2ASD

oxoG-modified Insertion Ternary Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.225

Literature

Macromolecules
Sequence Display for 2ASD

Classification: transferase / DNA

Total Structure Weight: 102428.42


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase IV A, B 360 Sulfolobus solfataricus EC#: 2.7.7.7 IUBMB
Gene Name(s): dbh dpo4 SSO2448
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3' D, H 13 synthetic Primer Strand (dideoxy-terminated at 3'-end)
5'-D(*CP*T*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3' E, J 19 synthetic oxoG-modified Template Strand

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DCP
Query on DCP

A, B 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B, D CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
DDG
Query on DDG
D, H DNA LINKING C10 H14 N5 O6 P DG
8OG
Query on 8OG
E, J DNA LINKING C10 H14 N5 O8 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.225
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 75.96 α = 90.00
b = 101.11 β = 97.14
c = 84.12 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-08-23
  • Released Date: 2006-01-10
  • Deposition author(s): Rechkoblit, O., Malinina, L., Cheng, Y., Kuryavyi, V., Broyde, S., Geacintov, N.E., Patel, D.J.

Revision History

  • 2008-04-30
    Type: Version format compliance
  • 2011-07-13
    Type: Advisory, Refinement description, Version format compliance