Solution Structure of a DNA Duplex Containing the Potent Anti-Poxvirus Agent Cidofovir
Polymer type: polydeoxyribonucleotide
Total | 1H | |
---|---|---|
All | 63.1 % (149 of 236) | 63.1 % (149 of 236) |
Suger, PO4 | 48.2 % (81 of 168) | 48.2 % (81 of 168) |
Nucleobase | 100.0 % (68 of 68) | 100.0 % (68 of 68) |
Aromatic | 100.0 % (48 of 48) | 100.0 % (48 of 48) |
Methyl | 100.0 % (4 of 4) | 100.0 % (4 of 4) |
1. Control DNA duplex chain A
CGCATGCTAC GC2. Control 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 | DNA duplex, chain_A | natural abundance | 2 mM | |
2 | 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 | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
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 | DNA duplex, chain_A | natural abundance | 2 mM | |
2 | 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 | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
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 | DNA duplex, chain_A | natural abundance | 2 mM | |
2 | 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 | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
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 | DNA duplex, chain_A | natural abundance | 2 mM | |
2 | 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 | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
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 | DNA duplex, chain_A | natural abundance | 2 mM | |
2 | 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 | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
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 | DNA duplex, chain_A | natural abundance | 2 mM | |
2 | 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 | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_17423_2l8q.nef |
Input source #2: Coordindates | 2l8q.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
NoneSequence alignments
--------10-- CGCATGCTACGC |||||||||||| CGCATGCTACGC
------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_17423_2l8q.nef
Assigned chemical shifts
--------10-- CGCATGCTACGC |||||||||||| CGCATGCTACGC
------20---- GCGTAGCATGCG |||| ||||| GCGT...ATGCG
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 120 | 78 | 65.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 84 | 42 | 50.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 36 | 36 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 2 | 2 | 100.0 |
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 | 53 | 45.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 84 | 29 | 34.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 32 | 24 | 75.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 2 | 2 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 9 | 6 | 66.7 |
Distance restraints
--------10-- CGCATGCTACGC |||||||||||| CGCATGCTACGC
------20---- GCGTAGCATGCG |||||||||||| GCGTAGCATGCG
--------10-- CGCATGCTACGC |||||||||||| CGCATGCTACGC
------20---- GCGTAGCATGCG |||||||||||| GCGTAGCATGCG
Dihedral angle restraints
--------10-- CGCATGCTACGC |||||||||||| CGCATGCTACGC
------20---- GCGTAGCATGCG |||||||||||| GCGTAGCATGCG