4GXJ

R283K DNA polymerase beta ternary complex with a templating 8OG and incoming dCTP analog

Structural Biology Knowledgebase: 4GXJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.292
  • R-Value Work: 0.231

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GXJ

Classification: Transferase / DNA

Total Structure Weight: 48626.99


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase beta A 335 Homo sapiens EC#: 2.7.7.7 IUBMB 4.2.99 IUBMB
Mutation: R283K
Gene Name(s): POLB Gene View
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*GP*TP*CP*GP*G)-3') D 5 Synthetic construct
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3') P 10 Synthetic construct
DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') T 16 Synthetic construct

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

A 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine
C10 H16 F2 N3 O12 P3
NCCTXZHZERSHKT-SHYZEUOFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, P, T MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, D SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
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: 2.2 Å
  • R-Value Free: 0.292
  • R-Value Work: 0.231
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 55.08 α = 90.00
b = 77.43 β = 114.45
c = 55.13 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-04
  • Released Date: 2013-01-16
  • Deposition author(s): Freudenthal, B.D., Beard, W.A., Wilson, S.H.

Revision History

  • 2013-02-27
    Type: Citation | Details: Citation update