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BMRB: 17422

2L8P

Solution Structure of a DNA Duplex Containing the Potent Anti-Poxvirus Agent Cidofovir

Authors

Julien, O., Beadle, J.R., Magee, W.C., Chatterjee, S., Hostetler, K.Y., Evans, D.H., Sykes, B.D.

Assembly

Cidofovir DNA duplex

Entity

1. Cidofovir DNA duplex chain A (polymer, Thiol state: not present), 12 monomers, 3658.330 Da Detail

CGCATGXTAC GC

2. Cidofovir DNA duplex chain B (polymer, Thiol state: not present), 12 monomers, 3766.388 Da Detail

GCGTAGCATG CG

Total weight

7424.718 Da

Max. entity weight

3766.388 Da

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.8 %, Completeness: 63.6 %, Completeness (bb): 52.8 % Detail

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 GC

2. Cidofovir DNA duplex chain B

GCGTAGCATG CG

Show sample condition

Sample

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

Release date

2011-02-08

Citation

Solution structure of a DNA duplex containing the potent anti-poxvirus agent cidofovir
Julien, O., Beadle, J.R., Magee, W.C., Chatterjee, S., Hostetler, K.Y., Evans, D.H., Sykes, B.D.
J. Am. Chem. Soc. (2011), 133, 2264-2274, PubMed 21280608 , DOI 10.1021/ja109823e , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 17423 released on 2011-02-08
Title Solution Structure of a DNA Duplex Containing the Potent Anti-Poxvirus Agent Cidofovir

Experiments performed 5 experiments Detail

1 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

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

2 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

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

3 2D DQF-COSY

Instrument

Varian INOVA - 600 MHz

Sample

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

4 2D DQF-COSY

Instrument

Varian INOVA - 500 MHz

Sample

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

5 2D 1H-13C HSQC

Instrument

Varian INOVA - 500 MHz

Sample

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

NMR combined restraints 5 contents Detail

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

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-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

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--
CGCATGXTACGC
||||||||||||
CGCATGXTACGC

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

------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

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	161		100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	189 (1)	noe	100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	51 (1)	hbond	100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	128 (128)	.	100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 157
  - ¹³C chemical shifts: 4
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of restraints: 189
- Weight of restraints: 1.0 (189)
- Potential type of restraints: upper-bound-parabolic (189)
- Range of distance target values: 2.45, 6.04 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
    - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
  - Total number of restraints: 51
  - Weight of restraints: 1.0 (51)
  - Potential type of restraints: upper-bound-parabolic (51)
  - Range of distance target values: 1.71, 2.85 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of restraints: 128
- Total number of restraints per polymer type: 128
- Weight of restraints: 1.0 (128)
- Potential type of restraints: square-well-parabolic (128)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords Cidofovir, DNA, dodecamer, duplex, HPMPC, poxvirus