5U2S

Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate incoming (-)3TC-TP and Ca2+.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.230

Literature

Macromolecules
Sequence Display for 5U2S

Classification: TRANSFERASE / DNA

Total Structure Weight: 49680.48


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase beta A 343 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-MER PHOSPHORYLATED DOWNSTREAM PRIMER D 5 Synthetic construct
10- MER PRIMER P 10 Synthetic construct
16- MER TEMPLATE T 16 Synthetic construct

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1RZ
Query on 1RZ

A [[(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin- 1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl- phosphoryl] phosphono hydrogen phosphate
C8 H14 N3 O12 P3 S
YLEQMGZZMCJKCN-NKWVEPMBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
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)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.230
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 54.63 α = 90.00
b = 79.45 β = 106.66
c = 55.17 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-11-30
  • Released Date: 2017-05-24
  • Deposition author(s): Vyas, R., Suo, Z.

Revision History

  • Version 1_0: 2017-05-24

    Type: Initial release

  • Version 1_1: 2017-06-14

    Type: Database references

  • Version 1_2: 2017-09-13

    Type: Author supporting evidence