Solution Structure of a DNA Duplex Containing the Potent Anti-Poxvirus Agent Cidofovir
Polymer type: polydeoxyribonucleotide
Total | 1H | |
---|---|---|
All | 63.6 % (143 of 225) | 63.6 % (143 of 225) |
Suger, PO4 | 52.8 % (85 of 161) | 52.8 % (85 of 161) |
Nucleobase | 90.6 % (58 of 64) | 90.6 % (58 of 64) |
Aromatic | 95.7 % (44 of 46) | 95.7 % (44 of 46) |
Methyl | 100.0 % (4 of 4) | 100.0 % (4 of 4) |
1. Cidofovir DNA duplex chain A
CGCATGXTAC GC2. Cidofovir DNA duplex chain B
GCGTAGCATG CGSolvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cidofovir DNA duplex, chain_A | natural abundance | 2 mM | |
2 | Cidofovir DNA duplex, chain_B | natural abundance | 2 mM | |
3 | NaCl | natural abundance | 50 mM | |
4 | Na2HPO4 | natural abundance | 20 mM | |
5 | EDTA | natural abundance | 1 mM | |
6 | DSS-d6 | natural abundance | 0.25 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cidofovir DNA duplex, chain_A | natural abundance | 2 mM | |
2 | Cidofovir DNA duplex, chain_B | natural abundance | 2 mM | |
3 | NaCl | natural abundance | 50 mM | |
4 | Na2HPO4 | natural abundance | 20 mM | |
5 | EDTA | natural abundance | 1 mM | |
6 | DSS-d6 | natural abundance | 0.25 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cidofovir DNA duplex, chain_A | natural abundance | 2 mM | |
2 | Cidofovir DNA duplex, chain_B | natural abundance | 2 mM | |
3 | NaCl | natural abundance | 50 mM | |
4 | Na2HPO4 | natural abundance | 20 mM | |
5 | EDTA | natural abundance | 1 mM | |
6 | DSS-d6 | natural abundance | 0.25 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cidofovir DNA duplex, chain_A | natural abundance | 2 mM | |
2 | Cidofovir DNA duplex, chain_B | natural abundance | 2 mM | |
3 | NaCl | natural abundance | 50 mM | |
4 | Na2HPO4 | natural abundance | 20 mM | |
5 | EDTA | natural abundance | 1 mM | |
6 | DSS-d6 | natural abundance | 0.25 mM |
Varian INOVA - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cidofovir DNA duplex, chain_A | natural abundance | 2 mM | |
2 | Cidofovir DNA duplex, chain_B | natural abundance | 2 mM | |
3 | NaCl | natural abundance | 50 mM | |
4 | Na2HPO4 | natural abundance | 20 mM | |
5 | EDTA | natural abundance | 1 mM | |
6 | DSS-d6 | natural abundance | 0.25 mM |
Varian INOVA - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cidofovir DNA duplex, chain_A | natural abundance | 2 mM | |
2 | Cidofovir DNA duplex, chain_B | natural abundance | 2 mM | |
3 | NaCl | natural abundance | 50 mM | |
4 | Na2HPO4 | natural abundance | 20 mM | |
5 | EDTA | natural abundance | 1 mM | |
6 | DSS-d6 | natural abundance | 0.25 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_17422_2l8p.nef |
Input source #2: Coordindates | 2l8p.cif |
Diamagnetism of the molecular assembly | True (excluding Oxygen atoms) |
Whether the assembly has a disulfide bond | None |
Whether the assembly has a other bond | None |
Whether the assembly contains a cyclic polymer | None |
Overall data processing status | Warning |
Disulfide bonds
NoneOther bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
A | 7 | L8P | ({[(2S)-1-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-hydroxypropan-2-yl]oxy}methyl)phosphonic acid | Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates |
Sequence alignments
--------10-- CGCATGXTACGC |||||||||||| CGCATGXTACGC
------20---- GCGTAGCATGCG |||||||||||| GCGTAGCATGCG --------10--
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 12 | 0 | 0 | 100.0 |
B | B | 12 | 0 | 0 | 100.0 |
Content subtype: combined_17422_2l8p.nef
Assigned chemical shifts
--------10-- CGCATGXTACGC |||||||||||| CGCATGXTACGC
------20---- GCGTAGCATGCG |||||||||||| GCGTAGCATGCG
Comp_index_ID | Comp_ID |
---|---|
7 | L8P |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 109 | 68 | 62.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 77 | 40 | 51.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 32 | 28 | 87.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 2 | 2 | 100.0 |
13C chemical shifts | 2 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 7 | 7 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 116 | 75 | 64.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 84 | 45 | 53.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 32 | 30 | 93.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 2 | 2 | 100.0 |
13C chemical shifts | 2 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 9 | 9 | 100.0 |
Distance restraints
--------10-- CGCATGXTACGC |||||||||||| CGCATGXTACGC
------20---- GCGTAGCATGCG |||||||||||| GCGTAGCATGCG
--------10-- CGCATGXTACGC |||||||||||| CGCATGXTACGC
------20---- GCGTAGCATGCG |||||||||||| GCGTAGCATGCG
Dihedral angle restraints
--------10-- CGCATGXTACGC |||||||||||| CGCATGXTACGC
------20---- GCGTAGCATGCG |||||||||||| GCGTAGCATGCG