Iron in PDB 6zfu: Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066
Enzymatic activity of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066
All present enzymatic activity of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066:
7.1.1.8;
Protein crystallography data
The structure of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066, PDB code: 6zfu
was solved by
K.Amporndanai,
P.M.O'neill,
W.D.Hong,
R.K.Amewu,
C.Pidathala,
N.G.Berry,
G.A.Biagini,
S.C.Leung,
S.S.Hasnain,
S.V.Antonyuk,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
89.85 /
3.50
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
210.74,
210.74,
343.935,
90,
90,
120
|
R / Rfree (%)
|
22.1 /
23.8
|
Other elements in 6zfu:
The structure of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066 also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066
(pdb code 6zfu). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066, PDB code: 6zfu:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 6zfu
Go back to
Iron Binding Sites List in 6zfu
Iron binding site 1 out
of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:104.8
occ:1.00
|
FE
|
C:HEM401
|
0.0
|
104.8
|
1.0
|
ND
|
C:HEM401
|
1.9
|
106.2
|
1.0
|
NA
|
C:HEM401
|
2.0
|
106.3
|
1.0
|
NC
|
C:HEM401
|
2.1
|
104.8
|
1.0
|
NB
|
C:HEM401
|
2.1
|
104.7
|
1.0
|
NE2
|
C:HIS83
|
2.2
|
106.4
|
1.0
|
NE2
|
C:HIS182
|
2.2
|
107.6
|
1.0
|
C4D
|
C:HEM401
|
2.9
|
107.3
|
1.0
|
C1D
|
C:HEM401
|
2.9
|
106.5
|
1.0
|
C1A
|
C:HEM401
|
3.0
|
107.2
|
1.0
|
C4C
|
C:HEM401
|
3.0
|
105.9
|
1.0
|
CE1
|
C:HIS83
|
3.1
|
107.4
|
1.0
|
C4A
|
C:HEM401
|
3.1
|
106.9
|
1.0
|
C1B
|
C:HEM401
|
3.1
|
105.4
|
1.0
|
C4B
|
C:HEM401
|
3.1
|
104.5
|
1.0
|
C1C
|
C:HEM401
|
3.1
|
104.4
|
1.0
|
CE1
|
C:HIS182
|
3.1
|
108.7
|
1.0
|
CD2
|
C:HIS83
|
3.2
|
108.5
|
1.0
|
CD2
|
C:HIS182
|
3.3
|
107.6
|
1.0
|
CHA
|
C:HEM401
|
3.3
|
107.8
|
1.0
|
CHD
|
C:HEM401
|
3.4
|
106.6
|
1.0
|
CHC
|
C:HEM401
|
3.5
|
104.4
|
1.0
|
CHB
|
C:HEM401
|
3.5
|
106.3
|
1.0
|
C2D
|
C:HEM401
|
4.2
|
107.1
|
1.0
|
C3D
|
C:HEM401
|
4.2
|
107.7
|
1.0
|
C2A
|
C:HEM401
|
4.2
|
108.2
|
1.0
|
ND1
|
C:HIS83
|
4.2
|
109.5
|
1.0
|
C3A
|
C:HEM401
|
4.3
|
107.8
|
1.0
|
C3C
|
C:HEM401
|
4.3
|
105.6
|
1.0
|
ND1
|
C:HIS182
|
4.3
|
108.1
|
1.0
|
C2C
|
C:HEM401
|
4.3
|
104.6
|
1.0
|
CG
|
C:HIS83
|
4.3
|
109.7
|
1.0
|
C2B
|
C:HEM401
|
4.3
|
105.1
|
1.0
|
C3B
|
C:HEM401
|
4.4
|
105.1
|
1.0
|
CG
|
C:HIS182
|
4.4
|
107.2
|
1.0
|
CA
|
C:GLY130
|
4.9
|
115.0
|
1.0
|
|
Iron binding site 2 out
of 5 in 6zfu
Go back to
Iron Binding Sites List in 6zfu
Iron binding site 2 out
of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe402
b:97.0
occ:1.00
|
