3T86 | pdb_00003t86

d(GCATGCT) + calcium

PDB DOI: https://doi.org/10.2210/pdb3T86/pdb
NAKB: 3T86

Classification: DNA
Mutation(s): No

Deposited: 2011-08-01 Released: 2012-06-13
Deposition Author(s): Cardin, C.J., Gan, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.279 (Depositor), 0.266 (DCC)
R-Value Work:
0.239 (Depositor), 0.237 (DCC)
R-Value Observed:
0.241 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3T86

This is version 1.3 of the entry. See complete history.

Literature

A novel structure for the d(GCATGCT) quadruplex in the presence of nickel and cobalt aqueous cations : comparison with the vanadium, barium and calcium-bound structural motif.

Gan, Y., Thorpe, J.H., Teixeira, S.C.M., Naseer, A., Cardin, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 2.19 kDa
Atom Count: 152
Modeled Residue Count: 7
Deposited Residue Count: 7
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (5'-D(GPCPAPTPGPCP*T)-3')	A	7	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.279 (Depositor), 0.266 (DCC)
R-Value Work: 0.239 (Depositor), 0.237 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 22.742	α = 90
b = 58.341	β = 90
c = 23.669	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
XFIT	data reduction
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-06-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-13
Type: Initial release
Version 1.1: 2014-11-12
Changes: Structure summary
Version 1.2: 2017-11-22
Changes: Database references
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.