5VRZ

Human DNA polymerase beta 8-oxoG:dC extension with dTTP after 60 s


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 5VRZ

Classification: transferase lyase / dna

Total Structure Weight: 49854.66


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase beta A 341 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*AP*(8OG)P*GP*CP*GP*CP*AP*TP*CP*AP*G)-3') T 16 Synthetic construct
DNA (5'-D(*CP*TP*GP*AP*TP*GP*CP*GP*CP*CP*T)-3') P 11 Synthetic construct
DNA (5'-D(P*GP*TP*CP*GP*G)-3') D 5 Synthetic construct

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TTP
Query on TTP

P THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PPV
Query on PPV

P PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IMD
Query on IMD

A IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
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)
MG
Query on MG

P MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

D 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
T DNA LINKING C10 H14 N5 O8 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.197
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 50.70 α = 90.00
b = 79.80 β = 107.20
c = 55.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-05-11
  • Released Date: 2017-07-19
  • Deposition author(s): Reed, A.J., Suo, Z.

Revision History

  • Version 1_0: 2017-07-19

    Type: Initial release

  • Version 1_1: 2017-07-26

    Type: Database references

  • Version 1_2: 2017-11-22

    Type: Refinement description