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legend  pdf

structure nameNIKR-OPERATOR DNA COMPLEX
(Nickel-responsive regulator)
referenceSchreiter et al. Proc.Natl.Acad.Sci.Usa 103 13676 2006
sourceEscherichia coli
experimentX-ray (resolution=3.10, R-factor=0.261)
structural superfamilyACT-like;Ribbon-helix-helix;
sequence familyNikR C terminal nickel binding domain; Ribbonhelixhelix protein, copG family;
multimeric complexes2hzv_ABCD 2hzv_EFGH
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureRTT

Estimated binding specificities ?

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# IC=4.250 IC/col=0.850 n_of_columns=5 specificity:   
A |  12  60   0  12  96
C |  12  12   0   0   0
G |  12  12   0  84   0
T |  60  12  96   0   0
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: NIKR
AATAATAPubMed2hzv_A(3.02e-03)
TATTATTPubMed2hzv_A(3.02e-03)
GTATGAPubMed2hzv_A(1.30e-07), 2hzv_ABCD(2.70e-03), 2hzv_EFGH(8.90e-07)

Dendrogram of similar interfaces ?

matrix format
  
  RGTTTT------------------------------------------   L                     +----------2hzv_A    
                                                                +----------1 
  --------------RA--------------------------------   L       +--2          +----------6mrj_D    
                                                             !  ! 
  ------TAFCAG----------------RC--------FA----RAEG   L     +-3  +---------------------6dg0_A    
                                                           ! ! 
  ------DGICLGWG----------------QGKTKGFG--FGRG----   L   +-4 +------------------------4y0f_A    
                                                         ! ! 
  ----------------------IC--RCKCICEC--RC----------   L --5 +-------------------------1zzi_A    
                                                         ! 
  ----------------NCKGCA--RA----------------------   L   +--------------------------2ayg_A

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updated Fri Sep 13 16:22:13 2024