InterPro : IPR007087

Name  Zinc finger, C2H2 Short Name  Znf_C2H2
Type  Domain Description  Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis(African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter [].This entry represents the classical C2H2 zinc finger domain.

Sequence Features

GO Displayer


InterPro protein domain ID --> Contigs



0 Child Features

1 Contains

Id Name Short Name Type
IPR015318 Zinc finger, GAGA-binding factor Znf_GAGA-bd_fac Domain

13 Found In

Id Name Short Name Type
IPR007042 Arsenite-resistance protein 2 Arsenite-R_2 Domain
IPR013087 Zinc finger C2H2-type/integrase DNA-binding domain Znf_C2H2/integrase_DNA-bd Domain
IPR004595 TFIIH C1-like domain TFIIH_C1-like_dom Domain
IPR016378 Transcription factor cyclic AMP-dependent, CRE-BP1-type TF_CRE-BP1-typ Family
IPR016766 Transcription regulator Tri6 Tscrpt_reg_Tri6 Family
IPR009170 Predicted retinoblastoma binding protein (RIZ) RIZ_retinblastoma-bd_prot Family
IPR017124 PR-domain zinc finger protein PRDM4 Znf_PRDM4 Family
IPR017125 PR-domain zinc finger protein PRDM5 Znf_PRDM5 Family
IPR017126 PR-domain zinc finger protein PRDM12 Znf_PRDM12 Family
IPR017083 RNA editing complex, nuclease subunit MP42 RNA_edit_cplx_Nase-su_MP42 Family
IPR017085 RNA editing complex, structural subunit MP81 RNA_edit_cplx_Nase-su_MP81 Family
IPR017086 RNA editing complex, structural subunit MP63 RNA_edit_cplx_Nase-su_MP63 Family
IPR017114 Transcription factor yin/yang TF_Yin_yang Family

1 Parent Features

Id Name Short Name Type
IPR015880 Zinc finger, C2H2-like Znf_C2H2-like Domain

7 Publications

First Author Title Year Journal Volume Pages
Matthews JM Zinc fingers--folds for many occasions. 2002 IUBMB Life 54 351-5
Gamsjaeger R Sticky fingers: zinc-fingers as protein-recognition motifs. 2007 Trends Biochem Sci 32 63-70
Hall TM Multiple modes of RNA recognition by zinc finger proteins. 2005 Curr Opin Struct Biol 15 367-73
Brown RS Zinc finger proteins: getting a grip on RNA. 2005 Curr Opin Struct Biol 15 94-8
Klug A Zinc finger peptides for the regulation of gene expression. 1999 J Mol Biol 293 215-8
Laity JH Zinc finger proteins: new insights into structural and functional diversity. 2001 Curr Opin Struct Biol 11 39-46
Marco E Assessment by molecular dynamics simulations of the structural determinants of DNA-binding specificity for transcription factor Sp1. 2003 J Mol Biol 328 9-32

To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)