1N56

Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.225

Literature

Macromolecules
Sequence Display for 1N56

Classification: TRANSFERASE / DNA

Total Structure Weight: 100331.25


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase IV A, B 352 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*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*AP*A)-3' C, E 14 synthetic Template
5'-D(*TP*CP*AP*TP*(3DR)P*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' D, F 17 synthetic primer

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

A, B ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
3DR
Query on 3DR
D, F DNA LINKING C5 H11 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.225
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 98.02 α = 90.00
b = 102.36 β = 90.00
c = 105.66 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-11-04
  • Released Date: 2004-02-24
  • Deposition author(s): Ling, H., Boudsocq, F., Woodgate, R., Yang, W.

Revision History

  • Version 1_0: 2004-02-24

    Type: Initial release

  • Version 1_1: 2008-04-28

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance