1MQ2

Human DNA Polymerase Beta Complexed With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine and dAMP

Structural Biology Knowledgebase: 1MQ2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.317
  • R-Value Work: 0.257

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1MQ2

Classification: TRANSFERASE / DNA

Total Structure Weight: 48084.54


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
5'-D(*CP*CP*GP*AP*CP*(8OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' T 16 synthetic
5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(2DA))-3' P 10 synthetic
5'-D(P*GP*TP*CP*GP*G)-3' D 5 synthetic

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

T 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
8OG
Query on 8OG
T DNA LINKING C10 H14 N5 O8 P DG
2DA
Query on 2DA
P DNA LINKING C10 H14 N5 O5 P DA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.317
  • R-Value Work: 0.257
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 55.20 α = 90.00
b = 81.00 β = 106.10
c = 55.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-09-13
  • Released Date: 2003-01-28
  • Deposition author(s): Krahn, J.M., Beard, W.A., Miller, H., Grollman, A.P., Wilson, S.H.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4