5V1N

DNA polymerase beta substrate complex with 8-oxoG:A at the primer terminus and incoming dCTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 5V1N

Classification: TRANSFERASE / DNA LIGASE / DNA

Total Structure Weight: 48389.10


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
DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') T 16 Synthetic construct
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3') P 10 Synthetic construct
DNA (5'-D(P*GP*TP*CP*GP*G)-3') D 5 Synthetic construct

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DCP
Query on DCP

A 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
8OG
Query on 8OG
P DNA LINKING C10 H14 N5 O8 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.181
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 50.55 α = 90.00
b = 79.22 β = 107.32
c = 55.54 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-03-02
  • Released Date: 2017-05-10
  • Deposition author(s): Freudenthal, B.D., Schaich, M.A., Whitaker, A.M., Smith, M.R.

Revision History

No revisions since initial release