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/pdb1f78/pdb
pdb_00001f78
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
8633.143
RNASE P RNA RIBOZYME, P4 DOMAIN
P4 STEM
1
syn
polymer
161.116
COBALT HEXAMMINE(III)
1
syn
non-polymer
no
no
GGAAGUCCGGUCUUCGGACCGGCUUCC
GGAAGUCCGGUCUUCGGACCGGCUUCC
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
45.755
1
19
A
1
A
27
-3.047
A_G1:C27_A
1
20.415
-0.273
-0.444
-0.339
7.996
1
19
A
2
A
26
-4.371
A_G2:C26_A
2
-2.819
-0.355
0.073
-0.266
-2.191
1
20
A
3
A
25
-1.003
A_A3:U25_A
3
-21.191
0.200
-0.824
-0.177
-3.528
1
20
A
4
A
24
-2.763
A_A4:U24_A
4
-5.000
0.063
-0.481
0.001
2.700
1
19
A
5
A
23
-2.327
A_G5:C23_A
5
-2.238
-0.222
-1.051
-0.401
-9.964
1
19
A
7
A
22
2.551
A_C7:G22_A
6
30.686
0.147
0.449
-0.186
-8.481
1
19
A
8
A
21
-8.819
A_C8:G21_A
7
7.807
-0.055
-1.097
-0.547
3.745
1
19
A
9
A
20
-4.977
A_G9:C20_A
8
4.757
0.061
-1.285
-0.644
-0.140
1
19
A
10
A
19
9.943
A_G10:C19_A
9
-19.688
-0.375
-1.117
-0.592
4.173
1
20
A
11
A
18
-3.586
A_U11:A18_A
10
-5.740
-0.300
-0.611
0.020
-29.827
1
19
A
12
A
17
-4.459
A_C12:G17_A
11
16.219
0.174
1.970
-0.633
37.976
2
A
13
A
16
-64.596
A_U13:G16_A
12
8.481
1.214
0.287
-5.464
3.910
31.598
A
A
1
2
41.964
A
A
27
26
5.728
20.922
-0.665
-0.698
AA_G1G2:C26C27_AA
1
-3.669
7.359
23.529
-7.887
0.062
2.785
40.097
A
A
2
3
26.656
A
A
26
25
3.808
17.634
0.282
-1.553
AA_G2A3:U25C26_AA
2
5.691
-8.603
35.716
-4.424
0.285
4.333
32.447
A
A
3
4
-24.651
A
A
25
24
4.294
-13.355
0.354
-1.165
AA_A3A4:U24U25_AA
3
-3.587
6.622
29.424
1.171
-1.509
1.900
30.339
A
A
4
5
32.974
A
A
24
23
3.280
16.371
0.055
-1.657
AA_A4G5:C23U24_AA
4
1.218
-2.453
25.602
-6.010
0.107
2.820
68.926
A
A
5
7
42.078
A
A
23
22
3.629
44.253
-1.968
-0.643
AA_G5C7:G22C23_AA
5
-13.950
13.264
52.460
-2.474
1.138
3.169
33.549
A
A
7
8
25.486
A
A
22
21
4.457
14.007
-1.054
-0.781
AA_C7C8:G21G22_AA
6
10.765
-19.587
28.635
-4.261
4.061
3.883
22.710
A
A
8
9
-0.870
A
A
21
20
3.866
-0.343
0.170
-0.898
AA_C8G9:C20G21_AA
7
0.936
-2.377
22.689
-2.135
-0.032
3.188
29.054
A
A
9
10
25.925
A
A
20
19
4.017
12.584
0.844
-1.150
AA_G9G10:C19C20_AA
8
1.760
-3.627
26.182
-5.504
-1.233
2.327
38.043
A
A
10
11
32.354
A
A
19
18
3.218
20.025
-0.890
-1.015
AA_G10U11:A18C19_AA
9
-5.079
8.206
32.120
-3.915
0.767
2.244
41.138
A
A
11
12
33.950
A
A
18
17
4.218
21.719
-0.641
-2.187
AA_U11C12:G17A18_AA
10
-18.753
29.314
29.794
-5.852
-1.453
2.145
100.094
A
A
12
13
-0.140
A
A
17
16
2.543
-0.213
2.092
-2.070
AA_C12U13:G16G17_AA
11
-23.362
15.314
98.049
-1.348
-1.632
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
1F6X shows the structure of the free wildtype P4 stem oligoribonucleotide
1F6Z shows the structure of the free C70U mutant P4 stem oligoribonucleotide
RCSB
Y
RCSB
2000-06-26
REL
REL
NCO
COBALT HEXAMMINE(III)
enzymatically 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 11 converged structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.7 Angstrom. A total of 266 NOE-derived intramolecular distance constraints, 164 dihedral restraint and 48 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 P4 RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O
90% H2O/10% D2O
2 mM P4 RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 99.96% D2O
99.96% D2O
2 mM P4 RNA; 100 mM sodium chloride; 10 mM magnesium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O
90% H2O/10% D2O
2 mM P4 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
3.84
Brunger
refinement
X-PLOR
3.84
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
C
7
n
7
C
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
minimized average
SOLUTION STRUCTURE OF RNASE P RNA (M1 RNA) P4 STEM OLIGORIBONUCLEOTIDE COMPLEXED WITH COBALT (III) HEXAMINE, 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
WATSON-CRICK
A
C
7
A
N3
C
7
1_555
A
G
22
A
N1
G
22
1_555
hydrog
WATSON-CRICK
A
C
7
A
N4
C
7
1_555
A
G
22
A
O6
G
22
1_555
hydrog
WATSON-CRICK
A
C
7
A
O2
C
7
1_555
A
G
22
A
N2
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, METAL BINDING SITE, METAL COMPLEX, COBALT (III) HEXAMMINE COMPLEX, RNA
1F78
PDB
1
1F78
1
27
1F78
1
27
1F78
A
1
1
27
BINDING SITE FOR RESIDUE NCO A 28
A
NCO
28
Software
3
A
G
5
A
G
5
3
1_555
A
C
8
A
C
8
3
1_555
A
G
21
A
G
21
3
1_555
1
P 1