3SPZ

DNA Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with dUpCpp Opposite dA (Ca2+)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 3SPZ

Classification: TRANSFERASE / DNA

Total Structure Weight: 113991.15


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 903 Escherichia virus rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: D222A, D327A, L415A, L561A, S565G, Y567A
Gene Name(s): 43
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(P*GP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3' T 16 synthetic template
5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3' P 13 synthetic primer

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

A 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine
C10 H17 N2 O13 P3
CLYYXAGDTAZMBH-LKEWCRSYSA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.200
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 78.17 α = 90.00
b = 119.06 β = 90.00
c = 130.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-07-04
  • Released Date: 2011-10-12
  • Deposition author(s): Xia, S., Konigsberg, W.H., Wang, J.

Revision History

  • Version 1_0: 2011-10-12

    Type: Initial release

  • Version 1_1: 2011-11-02

    Type: Database references