2GW0 | pdb_00002gw0

A D(TGGGGT)- sodium and calcium complex.

PDB DOI: https://doi.org/10.2210/pdb2GW0/pdb
NAKB: 2GW0

Classification: DNA
Mutation(s): No

Deposited: 2006-05-03 Released: 2007-05-15
Deposition Author(s): Lee, M.P.H., Parkinson, G.N., Neidle, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.224 (Depositor), 0.213 (DCC)
R-Value Work:
0.170 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Observation of the coexistence of sodium and calcium ions in a DNA G-quadruplex ion channel.

Lee, M.P., Parkinson, G.N., Hazel, P., Neidle, S.

(2007) J Am Chem Soc 129: 10106-10107

PubMed: 17661470 Search on PubMed
DOI: https://doi.org/10.1021/ja0740869
Primary Citation Related Structures:
2GW0

Organizational Affiliation

CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, U.K.

Macromolecule Content

Total Structure Weight: 15.45 kDa
Atom Count: 1,171
Modeled Residue Count: 48
Deposited Residue Count: 48
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
5'-D(TPGPGPGPGPT)-3'	A, B, C, D, E A, B, C, D, E, F, G, H	6	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 Q [auth D] SDF format, chain P [auth D] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A] K [auth A] L [auth A] M [auth A] N [auth B] J [auth A], K [auth A], L [auth A], M [auth A], N [auth B], O [auth B], P [auth D], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth D] Focus chain Q [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain I [auth A] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain I [auth A] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain I [auth A]	I [auth A], R [auth E], S [auth E], T [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Interactions & Density Focus chain I [auth A] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.224 (Depositor), 0.213 (DCC)
R-Value Work: 0.170 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.357	α = 89.11
b = 27.911	β = 75.63
c = 34.969	γ = 79.7

Software Package:

Software Name	Purpose
SHELXL-97	refinement
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-05-15

Deposition Author(s):

Lee, M.P.H.

Parkinson, G.N.

Neidle, S.

Revision History (Full details and data files)

Version 1.0: 2007-05-15
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2019-07-24
Changes: Data collection, Refinement description
Version 1.5: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description