5DAM | pdb_00005dam

Crystal Structure of p-iodoHoechst bound to d(CGCAAATTTGCG)

PDB DOI: https://doi.org/10.2210/pdb5DAM/pdb
NAKB: 5DAM

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

Deposited: 2015-08-20 Released: 2016-03-16
Deposition Author(s): Clark, G.R.
Funding Organization(s): Marsden Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.297 (Depositor), 0.288 (DCC)
R-Value Work:
0.178 (Depositor), 0.187 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal Structure of p-iodoHoechst bound to d(CGCAAATTTGCG)

(2016) Int J Radiat Biol

Macromolecule Content

Total Structure Weight: 7.88 kDa
Atom Count: 654
Modeled Residue Count: 24
Deposited Residue Count: 24
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (5'-D(CPGPCPAPAPAPTPTPTPGPCPG)-3')	A, B	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
58F Query on 58F 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]	p-iodo Hoechst C₂₅ H₂₃ I N₆ WSBVZEKIZWIJQO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.297 (Depositor), 0.288 (DCC)
R-Value Work: 0.178 (Depositor), 0.187 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.638	α = 90
b = 40.408	β = 90
c = 64.344	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-03-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Marsden Fund	New Zealand	--

Revision History (Full details and data files)

Version 1.0: 2016-03-16
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2026-03-04
Changes: Refinement description, Structure summary

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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.