3V6H

Replication of N2,3-Ethenoguanine by DNA Polymerases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Replication of n(2) ,3-ethenoguanine by DNA polymerases.

Zhao, L.Christov, P.P.Kozekov, I.D.Pence, M.G.Pallan, P.S.Rizzo, C.J.Egli, M.Guengerich, F.P.

(2012) Angew.Chem.Int.Ed.Engl. 51: 5466-5469


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase IV
A, B
348Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: dbh (dpo4)
EC: 2.7.7.7
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q97W02
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*AP*CP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')T,C18N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC))-3')P,D13N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCP
Query on DCP

Download SDF File 
Download CCD File 
A, B
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
EFG
Query on EFG
C, T
NON-POLYMERC12 H13 F N5 O7 PDG
DOC
Query on DOC
D, P
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.532α = 90.00
b = 111.267β = 102.68
c = 98.942γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-12-19 
  • Released Date: 2012-04-25 
  • Deposition Author(s): Zhao, L.

Revision History 

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2012-06-06
    Type: Database references