1ZX7 | pdb_00001zx7

Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative

• PDB DOI: https://doi.org/10.2210/pdb1ZX7/pdb
• NAKB: 1ZX7

• Classification: RNA
• Mutation(s): No 


• Deposited: 2005-06-07 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: 2.15 Å
• R-Value Free: 
  0.292 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.261 (DCC) 
• R-Value Observed: 
  0.262 (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 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.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.14 kDa 
• Atom Count: 2,548 
• Modeled Residue Count: 116 
• Deposited Residue Count: 116 
• 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, E, G	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, F, H	14	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.292 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.261 (DCC) 
• R-Value Observed: 0.262 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.65	α = 90
b = 153.2	β = 90.1
c = 32.74	γ = 90

Software Package:

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

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