216D | pdb_0000216d

CRYSTAL STRUCTURES OF THE B-FORM DNA-RNA CHIMER (5'-D(*IP*)-R(*CP*)-D(*IP*CP*IP*CP*IP*C)-3') COMPLEXED WITH DISTAMYCIN

• PDB DOI: https://doi.org/10.2210/pdb216D/pdb
• NAKB: 216D

• Classification: DNA-RNA HYBRID
• Mutation(s): No 


• Deposited: 1995-07-18 Released: 1996-01-29 
• Deposition Author(s): Chen, X., Ramakrishnan, B., Sundaralingam, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Work: 
  0.152 (Depositor), 0.138 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Literature

Crystal structures of B-form DNA-RNA chimers complexed with distamycin.

Chen, X., Ramakrishnan, B., Sundaralingam, M.

(1995) Nat Struct Biol 2: 733-735

• PubMed: 7552741 
• DOI: https://doi.org/10.1038/nsb0995-733
• Primary Citation Related Structures: 
  216D, 217D


• PubMed Abstract: 
  

  Two DNA-RNA chimers, complexed with DNA minor groove binding drugs, have been observed to adopt the B-form conformation for the first time. Thus, the RNA duplex may assume the B-DNA conformation when interacting with drugs, peptides or proteins.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.89 kDa 
• Atom Count: 237 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-D(*IP*)-R(*CP*)-D(*IP*CP*IP*CP*IP*C)-3')	A	8	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMY	B [auth A]	DISTAMYCIN A C22 H27 N9 O4 UPBAOYRENQEPJO-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Work:  0.152 (Depositor), 0.138 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.92	α = 90
b = 27.92	β = 90
c = 57.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-01-29 
Deposition Author(s): Chen, X., Ramakrishnan, B., Sundaralingam, M.

Revision History  

• Version 1.0: 1996-01-29
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations