CYTOCHROME bc 1 : A BACTERIAL CYTOCHROME 403
formed between the SMA hydroxyl group and atom O ε 1 of glu271 (O 8
(OH) · · · O ε 1 = 2.7 Å ). Stigmatellin A binding turns the side chain of glu271 about
180 ° about the χ^1 dihedral angle compared to the native protein. The mostly
hydrophobic SMA tail interacts with phe274, met124, ala125, and met129. The
closest approach of SMA to a heme metal ion [between the O 8 position of
SMA and the iron ion in heme b L (O 8 · · · Fe = 14.6 Å )] is 4 Å longer than the
distance for the inhibitor myxothiazol. The reference 88 authors believe that
the PDB: 1SQX structure presents stigmatellin A in a stereochemically correct
manner, whereas earlier X - ray crystallographic structures (including PDB:
3BCC) may have represented stigmatellin incorrectly or incompletely. Muta-
tions in or near stigmatellin A ’ s binding pocket in cytochrome bc 1 are known
to cause resistance to the fungicide, probably because the shape of the Q o
pocket changes and SMA binding is decreased or eliminated. In the PDB:
1SQX structure, a ubiquinone - 2 (UQ2; see Figure 7.29 ) molecule is located
near heme b H in the Q i pocket. Table 7.7 lists the interactions of this Q i site
ubiquinone - 2 molecule: (1) a carboxyl oxygen of UQ2 interacts with the
hydroxyl group of ser35 (O 1 · · · S35 O γ = 4.3 Å ); (2) a water molecule intervenes
to hydrogen bond the N ε 2 nitrogen of his201 with the UQ2 ’ s opposite carboxyl
oxygen (O 4 · · · H 2 O = 2.5 Å , H 2 O · · · H201 N (^) ε 2 = 2.6 Å ); (3) a methoxy oxygen of
UQ2 hydrogen bonds to the hydroxyl OH of ser205 (O 3 · · · S205 O γ = 3.5 Å );
and (4) a carboxyl oxygen hydrogen bonds to the O δ 2 atom of asp228 (O 1 · · · D228
Oδ 2 = 2.7 Å ). In the last case, one must assume that the O δ 2 atom of asp228 is
protonated and is the H - donor to the hydrogen bond. At physiological pH, an
aspartic acid residue is normally believed to be deprotonated, making the
side - chain carboxylic acid oxygens always hydrogen - bond acceptors. One solu-
tion is to project an intervening water molecule; however, these may not be
present at the needed site, even in crystallographic structures of suffi cient
resolution to pinpoint their positions. The conclusion must be that interpreta-
tion of hydrogen bonding scenarios for inhibitor molecules and their interac-
tions with side - chain or backbone amino acid residue atoms should be carried
out with caution. Even if the atoms are close enough to engage in hydrogen
bonding, the necessary hydrogen atom may not be present. Also, since the
crystals being studied have not necessarily been formed at physiological pH,
but instead below this, the aspartic acid residues may indeed be protonated in
the crystal with hydrogen ’ s available as H - donors to hydrogen bonds. In Table
7.7 , a footnote has been added where questions should be asked about hydro-
gen bonding partners.
In 2003, the Di Xia group published an X - ray crystallographic study of
substrate and inhibitor molecules at the Q o and Q i site.^86 They intended to
compare the structure of the native enzyme (PDB: 1NTM) with the cyto-
chrome bc 1 complex having substrate or inhibitors in the Q o and/or Q i sites.
The complex with substrate ubiquinone UQ2 (PDB: 1NTZ) was discussed
previously in this section. The complex with the inhibitor antimycin A 1 (PDB:
1NTK) will be discussed here. A fourth complex with the ubiquinone - model