2NP6

Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing an abasic site analog at the target position


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.286
  • R-Value Work: 0.228

Literature

Macromolecules
Sequence Display for 2NP6

Classification: TRANSFERASE / DNA

Total Structure Weight: 108819.48


Macromolecule Entities
Molecule Chains Length Organism Details
Modification methylase TaqI A, D 421 Thermus aquaticus EC#: 2.1.1.72 IUBMB
Gene Name(s): taqIM
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*TP*TP*CP*GP*(3DR)P*TP*GP*TP*C)-3' B, E 10 synthetic DNA target strand containing an abasic site analog at the target position
5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3' C, F 10 synthetic DNA partner strand containing N6-methyladenine

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

A, D 5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE
C12 H18 N6 O3 S
APAPOJUCRZTCHD-WOUKDFQISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IPA
Query on IPA

A, B, E ISOPROPYL ALCOHOL
2-PROPANOL (Synonym)
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
3DR
Query on 3DR
B, E DNA LINKING C5 H11 O6 P --
6MA
Query on 6MA
C, F DNA LINKING C11 H16 N5 O6 P A

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.286
  • R-Value Work: 0.228
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 59.34 α = 90.00
b = 68.82 β = 92.22
c = 114.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-10-26
  • Released Date: 2007-11-13
  • Deposition author(s): Lenz, T., Scheidig, A.J., Weinhold, E.

Revision History

  • Version 1_0: 2007-11-13

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Non-polymer description, Version format compliance

  • Version 1_2: 2017-10-18

    Type: Refinement description