5VEZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 5VEZ

Classification: TRANSFERASE / DNA LIGASE / DNA

Total Structure Weight: 48306.35


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 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
XC5
Query on XC5

A 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine
C10 H18 N3 O12 P3
YSCOIIOUWFAHFY-LKEWCRSYSA-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)
NA
Query on NA

A, P 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: 2.04 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.187
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 50.47 α = 90.00
b = 79.71 β = 107.50
c = 55.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-04-06
  • 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