3L8B

Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.219

Literature

Macromolecules
Sequence Display for 3L8B

Classification: transferase / DNA

Total Structure Weight: 229359.69


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A, B 906 Escherichia virus rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: D222A, D327A
Gene Name(s): 43
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*AP*C*TP*(G35)P*TP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') C, E 18 synthetic DNA template
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*A)-3') D, F 13 synthetic DNA primer

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
G35
Query on G35
C, E DNA linking C9 H16 N5 O8 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.219
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 78.28 α = 90.00
b = 120.25 β = 95.96
c = 136.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-12-30
  • Released Date: 2010-03-09
  • Deposition author(s): Aller, P., Ye, Y., Wallace, S.S., Burrows, C.J., Doublie, S.

Revision History

  • Version 1_0: 2010-03-09

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance