4B21

Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog Mag2

Structural Biology Knowledgebase: 4B21 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.207

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4B21

Classification: HYDROLASE / DNA

Total Structure Weight: 33137.55


Macromolecule Entities
Molecule Chains Length Organism Details
PROBABLE DNA-3-METHYLADENINE GLYCOSYLASE 2 A 232 Schizosaccharomyces pombe EC#: 3.2.2.21 IUBMB
Gene Name(s): mag2 SPBC23G7.11
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*CP*TP*AP*CP*3DRP*GP*AP*TP*CP*GP)-3' X 11 Synthetic construct
5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP)-3' Y 10 Synthetic construct

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

A BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, Y PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
3DR
Query on 3DR
X DNA LINKING C5 H11 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.207
  • Space Group: I 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.93 α = 90.00
b = 84.75 β = 90.00
c = 126.71 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-12
  • Released Date: 2013-01-09
  • Deposition author(s): Dalhus, B., Nilsen, L., Korvald, H., Huffman, J., Forstrom, R.J., Mcmurray, C.T., Alseth, I., Tainer, J.A., Bjoras, M.

Revision History

  • 2013-01-30
    Type: Citation | Details: JRNL