1HD7

A SECOND DIVALENT METAL ION IN THE ACTIVE SITE OF A NEW CRYSTAL FORM OF HUMAN APURINIC/APYRIDINIMIC ENDONUCLEASE, APE1, AND ITS IMPLICATIONS FOR THE CATALYTIC MECHANISM

Structural Biology Knowledgebase: 1HD7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.205

Literature

Macromolecules
Sequence Display for 1HD7

Classification: DNA REPAIR

Total Structure Weight: 35814.04

Macromolecule Entities
Molecule Chains Length Organism Details
DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE A 318 Homo sapiens EC#: 3.1 IUBMB 4.2.99.18 IUBMB
Gene Name(s): APEX1 Gene View APE APE1 APEX APX HAP1 Gene View REF1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PB
Query on PB

A LEAD (II) ION
Pb
RVPVRDXYQKGNMQ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.205
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 128.39 α = 90.00
b = 44.85 β = 124.54
c = 78.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-11-09
  • Released Date: 2001-02-16
  • Deposition author(s): Beernink, P.T., Segelke, B.W., Rupp, B.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4