3V6H

Replication of N2,3-Ethenoguanine by DNA Polymerases

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

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Ligand Structure Quality Assessment 


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

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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase IVE [auth A],
F [auth B]		348Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: dbh, dpo4, SSO2448
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
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*AP*CP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')A [auth T],
C		18N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC))-3')B [auth P],
D		13N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DCP
Query on DCP
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H [auth A],
L [auth B]		2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
CA
Query on CA
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G [auth D],
K [auth A],
N [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
M [auth B],
O [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.532α = 90
b = 111.267β = 102.68
c = 98.942γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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