FE
|
C:HEM402
|
0.0
|
97.0
|
1.0
|
ND
|
C:HEM402
|
1.9
|
99.2
|
1.0
|
NA
|
C:HEM402
|
2.0
|
99.5
|
1.0
|
NC
|
C:HEM402
|
2.1
|
99.8
|
1.0
|
NB
|
C:HEM402
|
2.1
|
99.1
|
1.0
|
NE2
|
C:HIS196
|
2.2
|
92.1
|
1.0
|
NE2
|
C:HIS97
|
2.2
|
98.4
|
1.0
|
C4D
|
C:HEM402
|
2.9
|
100.1
|
1.0
|
C1D
|
C:HEM402
|
2.9
|
99.8
|
1.0
|
C1A
|
C:HEM402
|
3.0
|
100.5
|
1.0
|
C4C
|
C:HEM402
|
3.0
|
100.2
|
1.0
|
C4A
|
C:HEM402
|
3.1
|
99.9
|
1.0
|
CE1
|
C:HIS97
|
3.1
|
99.9
|
1.0
|
C4B
|
C:HEM402
|
3.1
|
99.9
|
1.0
|
C1B
|
C:HEM402
|
3.1
|
99.4
|
1.0
|
CD2
|
C:HIS196
|
3.1
|
91.6
|
1.0
|
C1C
|
C:HEM402
|
3.1
|
100.8
|
1.0
|
CE1
|
C:HIS196
|
3.2
|
91.8
|
1.0
|
CD2
|
C:HIS97
|
3.3
|
99.3
|
1.0
|
CHA
|
C:HEM402
|
3.3
|
100.5
|
1.0
|
CHD
|
C:HEM402
|
3.4
|
100.3
|
1.0
|
CHB
|
C:HEM402
|
3.5
|
100.4
|
1.0
|
CHC
|
C:HEM402
|
3.5
|
101.0
|
1.0
|
C3D
|
C:HEM402
|
4.2
|
100.8
|
1.0
|
C2D
|
C:HEM402
|
4.2
|
100.0
|
1.0
|
C2A
|
C:HEM402
|
4.2
|
101.1
|
1.0
|
C3A
|
C:HEM402
|
4.2
|
100.5
|
1.0
|
ND1
|
C:HIS97
|
4.2
|
100.9
|
1.0
|
C3C
|
C:HEM402
|
4.3
|
100.6
|
1.0
|
CG
|
C:HIS196
|
4.3
|
92.0
|
1.0
|
ND1
|
C:HIS196
|
4.3
|
92.0
|
1.0
|
C2C
|
C:HEM402
|
4.3
|
100.7
|
1.0
|
CG
|
C:HIS97
|
4.3
|
100.5
|
1.0
|
C2B
|
C:HEM402
|
4.4
|
98.9
|
1.0
|
C3B
|
C:HEM402
|
4.4
|
99.4
|
1.0
|
NH2
|
C:ARG100
|
5.0
|
99.7
|
1.0
|
|
Iron binding site 3 out
of 5 in 6zfu
Go back to
Iron Binding Sites List in 6zfu
Iron binding site 3 out
of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:153.6
occ:1.00
|
FE
|
D:HEC501
|
0.0
|
153.6
|
1.0
|
NC
|
D:HEC501
|
2.1
|
158.6
|
1.0
|
NB
|
D:HEC501
|
2.1
|
153.2
|
1.0
|
NA
|
D:HEC501
|
2.1
|
151.8
|
1.0
|
NE2
|
D:HIS41
|
2.1
|
160.3
|
1.0
|
ND
|
D:HEC501
|
2.1
|
156.1
|
1.0
|
SD
|
D:MET160
|
2.4
|
171.2
|
1.0
|
CE1
|
D:HIS41
|
2.9
|
161.7
|
1.0
|
C4C
|
D:HEC501
|
3.1
|
160.8
|
1.0
|
C1C
|
D:HEC501
|
3.1
|
161.4
|
1.0
|
C4A
|
D:HEC501
|
3.1
|
151.1
|
1.0
|
C1B
|
D:HEC501
|
3.1
|
151.5
|
1.0
|
C4B
|
D:HEC501
|
3.1
|
155.9
|
1.0
|
C1D
|
D:HEC501
|
3.1
|
159.4
|
1.0
|
C4D
|
D:HEC501
|
3.1
|
155.9
|
1.0
|
C1A
|
D:HEC501
|
3.1
|
151.3
|
1.0
|
CD2
|
D:HIS41
|
3.3
|
162.6
|
1.0
|
CHB
|
D:HEC501
|
3.5
|
150.8
|
1.0
|
CHC
|
D:HEC501
|
3.5
|
159.4
|
1.0
|
CHD
|
D:HEC501
|
3.5
|
160.5
|
1.0
|
CHA
|
D:HEC501
|
3.5
|
153.2
|
1.0
|
CE
|
D:MET160
|
3.7
|
176.0
|
1.0
|
CG
|
D:MET160
|
3.8
|
174.8
|
1.0
|
ND1
|
D:HIS41
|
4.1
|
161.9
|
1.0
|
CG
|
D:HIS41
|
4.3
|
162.2
|
1.0
|
C3C
|
D:HEC501
|
4.4
|
163.4
|
1.0
|
C3B
|
D:HEC501
|
4.4
|
155.4
|
1.0
|
C3A
|
D:HEC501
|
4.4
|
149.8
|
1.0
|
C2C
|
D:HEC501
|
4.5
|
164.8
|
1.0
|
CB
|
D:MET160
|
4.5
|
172.6
|
1.0
|
C2B
|
D:HEC501
|
4.5
|
151.9
|
1.0
|
C2D
|
D:HEC501
|
4.5
|
160.7
|
1.0
|
