5U9H

DNA polymerase beta product complex with inserted Sp-isomer of dCTP-alpha-S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 5U9H

Classification: TRANSFERASE / DNA

Total Structure Weight: 48433.83


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*GP*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*CP*(C7R))-3') P 11 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
PPV
Query on PPV

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

A, T MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-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)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
C7R
Query on C7R
P DNA linking C9 H14 N3 O6 P S DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.194
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 50.98 α = 90.00
b = 80.05 β = 108.05
c = 55.07 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-12-16
  • Released Date: 2017-02-08
  • Deposition author(s): Freudenthal, B.D., Wilson, S.H., Beard, W.A.

Revision History

  • 2017-05-03
    Type: Database references