1D9F

CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA TETRAMER CARRYING 2'-O-(3-AMINOPROPYL)-RNA MODIFICATION 5'-D(TT)-AP(U)-D(T)-3'


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.224

Literature

Macromolecules
Sequence Display for 1D9F

Classification: TRANSFERASE / DNA RNA

Total Structure Weight: 69874.30

Macromolecule Entities
Molecule Chains Length Organism Details
DNA POLYMERASE I A 605 Escherichia coli EC#: 2.7.7.7 IUBMB
Fragment: KLENOW FRAGMENT
Mutation: V324M
Gene Name(s): polA resA b3863 JW3835
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA/RNA (5'-D(*TP*TP)-R(*(U31)P)-D(*T)-3') B 4 synthetic URACIL HAS 3-AMINOPROPYL BOUND TO O2*

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
U31
Query on U31
B RNA LINKING C12 H20 N3 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.224
  • Space Group: P 43

Unit Cell:

Length (Å) Angle (°)
a = 102.65 α = 90.00
b = 102.65 β = 90.00
c = 86.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-10-27
  • Released Date: 1999-12-02
  • Deposition author(s): Teplova, M., Wallace, S.T., Tereshko, V., Minasov, G., Simons, A.M., Cook, P.D., Manoharan, M., Egli, M.

Revision History

  • Version 1_0: 1999-12-02

    Type: Initial release

  • Version 1_1: 2008-04-27

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance