2A04

Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative

• PDB DOI: https://doi.org/10.2210/pdb2A04/pdb
• NAKB: 2A04

• Classification: RNA
• Mutation(s): No 


• Deposited: 2005-06-15 Released: 2005-09-20 
• Deposition Author(s): Zhao, Q., Zhao, F., Blount, K.F., Han, Q., Tor, Y., Hermann, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.318 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.298 (Depositor) 

Literature

Molecular recognition of RNA by neomycin and a restricted neomycin derivative

Zhao, F., Zhao, Q., Blount, K.F., Han, Q., Tor, Y., Hermann, T.

(2005) Angew Chem Int Ed Engl 44: 5329-5334

• PubMed: 16037995 
• DOI: https://doi.org/10.1002/anie.200500903
• Primary Citation of Related Structures:  
  1ZX7, 1ZZ5, 2A04

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, 92093, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21.08 kDa 
• Atom Count: 1,418 
• Modelled Residue Count: 58 
• Deposited Residue Count: 58 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'	A, C	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)-3'	B, D	14	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NMY	E [auth A], F [auth A], H [auth C], I [auth C]	NEOMYCIN C23 H46 N6 O13 PGBHMTALBVVCIT-VCIWKGPPSA-N
MG	G [auth A], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.318 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.298 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.8	α = 90
b = 49.9	β = 90
c = 144.6	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-20 
Deposition Author(s): Zhao, Q., Zhao, F., Blount, K.F., Han, Q., Tor, Y., Hermann, T.

Revision History  

• Version 1.0: 2005-09-20
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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