
G
21
A
O6
G
21
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
A
G
21
A
N2
G
21
1_555
hydrog
WATSON-CRICK
A
G
9
A
N1
G
9
1_555
A
C
20
A
N3
C
20
1_555
hydrog
WATSON-CRICK
A
G
9
A
N2
G
9
1_555
A
C
20
A
O2
C
20
1_555
hydrog
WATSON-CRICK
A
G
9
A
O6
G
9
1_555
A
C
20
A
N4
C
20
1_555
hydrog
WATSON-CRICK
A
G
10
A
N1
G
10
1_555
A
C
19
A
N3
C
19
1_555
hydrog
WATSON-CRICK
A
G
10
A
N2
G
10
1_555
A
C
19
A
O2
C
19
1_555
hydrog
WATSON-CRICK
A
G
10
A
O6
G
10
1_555
A
C
19
A
N4
C
19
1_555
hydrog
WATSON-CRICK
A
U
11
A
N3
U
11
1_555
A
A
18
A
N1
A
18
1_555
hydrog
WATSON-CRICK
A
U
11
A
O4
U
11
1_555
A
A
18
A
N6
A
18
1_555
hydrog
WATSON-CRICK
A
C
12
A
N3
C
12
1_555
A
G
17
A
N1
G
17
1_555
hydrog
WATSON-CRICK
A
C
12
A
N4
C
12
1_555
A
G
17
A
O6
G
17
1_555
hydrog
WATSON-CRICK
A
C
12
A
O2
C
12
1_555
A
G
17
A
N2
G
17
1_555
hydrog
U-G MISPAIR
A
U
13
A
O2
U
13
1_555
A
G
16
A
N1
G
16
1_555
RNA
RIBONUCLEASE P, RIBOZYME, TRANSFER RNA PROCESSING, P4 STEM, C70U MUTANT, METAL BINDING SITE, METAL COMPLEX, COBALT (III) HEXAMMINE COMPLEX, RNA
1F79
PDB
1
1F79
1
27
1F79
1
27
1F79
A
1
1
27
BINDING SITE FOR RESIDUE NCO A 28
A
NCO
28
Software
5
A
G
5
A
G
5
5
1_555
A
U
6
A
U
6
5
1_555
A
C
20
A
C
20
5
1_555
A
G
21
A
G
21
5
1_555
A
C
23
A
C
23
5
1_555
1
P 1