6BST

CRYSTAL STRUCTURE OF Z-DNA WITH UNTYPICALLY COORDINATED CA2+ ION

• PDB DOI: https://doi.org/10.2210/pdb6BST/pdb
• Entry: 6BST supersedes: 6B01
• NAKB: 6BST

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


• Deposited: 2017-12-04 Released: 2017-12-20 
• Deposition Author(s): LUO, Z., DAUTER, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.172 
• R-Value Work: 0.121 
• R-Value Observed: 0.121 

Literature

The crystal structure of Z-DNA with untypically coordinated Ca

Luo, Z., Dauter, Z.

(2018) J Biol Inorg Chem 23: 253-259

• PubMed: 29270817 
• DOI: https://doi.org/10.1007/s00775-017-1526-4
• Primary Citation of Related Structures:  
  6BST


• PubMed Abstract: 
  

  DNA oligomer duplexes with alternating cytosines and guanines in their sequence tend to form helices of the Z-DNA type, where the sugar and phosphate backbone forms a left-handed helix in a zigzag fashion with a repeat of two successive Watson-Crick pairs of nucleotides. Z-DNA duplexes often crystallize in complexes with diverse metal ions interacting with polar DNA atoms in various ways. This work describes the high-resolution crystal structure of a Z-DNA d(CGCGCG) ₂ duplex in complex with Ca ²⁺ ions, unusually coordinated as an approximate pentagonal bipyramid by two neighboring guanines through their O6 and N7 atoms and a water molecule in the equatorial plane and a phosphate oxygen atom and another water molecule in the apical positions.

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Organizational Affiliation: 

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL, 60439, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 3.81 kDa 
• Atom Count: 289 
• Modelled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')	A, B	6	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SR0	C [auth A]	N~1~-(3-azaniumylpropyl)butane-1,4-diaminium C7 H22 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-Q
CA	D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.172 
• R-Value Work: 0.121 
• R-Value Observed: 0.121 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.76	α = 90
b = 28.82	β = 90
c = 42.36	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): LUO, Z., DAUTER, Z.
• This entry supersedes: 6B01

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2018-01-10
  Changes: Database references
• Version 1.2: 2018-02-28
  Changes: Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description