2OZM

Crystal structure of RB69 gp43 in complex with DNA with 5-NITP opposite an abasic site analog

Structural Biology Knowledgebase: 2OZM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.204

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2OZM

Classification: transferase / DNA

Total Structure Weight: 114871.86


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 903 Enterobacteria phage rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: D222A, D327A
Gene Name(s): 43
Macromolecule Entities
Molecule Chains Length Organism Details
Template DNA T 18 synthetic
Primer DNA P 14 synthetic

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

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
N5P
Query on N5P

A 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]- BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO-1H- INDOLE
5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE (Synonym)
C13 H17 N2 O14 P3
JJJBDAFRCKSXDR-YNEHKIRRSA-N
Ligand Explorer
 
JSmol
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
3DR
Query on 3DR
T DNA LINKING C5 H11 O6 P --
DDG
Query on DDG
P DNA LINKING C10 H14 N5 O6 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.204
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 81.23 α = 90.00
b = 117.49 β = 90.00
c = 126.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-02-26
  • Released Date: 2007-10-23
  • Deposition author(s): Zahn, K.E., Belrhali, H., Wallace, S.S., Doublie, S.

Revision History

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