4IEM

Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+

Structural Biology Knowledgebase: 4IEM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.208

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4IEM

Classification: HYDROLASE LYASE / DNA

Total Structure Weight: 168497.25


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-(apurinic or apyrimidinic site) lyase A, B, C, D 317 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
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*CP*TP*AP*C)-3') E, H, K, N 5 Synthetic construct
DNA (5'-D(P*(3DR)P*GP*AP*TP*CP*G)-3') F, I, L, O 6 Synthetic construct
DNA (5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*C)-3') G, J, M, P 11 Synthetic construct

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

A, B, C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B, D, E, F, N SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
3DR
Query on 3DR
F, I, L, O DNA LINKING C5 H11 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.208
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 104.64 α = 90.00
b = 74.09 β = 111.98
c = 112.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-13
  • Released Date: 2013-01-23
  • Deposition author(s): Tsutakawa, S.E., Mol, C.D., Arvai, A.S., Tainer, J.A.

Revision History

  • 2013-04-10
    Type: Citation | Details: Citation update
  • 2013-02-13
    Type: Binding sites and description | Details: Update binding sites with changing Mg chain labels
  • 2013-02-13
    Type: Linkage | Details: Update links with changing Mg chain labels
  • 2013-02-13
    Type: Citation | Details: Citation update
  • 2013-02-13
    Type: Other | Details: Change Mg chain labels to the protein chain and not a random DNA chain nearby