BMRB Entry 17791

Name: Structure of the duplex containing HNE derived (6S,8R,11S) gamma-HO-PdG when placed opposite dT
Published: 2012-08-30

Click here to enlarge.

PDB ID: 2lg3
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17791
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Structure of the duplex containing HNE derived (6S,8R,11S) gamma-HO-PdG when placed opposite dT

Deposition date:

2011-07-19

Original release date:

2012-08-30

Authors:

Huang, Hai; Wang, Hao; Kozekova, Albena; LLoyd, R.; Rizzo, Carmelo; Stone, Michael

Citation:

Citation: Huang, Hai; Wang, Hao; Kozekova, Albena; LLoyd, R.; Rizzo, Carmelo; Stone, Michael. "Ring-chain tautomerization of trans-4-hydroxynonenal derived (6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct when placed opposite 2'-deoxythymidine in duplex" .

Assembly members:

Assembly members:
DNA_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'), polymer, 12 residues, 3663.422 Da.
DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3'), polymer, 12 residues, 3678.433 Da.
HNE, non-polymer, 156.222 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'): GCTAGCGAGTCC
DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3'): GGACTTGCTAGC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	141

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA_(5'-D(GPCPTPAPGPCPGPAPGPTPCPC)-3')	1
2	DNA_(5'-D(GPGPAPCPTPTPGPCPTPAPGPC)-3')	2
3	HNE	3

Entities:

Entity 1, DNA_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3') 12 residues - 3663.422 Da.

1

DG

DC

DT

DA

DG

DC

DG

DA

DG

DT

2

DC

Entity 2, DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3') 12 residues - 3678.433 Da.

1

DG

DA

DC

DT

DG

DC

DT

DA

2

DG

DC

Entity 3, HNE - C9 H16 O2 - 156.222 Da.

1

HNE

Samples:

sample_1: DNA_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3') 1 mM; DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3') 1 mM; HNE 1 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMR spectrometers:

Bruker Avance 800 MHz