363D

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
R-Value Work: 0.192
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

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)PDG)-3'	A, B, C, D, E A, B, C, D, E, F	12	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain DA [auth D] SDF format, chain GA [auth E] SDF format, chain I [auth A] SDF format, chain JA [auth E] SDF format, chain L [auth A] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain PA [auth F] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain X [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain X [auth C]	AA [auth D] DA [auth D] GA [auth E] I [auth A] JA [auth E] 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		Interactions Focus chain AA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain I [auth A] Focus chain JA [auth E] Focus chain L [auth A] Focus chain NA [auth F] Focus chain O [auth B] Focus chain PA [auth F] Focus chain R [auth B] Focus chain U [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain I [auth A] Focus chain JA [auth E] Focus chain L [auth A] Focus chain NA [auth F] Focus chain O [auth B] Focus chain PA [auth F] Focus chain R [auth B] Focus chain U [auth C] Focus chain X [auth C]
NH4 Query on NH4 Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain EA [auth E] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth F] SDF format, chain LA [auth F] SDF format, chain M [auth B] SDF format, chain MA [auth F] SDF format, chain N [auth B] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain FA [auth E] SDF format, chain J [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain J [auth A]	BA [auth D] CA [auth D] EA [auth E] FA [auth E] G [auth A] 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		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain M [auth B] Focus chain MA [auth F] Focus chain N [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain M [auth B] Focus chain MA [auth F] Focus chain N [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.247
R-Value Work: 0.192
R-Value Observed: 0.192
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 1997-12-15

Deposition Author(s):

Tereshko, V.

Gryaznov, S.

Egli, M.

Revision History (Full details and data files)

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