Sinkkisormi Zinc Finger. Xenopus laevis

When you go to the PDB to explore zinc fingers, try not to be overwhelmed: there are currently over a thousand structures containing all sorts of zinc fingers, knuckles, treble clefs, ribbons, and other fanciful folds. The structure shown here on the left, from PDB entry 1znf , shows a classic zinc finger. Since it's such a small structure, with only 25 amino acids, it's worth taking a closer look at what each part is doing. The two cysteines (C, C)  and two histidines (H, H)  are shown at the bottom, arranged in a tetrahedron around the zinc (Zn). Just above them, a phenylalanine (F)  and a leucine (L) form a tiny hydrophobic core inside the small folded chain. The rest of the amino acids all face more-or-less outwards, and can be used for various functional tasks. For DNA binding proteins, the amino acids at the top of the alpha helix are typically used for recognition. This is shown on the structure at right, from PDB entry 1zaa . It contains three linked zinc fingers bound to DNA. The amino acids shown in red extend towards the DNA and read the base sequence, as shown in the lower figure where the DNA is removed.

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Classic Zinc Finger
 https://www.rcsb.org/structure/1znf

Chain A, 31ST ZINC FINGER FROM XFIN

PDB: 1ZNF_A

Identical Proteins FASTA Graphics

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LOCUS       1ZNF_A                    27 aa            linear   VRT 07-MAY-2018
DEFINITION  Chain A, 31ST ZINC FINGER FROM XFIN.
ACCESSION   1ZNF_A
VERSION     1ZNF_A
DBSOURCE    pdb: molecule 1ZNF, chain 65, release Nov 29, 2017;
            deposition: Sep 25, 1989;
            class: ZINC FINGER DNA BINDING DOMAIN;
            source: Mmdb_id: 106075, Pdb_id 1: 1ZNF;
            Exp. method: Solution NMR.
KEYWORDS    .
SOURCE      Xenopus laevis (African clawed frog)
  ORGANISM  Xenopus laevis
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae;
            Xenopus; Xenopus.
REFERENCE   1  (residues 1 to 27)
  AUTHORS   Lee,M.S., Gippert,G.P., Soman,K.V., Case,D.A. and Wright,P.E.
  TITLE     Three-dimensional solution structure of a single zinc finger
            DNA-binding domain
  JOURNAL   Science 245 (4918), 635-637 (1989)
   PUBMED   2503871
REFERENCE   2  (residues 1 to 27)
  AUTHORS   Lee,M.S., Cavanagh,J. and Wright,P.E.
  TITLE     Complete assignment of the 1H NMR spectrum of a synthetic zinc
            finger from Xfin. Sequential resonance assignments and secondary
            structure
  JOURNAL   FEBS Lett. 254 (1-2), 159-164 (1989)
   PUBMED   2506074
REFERENCE   3  (residues 1 to 27)
  AUTHORS   Lee,M.S., Gippert,G.P., Soman,K.V., Case,D.A. and Wright,P.E.
  TITLE     Proton Nuclear Magnetic Resonance Assignments and Solution
            Structure of a Synthetic Zinc Finger from Xfin
  JOURNAL   (in) Lee,M.S., Gippert,G.P., Soman,K.V., Case,D.A. and Wright,P.E.
            (Eds.);
            STRUCTURE AND METHODS. V. 2. DNA PROTEIN COMPLEXES AND PROTEINS:
            83;
            Adenine Press, Albany, New York (1990)
REFERENCE   4  (residues 1 to 27)
  AUTHORS   Lee,M.S., Gippert,G.P., Soman,K.V., Case,D.A. and Wright,P.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-SEP-1989)
COMMENT     On Dec 27, 2012 this sequence version replaced gi:157834402.
            THREE-DIMENSIONAL SOLUTION STRUCTURE OF A SINGLE ZINC FINGER
            DNA-BINDING DOMAIN.
FEATURES             Location/Qualifiers
     source          1..27
                     /organism="Xenopus laevis"
                     /db_xref="taxon:8355"
     SecStr          2..5
                     /sec_str_type="sheet"
                     /note="strand 1"
     Region          4..24
                     /region_name="C2H2 Zn finger"
                     /note="C2H2 Zn finger [structural motif]"
                     /db_xref="CDD:275368"
     Het             join(bond(4),bond(7),bond(20),bond(24))
                     /heterogen="(ZN,424)"
     Site            order(4,7,20,24)
                     /site_type="other"
                     /note="Zn binding site [ion binding]"
                     /db_xref="CDD:275368"
     SecStr          7..10
                     /sec_str_type="sheet"
                     /note="strand 2"
     SecStr          13..21
                     /sec_str_type="helix"
                     /note="helix 1"
ORIGIN      
        1 xykcglcers fveksalsrh qrvhknx
//