C2A
|
D:HEC501
|
4.5
|
149.3
|
1.0
|
C3D
|
D:HEC501
|
4.5
|
157.9
|
1.0
|
|
Iron binding site 4 out
of 5 in 6zfu
Go back to
Iron Binding Sites List in 6zfu
Iron binding site 4 out
of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:288.1
occ:1.00
|
FE1
|
E:FES201
|
0.0
|
288.1
|
1.0
|
S1
|
E:FES201
|
2.2
|
291.5
|
1.0
|
S2
|
E:FES201
|
2.2
|
295.2
|
1.0
|
SG
|
E:CYS158
|
2.7
|
219.0
|
1.0
|
FE2
|
E:FES201
|
3.1
|
306.9
|
1.0
|
SG
|
E:CYS139
|
3.2
|
247.8
|
1.0
|
CB
|
E:CYS160
|
3.5
|
246.9
|
1.0
|
SG
|
E:CYS144
|
3.8
|
258.6
|
1.0
|
CB
|
E:CYS158
|
3.9
|
223.6
|
1.0
|
CB
|
E:CYS139
|
4.0
|
242.4
|
1.0
|
N
|
E:HIS161
|
4.1
|
252.3
|
1.0
|
SG
|
E:CYS160
|
4.3
|
256.4
|
1.0
|
CB
|
E:HIS161
|
4.5
|
257.2
|
1.0
|
CB
|
E:CYS144
|
4.5
|
245.5
|
1.0
|
ND1
|
E:HIS161
|
4.5
|
252.9
|
1.0
|
CA
|
E:CYS160
|
4.5
|
244.7
|
1.0
|
N
|
E:CYS160
|
4.7
|
239.8
|
1.0
|
C
|
E:CYS160
|
4.7
|
248.2
|
1.0
|
OG
|
E:SER163
|
4.8
|
242.7
|
1.0
|
CA
|
E:HIS161
|
4.9
|
256.4
|
1.0
|
CG
|
E:HIS161
|
4.9
|
256.6
|
1.0
|
CB
|
E:SER163
|
4.9
|
244.8
|
1.0
|
CB
|
E:HIS141
|
5.0
|
277.2
|
1.0
|
|
Iron binding site 5 out
of 5 in 6zfu
Go back to
Iron Binding Sites List in 6zfu
Iron binding site 5 out
of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor RKA066 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:306.9
occ:1.00
|
FE2
|
E:FES201
|
0.0
|
306.9
|
1.0
|
S1
|
E:FES201
|
2.2
|
291.5
|
1.0
|
S2
|
E:FES201
|
2.2
|
295.2
|
1.0
|
ND1
|
E:HIS141
|
2.9
|
292.4
|
1.0
|
CB
|
E:HIS161
|
3.0
|
257.2
|
1.0
|
CG
|
E:HIS161
|
3.0
|
256.6
|
1.0
|
FE1
|
E:FES201
|
3.1
|
288.1
|
1.0
|
ND1
|
E:HIS161
|
3.2
|
252.9
|
1.0
|
CB
|
E:HIS141
|
3.3
|
277.2
|
1.0
|
CG
|
E:HIS141
|
3.4
|
287.7
|
1.0
|
CD2
|
E:HIS161
|
3.7
|
258.2
|
1.0
|
CE1
|
E:HIS161
|
3.9
|
254.8
|
1.0
|
CG
|
E:PRO175
|
4.0
|
232.6
|
1.0
|
CE1
|
E:HIS141
|
4.0
|
293.7
|
1.0
|
NE2
|
E:HIS161
|
4.2
|
258.1
|
1.0
|
CA
|
E:HIS161
|
4.3
|
256.4
|
1.0
|
N
|
E:LEU142
|
4.3
|
256.0
|
1.0
|
N
|
E:HIS161
|
4.4
|
252.3
|
1.0
|
CA
|
E:HIS141
|
4.6
|
266.5
|
1.0
|
CD2
|
E:HIS141
|
4.6
|
291.4
|
1.0
|
CB
|
E:PRO175
|
4.6
|
236.5
|
1.0
|
CB
|
E:LEU142
|
4.8
|
248.9
|
1.0
|
CG
|
E:LEU142
|
4.8
|
245.6
|
1.0
|
C
|
E:HIS141
|
4.8
|
264.1
|
1.0
|
NE2
|
E:HIS141
|
4.9
|
294.3
|
1.0
|
OG
|
E:SER163
|
4.9
|
242.7
|
1.0
|
CD1
|
E:LEU142
|
5.0
|
244.2
|
1.0
|
|
Reference:
K.Amporndanai,
P.M.O'neill,
W.D.Hong,
R.K.Amewu,
C.Pidathala,
N.Berry,
G.A.Biangini,
S.C.Leung,
S.S.Hasnain,
S.V.Antonyuk.
Targeting the Ubiquinol-Reduction (Qi) Site of the Mitochondrial Cytochrome BC1 Complex For the Development of Next Generation Quinolone Antimalarials To Be Published.
Page generated: Wed Aug 7 18:24:28 2024
|