5OV2

2'F-ANA-G modified quadruplex with a flipped tetrad

PDB DOI: https://doi.org/10.2210/pdb5OV2/pdb
NAKB: 5OV2
BMRB: 34174

Classification: DNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2017-08-27 Released: 2017-10-18
Deposition Author(s): Dickerhoff, J., Weisz, K.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 10
Conformers Submitted: 10
Selection Criteria: all calculated structures submitted

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Nonconventional C-HF Hydrogen Bonds Support a Tetrad Flip in Modified G-Quadruplexes.

Dickerhoff, J., Weisz, K.

(2017) J Phys Chem Lett 8: 5148-5152

PubMed: 28976755 Search on PubMed
DOI: https://doi.org/10.1021/acs.jpclett.7b02428
Primary Citation of Related Structures:
5OV2

PubMed Abstract:
A G-quadruplex adopting a (3 + 1)-hybrid structure was substituted at its 5'-tetrad by 2'-deoxy-2'-fluoro-arabinoguanosine ( ^FaraG) analogs. Incorporation of anti-favoring ^FaraG at syn-positions of the 5'-outer tetrad induced a reversal of the tetrad polarity without noticeably compromising the quadruplex stability. This conformational change is shown to be promoted by nonconventional C-H···F hydrogen bonds acting within the anti- ^FaraG residues.

Organizational Affiliation

Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany.

Macromolecule Content

Total Structure Weight: 7.03 kDa
Atom Count: 468
Modelled Residue Count: 22
Deposited Residue Count: 22
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
artificial quadruplex with propeller, diagonal, and lateral loop	A [auth X]	22	synthetic construct
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 10
Conformers Submitted: 10
Selection Criteria: all calculated structures submitted

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-10-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-10-18
Type: Initial release
Version 1.1: 2017-11-01
Changes: Database references
Version 1.2: 2019-05-08
Changes: Data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.