2FMP

DNA Polymerase beta with a terminated gapped DNA substrate and ddCTP with sodium in the catalytic site

Structural Biology Knowledgebase: 2FMP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.179

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2FMP

Classification: TRANSFERASE / DNA

Total Structure Weight: 48282.74


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase beta A 335 Homo sapiens EC#: 2.7.7.7 IUBMB 4.2.99 IUBMB
Gene Name(s): POLB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' T 16 synthetic
5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3' P 10 synthetic
5'-D(P*GP*TP*CP*GP*G)-3' D 5 synthetic

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

A 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
C9 H16 N3 O12 P3
ARLKCWCREKRROD-POYBYMJQSA-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)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
DOC
Query on DOC
P DNA LINKING C9 H14 N3 O6 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.179
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 50.90 α = 90.00
b = 80.40 β = 107.50
c = 55.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-01-09
  • Released Date: 2006-04-25
  • Deposition author(s): Batra, V.K., Beard, W.A., Shock, D.D., Krahn, J.M., Pedersen, L.C., Wilson, S.H.

Revision History

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