2KFN

KLENOW FRAGMENT WITH BRIDGING-SULFUR SUBSTRATE AND MANGANESE

Structural Biology Knowledgebase: 2KFN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.214

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2KFN

Classification: TRANSFERASE / DNA

Total Structure Weight: 70600.34


Macromolecule Entities
Molecule Chains Length Organism Details
KLENOW FRAGMENT OF DNA POLYMERASE I A 605 Escherichia coli EC#: 2.7.7.7 IUBMB
Fragment: LARGE 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(*GP*CP*TP*TP*AP*(US1)P*G)-3' B 7 synthetic

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

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
US1
Query on US1
B DNA LINKING C9 H13 N2 O7 P S DU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.214
  • Space Group: P 43
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 102.90 α = 90.00
b = 102.90 β = 90.00
c = 86.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-07-01
  • Released Date: 1998-11-11
  • Deposition author(s): Brautigam, C.A., Sun, S., Piccirilli, J.A., Steitz, T.A.

Revision History

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