363D | pdb_0000363d

High-resolution crystal structure of a fully modified N3'-> P5' phosphoramidate DNA dodecamer duplex

• PDB DOI: https://doi.org/10.2210/pdb363D/pdb
• NAKB: 363D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1997-11-26 Released: 1997-12-15 
• Deposition Author(s): Tereshko, V., Gryaznov, S., Egli, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.247 (Depositor) 
• R-Value Work: 
  0.192 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: in silico

Literature

Consequences of Replacing the DNA 3'-Oxygen by an Amino Group: High-Resolution Crystal Structure of a Fully Modified N3'--> P5' Phosphoramidate DNA Dodecamer Duplex

Tereshko, V., Gryaznov, S., Egli, M.

(1998) J Am Chem Soc 120: 269-283

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.

Macromolecule Content 

• Total Structure Weight: 22.77 kDa 
• Atom Count: 1,694 
• Modeled Residue Count: 72 
• Deposited Residue Count: 72 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'	A, B, C, D, E, F	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	AA [auth D], DA [auth D], GA [auth E], I [auth A], JA [auth E], L [auth A], NA [auth F], O [auth B], PA [auth F], R [auth B], U [auth C], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NH4	BA [auth D], CA [auth D], EA [auth E], FA [auth E], G [auth A], H [auth A], HA [auth E], IA [auth E], J [auth A], K [auth A], KA [auth F], LA [auth F], M [auth B], MA [auth F], N [auth B], OA [auth F], P [auth B], Q [auth B], S [auth C], T [auth C], V [auth C], W [auth C], Y [auth D], Z [auth D]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.247 (Depositor) 
• R-Value Work:  0.192 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.15	α = 90
b = 40.15	β = 90
c = 304.21	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-12-15 
Deposition Author(s): Tereshko, V., Gryaznov, S., Egli, M.

Revision History  

• Version 1.0: 1997-12-15
  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: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description