3K5M

Crystal structure of E.coli Pol II-abasic DNA-ddGTP Lt(-2, 2) ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.243

Literature

Macromolecules
Sequence Display for 3K5M

Classification: TRANSFERASE / DNA

Total Structure Weight: 101033.55


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase II A 786 Escherichia coli EC#: 2.7.7.7 IUBMB
Mutation: D335N
Gene Name(s): polB dinA b0060 JW0059
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*AP*GP*TP*CP*CP*TP*GP*(3DR)P*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3') T 20 synthetic Abasic Lt(-2, 2) template
DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*GP*CP*GP*TP*AP*G)-3') P 13 synthetic Primer

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DG3
Query on DG3

A 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
HDRRAMINWIWTNU-NTSWFWBYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-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
T DNA LINKING C5 H11 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.243
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 73.11 α = 90.00
b = 95.23 β = 90.00
c = 144.74 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-10-07
  • Released Date: 2010-02-02
  • Deposition author(s): Yang, W., Wang, F.

Revision History

  • Version 1_0: 2010-02-02

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance