BIOINORGANIC CHEMISTRY A Short Course Second Edition

CYTOCHROME bc 1 : A BACTERIAL CYTOCHROME 401

Q

Site o

PDB No.(Substrate/Inhibitor)

Ar - Ar or

hydrophobic

contacts

his161 (H161)

(from ISP, [2Fe - 2S]

ligand) (

Å )

glu271 (E271) (from cyto b, EF loop) ( Å )

tyr273 (Y273) (from cyto b, EF loop) ( Å )

Q

Site i

PDB(substrate/inhibitor)

Ar - Ar or

hydrophobic

contacts

ser35 S35

(from helix A)

his201 H201(from helix D)

ser205 S205

(from helix D)

lys227 K227(from helix E)

asp228 D228(from helix E)

1NTZ(substrate

ubiquinone - 2 (UQ2)

Ar - Ar with

phe220

O

· · · H 4

O = 3.4, 2

H

O · · · H201 N 2

= 2.6 ε 2

O

· · · S205 O 4

= γ

4.0,

O

· · · S205 O 3

= γ

2.7 Å

O

· · · H 1

O = 3.6, 2

H

O · · · K227 N 2

ζ

= 3.3

O

· · · D228 O 1

δ^2

= 2.5

a

1SQX(substrate

ubiquinone - 2, UQ2)

O

· · · S35 O 1

= 4.3 γ

O

· · · H 4

O = 2.5, 2

H

O · · · H201 N 2

= 2.6 ε 2

O

· · · S205 O 3

= γ

3.5

not involved

O

· · · D228 O 1

δ^2

= 2.7

a

1PP9(substrate

ubiquinone - 10, UQ)

Ar - Ar with

phe220

O

· · · H 1

O = 3.2, 2

H

O · · · S35 O 2

= 3.0 γ

O

· · · H201 N 4

= 2.3 ε 2

O

· · · S205 O 3

= γ

3.7

not involved

O

· · · D228 O 1

δ^2

= 2.2

a

1NTK(inhibitor

anitmycin A, AY1)

Ar - Ar with

phe220

O

· · · S35 O 3

= 3.0,γ

O

· · · S35 O 7

= 3.7 γ

N

· · · H 2

O = 2.5, 2

H

O · · · H 2

O = 2.8, 2

H

O · · · H201 N 2

= 2.5 ε 2

not involved

O

· · · K227 N 1

= ζ

3.7

O

· · · D228 O 2

δ^2

= 2.3

b

N

· · · D228 O 1

δ^1

= 3.0

1PPJ(inhibitor

antimycin A, ANY)

O

· · · H 1

O 2

222

= 2.9,

H

O 2

222

· · · S35 O

= γ

3.0

O

· · · H 3

O = 2.8 2

H

O 2

1473

· · · H201 N

= ε 2

2.7

not involved

O

· · · H 2

O 2

119

=

2.6,

H

O 2

119

· · · K227

N

= 2.7 ζ

O

· · · D228 O 1

δ^2

= 2.6,

N

· · · D228 O 1

δ^1

= 2.8

a The H - donor is questionable in these hydrogen bonds. b The H atoms of the salicylamine hydroxyl OH (O

) must be the H - donor for both the intramolecular hydrogen bond with the amide linker carbonyl 2

group (O

) and the O 3

carboxylic acid oxygen of asp228 assuming the carboxylic acid group is deprotonated. δ 2