structure nameCRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE ECORII CATALYTIC C- TERMINAL DOMAIN IN COMPLEX WITH COGNATE DNA
(Type-2 restriction enzyme EcoRII)
referenceTamulaitiene et al.
sourceEscherichia coli
experimentX-ray (resolution=2.60, R-factor=0.242)
structural superfamilyRestriction endonuclease-like;
sequence familyEcoRII C terminal;
reference complex3hqf_A
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureREYFRKSRASKDR

Estimated binding specificities ?

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# IC=5.105 IC/col=1.021 n_of_columns=5 specificity:   
A |  19   0  96   0   2
C |  38  96   0   0   2
G |  19   0   0  96  90
T |  20   0   0   0   2
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: EcoRII
CCNGGPubMed3hqg_A(1.35e-04)
CCAGGPubMed3hqg_A(2.56e-08)
CCTGGPubMed3hqg_A(2.56e-08)
CCATGGPubMed3hqg_A(2.63e-03)
CCTAGGPubMed3hqg_A(2.63e-03)
ACTGGGPubMed3hqg_A(3.56e-04)
CCNGGAPubMed3hqg_A(3.56e-04)
CCGGGPubMed3hqg_A(1.18e-03)

Dendrogram of similar interfaces ?

matrix format
  
  RAEAYAFA--------RAKCSCRAAASA----KGDGRG--   L            +------------------3hqg_A    
                                                   +------1 
  --------QGFCACKG--------------RGKGECVCRT   L   +-2      +------------------6eko_A    
                                                 ! ! 
  ----------------LT----------RT--EG------     --3 +-------------------------5gke_A    
                                                 ! 
  ------------------------------------ET--       +---------------------------6g3b_A

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updated Thu Jan 8 21:44:46 2026