1ZYQ

T7 DNA polymerase in complex with 8oG and incoming ddATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.272
  • R-Value Work: 0.224

Literature

Macromolecules
Sequence Display for 1ZYQ

Classification: TRANSFERASE / ELECTRON TRANSPORT / DNA

Total Structure Weight: 105970.63


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 698 Escherichia virus t7 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: ΔK118, ΔR119, ΔF120, ΔG121, ΔS122, ΔH123, K536A
Gene Name(s): 5
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Thioredoxin 1 B 108 Escherichia coli Gene Name(s): trxA fipA tsnC b3781 JW5856
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(DDG))-3' P 22 synthetic PRIMER STRAND
5'-D(*CP*CP*CP*(8OG)P*CP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3' T 26 synthetic TEMPLATE STRAND

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

A 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O11 P3
OAKPWEUQDVLTCN-RQJHMYQMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
DDG
Query on DDG
P DNA LINKING C10 H14 N5 O6 P DG
8OG
Query on 8OG
T DNA LINKING C10 H14 N5 O8 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.272
  • R-Value Work: 0.224
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 106.15 α = 90.00
b = 213.01 β = 90.00
c = 52.99 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-06-10
  • Released Date: 2005-11-22
  • Deposition author(s): Brieba, L.G., Kokoska, R.J., Bebenek, K., Kunkel, T.A., Ellenberger, T.

Revision History

  • Version 1_0: 2005-11-22

    Type: Initial release

  • Version 1_1: 2008-04-30

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance