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/pdb1f7i/pdb
pdb_00001f7i
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
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
5.257
1
19
A
2
A
26
-6.246
A_G2:C26_A
1
-0.087
-0.262
0.923
-0.404
0.962
1
20
A
3
A
25
-4.170
A_A3:U25_A
2
-20.400
0.032
-0.309
-0.067
4.215
1
20
A
4
A
24
-4.362
A_A4:U24_A
3
-1.324
0.000
-0.857
-0.175
-12.717
1
19
A
5
A
23
-0.309
A_G5:C23_A
4
-21.848
-0.153
-0.655
-0.159
-10.792
1
28
A
6
A
22
5.509
A_U6:G22_A
5
-4.345
2.374
0.000
-0.387
-14.353
1
19
A
8
A
21
-0.809
A_C8:G21_A
6
-15.367
0.076
-0.386
-0.381
15.446
1
19
A
9
A
20
-3.726
A_G9:C20_A
7
5.856
-0.262
1.140
-0.381
-3.353
1
19
A
10
A
19
8.957
A_G10:C19_A
8
-24.941
-0.402
-0.913
-0.484
0.902
1
20
A
11
A
18
-2.333
A_U11:A18_A
9
-29.223
0.038
-0.631
-0.307
-5.664
1
19
A
12
A
17
-1.172
A_C12:G17_A
10
-8.396
0.484
0.105
-0.219
17.843
6
A
13
A
16
-81.303
A_U13:G16_A
11
-12.041
1.423
0.049
-5.467
3.787
32.926
A
A
2
3
6.820
A
A
26
25
4.005
3.825
0.273
-1.360
AA_G2A3:U25C26_AA
1
7.451
-13.284
31.871
-3.190
1.057
3.994
35.314
A
A
3
4
-9.046
A
A
25
24
3.842
-5.466
0.402
-1.249
AA_A3A4:U24U25_AA
2
0.859
-1.421
34.891
-1.084
-0.510
4.630
29.334
A
A
4
5
6.685
A
A
24
23
4.753
3.376
0.583
-1.066
AA_A4G5:C23U24_AA
3
1.962
-3.886
29.079
-3.153
-0.541
2.177
44.525
A
A
5
6
32.155
A
A
23
22
3.119
23.258
0.923
-0.959
AA_G5U6:G22C23_AA
4
-1.730
2.392
38.196
-3.151
-1.358
2.122
32.777
A
A
6
8
46.457
A
A
22
21
3.933
23.142
0.643
-0.909
AA_U6C8:G21G22_AA
5
9.793
-19.658
21.216
-6.143
0.778
1.975
33.939
A
A
8
9
20.863
A
A
21
20
2.422
11.790
-0.427
-0.965
AA_C8G9:C20G21_AA
6
-8.987
15.902
30.617
-2.994
-0.290
3.172
44.946
A
A
9
10
44.450
A
A
20
19
4.150
30.475
1.398
-0.154
AA_G9G10:C19C20_AA
7
13.516
-19.713
30.585
-3.952
-0.165
2.440
39.882
A
A
10
11
21.311
A
A
19
18
2.913
14.237
-0.415
-0.893
AA_G10U11:A18C19_AA
8
-1.432
2.143
37.325
-2.702
0.468
2.911
33.885
A
A
11
12
27.382
A
A
18
17
3.599
15.357
-0.599
-0.813
AA_U11C12:G17A18_AA
9
-4.493
8.011
29.967
-4.016
0.261
3.082
102.888
A
A
12
13
-1.088
A
A
17
16
3.499
-1.696
2.667
-1.806
AA_C12U13:G16G17_AA
10
-21.255
13.641
101.274
-1.129
-2.022
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
contains the average complex structure calculated from this ensemble
RCSB
Y
RCSB
2000-06-27
REL
REL
NCO
COBALT HEXAMMINE(III)
synthesized from DNA oligonucleotide template by T7 RNA polymerase
sample
This structure was determined using standard 2D homonuclear techniques and 13C and 31P heteronuclear techniques at natural abundance. Distance constraints derived from intermolecular NOE crosspeaks between RNA protons and cobalt (III) hexammine protons were used to determine the site of cobalt (III) hexammine binding in the complex structure
structures with the least restraint violations
50
12
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 structures are based on a total of 268 NOE derived distance constraints, 171 dihedral restraints and 49 distance restraints from hydrogen bonds. 12 NOE derived intermolecular distance constraints were used to localize the bound cobalt(III) hexammine. The 12 structures with lowest NOE and dihedral angle violation energies are presented
restrained molecular dynamics; simulated annealing
7
closest to the average
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
H41
O6
C
G
8
21
1.59
9
A
A
HO2'
O5'
U
C
14
15
1.46
10
A
A
O6
H41
G
C
2
26
1.59
SOLUTION STRUCTURE OF THE RNASE P RNA (M1 RNA) P4 STEM C70U MUTANT OLIGORIBONUCLEOTIDE COMPLEXED WITH COBALT (III) HEXAMINE ,NMR, ENSEMBLE OF 12 STRUCTURES
1
N
N
2
N
N
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
1F7I
PDB
1
1F7I
1
27
1F7I
1
27
1F7I
A
1
1
27
BINDING SITE FOR RESIDUE NCO A 28
A
NCO
28
Software
4
A
G
5
A
G
5
4
1_555
A
U
6
A
U
6
4
1_555
A
G
21
A
G
21
4
1_555
A
G
22
A
G
22
4
1_555
1
P 1