BIOINORGANIC CHEMISTRY A Short Course Second Edition

72 BIOCHEMISTRY FUNDAMENTALS

atoms of two histidines from theα - helical region — his129 and his134 — and the
Sγ atoms of two cysteines from the β - sheet and loop region — cys113 and
cys116. In F2, the Zn(II) ion (shown in stick form) is coordinated by the N ε 2
atoms of two histidines from anα - helical region — his159 and his164 — and the
Sγ atoms of two cysteines from the β - sheet and loop region — cys143 and
cys146. Bond and interaction distances are collected in Table 2.4.
The position of amino acids in sequence, with beginning and ending residue
numbers shown, for F1 is — Y(111)X C X 2 C X 3 YX 5 FX 2 H X 4 H X 6 Y(141) — with
the zinc ion ligand atoms shown in boldface. The amino acid sequence for F2,
beginning with the right hand ending Y from the F1 sequence, is — Y(141)X C
X 2 C FX 2 FX 8 H X 4 H X 2 (166) —. The α - helical region of F1 runs from residues 123
to 134, encompassing all its DNA strand contacts and the histidine Zn(II)
ligands. The α - helical region of F2 runs from residues 153 to 164, encompassing
all its DNA strand contacts and the histidine Zn(II) ligands.
Shi and Berg have reported on zinc - fi nger proteins that bind to DNA – RNA
hybrids as well as those that bind to dsDNA.^39 Previous X - ray crystallographic
structures such as that reported in references 31 , 37 , and 38 have indicated
that zinc - fi nger proteins have more contacts with one strand of dsDNA than
with the other. Also, the structures of the DNA strands in complexes with
zinc - fi nger proteins have characteristics of both A - and B - form DNA. These
fi ndings led Shi and Berg to examine the binding of two different zinc - fi nger
proteins (Sp1, a human transcription factor that contains three zinc fi ngers,
and ZF - QQR) to dsDNA, to double - stranded RNA, and to DNA – RNA
hybrids. RNA, of course, differs from DNA in the presence of the 2 ′ - OH group

TABLE 2.4 Selected Bond Lengths for the Tramtrack Zinc - Finger Protein

Coordinate - Covalent Bonds

Cysteine Histidine

S γ – Zn(II)( Å ) N ε 2 – Zn(II)( Å )
cys143 2.26 his159 2.03
cys146 2.28 his164 1.95

Hydrogen Bonds in the F1 Zinc - Finger Domain

Bonding Atoms Bond Length ( Å )

ser124 (H of OH group, O γ ) with T11 (O at position 4, O 4 ) 2.89
asn125 O δ 1 with A10 (H of NH 2 at position 6, N 6 ) 2.97
arg128 (H of NH 2 side chain, N H1 ) with G9 (O at position 6, O 6 ) 2.73

Hydrogen Bonds in the F2 Zinc - Finger Domain

Bonding Atoms Bond Length ( Å )

arg152 (H of NH 2 side chain, N H2 ) with G8 (O at position 6, O 6 ) 2.80
asp154 O δ 2 with C32 (H of NH 2 at position 4, N 4 ) 2.98
asn155 O δ 1 with A10 (H of NH 2 at position 6, N 6 ) 3.17