3LZI

RB69 DNA Polymerase (Y567A) ternary complex with dATP Opposite 7,8-dihydro-8-oxoguanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.206

Literature

Macromolecules
Sequence Display for 3LZI

Classification: TRANSFERASE / DNA

Total Structure Weight: 114763.80


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, Y567A
Gene Name(s): 43
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*TP*CP*AP*(8OG)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') T 18 synthetic Template DNA strand
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3') P 13 synthetic Primer DNA strand

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

A 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-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 2 Unique
ID Chains Type Formula 2D Diagram Parent
8OG
Query on 8OG
T DNA LINKING C10 H14 N5 O8 P DG
DOC
Query on DOC
P DNA LINKING C9 H14 N3 O6 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.206
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 78.15 α = 90.00
b = 117.60 β = 90.00
c = 130.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-03-01
  • Released Date: 2010-05-12
  • Deposition author(s): Wang, M., Beckman, J., Blaha, G., Wang, J., Konigsberg, W.H.

Revision History

  • Version 1_0: 2010-05-12

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Advisory, Version format compliance