1D9D

CRYSTALL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH SHORT DNA FRAGMENT CARRYING 2'-0-AMINOPROPYL-RNA MODIFICATIONS 5'-D(TCG)-AP(AUC)-3'

Structural Biology Knowledgebase: 1D9D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.215

Literature

Macromolecules
Sequence Display for 1D9D

Classification: TRANSFERASE / DNA RNA

Total Structure Weight: 70780.91

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
5'-D(*TP*CP*GP)-R(AP*(U31)P*(C31))-3' B 6 synthetic 3'-TERMINAL ADENOSINE, URACIL, AND CYTOSINE NUCLEOTIDES HAVE 3-AMINOPROPYL BOUND TO O2*

Small Molecules
Ligands 3 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)
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
U31
Query on U31
B RNA LINKING C12 H20 N3 O9 P U
C31
Query on C31
B RNA LINKING C12 H21 N4 O8 P C

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.215
  • Space Group: P 43

Unit Cell:

Length (Å) Angle (°)
a = 102.55 α = 90.00
b = 102.55 β = 90.00
c = 86.28 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

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4