3V6K

Replication of N2,3-Ethenoguanine by DNA Polymerases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.234 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase IVA,
B [auth J]
347Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: dbhdpo4SSO2448
EC: 2.7.7.7
UniProt
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97W02 
Go to UniProtKB:  Q97W02
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97W02
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*AP*AP*GP*GP*AP*TP*TP*CP*(2DT))-3')C [auth P],
E [auth K]
10N/A
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*AP*CP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*C)-3')D [auth B],
F [auth M]
14N/A
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
N [auth J]
P [auth J]
I [auth A],
J [auth A],
K [auth A],
N [auth J],
P [auth J],
Q [auth J],
R [auth J]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
M [auth J],
O [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
L [auth A],
S [auth J],
T [auth P],
U [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.855α = 90
b = 110.953β = 102.7
c = 100.238γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2012-06-06
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description