my $xyz_fmt = '@30a7 @38a6 @46a6';
while ($pdbline = <IN>) {
    if ($pdbline =~ m/ZN1  LG1 X/) 
    {
        @Zn = unpack $xyz_fmt, $pdbline;
        next;
    }
    if ($pdbline =~ /^ATOM.*(OD2 ASP|NE2 HIS)/)
    {
        push @Atoms, [unpack $xyz_fmt, $pdbline];
        ...
    }
}
# ... do the calculations once we have all data.