Iron in PDB 6zfs: Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4
Enzymatic activity of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4
All present enzymatic activity of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4:
7.1.1.8;
Protein crystallography data
The structure of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4, PDB code: 6zfs
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)
|
90.74 /
3.50
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
209.56,
209.56,
343.348,
90,
90,
120
|
R / Rfree (%)
|
21.7 /
24.6
|
Other elements in 6zfs:
The structure of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4 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 Wdh-1U-4
(pdb code 6zfs). 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 Wdh-1U-4, PDB code: 6zfs:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 6zfs
Go back to
Iron Binding Sites List in 6zfs
Iron binding site 1 out
of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4
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 Wdh-1U-4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:107.7
occ:1.00
|
FE
|
C:HEM401
|
0.0
|
107.7
|
1.0
|
ND
|
C:HEM401
|
1.9
|
109.3
|
1.0
|
NA
|
C:HEM401
|
2.0
|
109.0
|
1.0
|
NC
|
C:HEM401
|
2.1
|
108.0
|
1.0
|
NB
|
C:HEM401
|
2.1
|
107.9
|
1.0
|
NE2
|
C:HIS83
|
2.2
|
108.7
|
1.0
|
NE2
|
C:HIS182
|
2.2
|
108.5
|
1.0
|
C4D
|
C:HEM401
|
2.9
|
110.0
|
1.0
|
C1D
|
C:HEM401
|
2.9
|
109.3
|
1.0
|
C1A
|
C:HEM401
|
3.0
|
109.8
|
1.0
|
C4C
|
C:HEM401
|
3.0
|
108.7
|
1.0
|
CE1
|
C:HIS83
|
3.1
|
109.0
|
1.0
|
C4A
|
C:HEM401
|
3.1
|
109.2
|
1.0
|
CE1
|
C:HIS182
|
3.1
|
109.0
|
1.0
|
C4B
|
C:HEM401
|
3.1
|
107.9
|
1.0
|
C1B
|
C:HEM401
|
3.1
|
108.2
|
1.0
|
C1C
|
C:HEM401
|
3.1
|
108.2
|
1.0
|
CD2
|
C:HIS83
|
3.2
|
110.0
|
1.0
|
CD2
|
C:HIS182
|
3.3
|
108.6
|
1.0
|
CHA
|
C:HEM401
|
3.3
|
110.1
|
1.0
|
CHD
|
C:HEM401
|
3.4
|
109.0
|
1.0
|
CHB
|
C:HEM401
|
3.5
|
108.7
|
1.0
|
CHC
|
C:HEM401
|
3.5
|
107.9
|
1.0
|
C3D
|
C:HEM401
|
4.2
|
110.2
|
1.0
|
C2D
|
C:HEM401
|
4.2
|
109.7
|
1.0
|
C2A
|
C:HEM401
|
4.2
|
110.4
|
1.0
|
ND1
|
C:HIS83
|
4.2
|
110.0
|
1.0
|
ND1
|
C:HIS182
|
4.2
|
109.0
|
1.0
|
C3A
|
C:HEM401
|
4.2
|
110.1
|
1.0
|
C3C
|
C:HEM401
|
4.3
|
109.0
|
1.0
|
C2C
|
C:HEM401
|
4.3
|
108.7
|
1.0
|
CG
|
C:HIS83
|
4.3
|
110.4
|
1.0
|
C2B
|
C:HEM401
|
4.3
|
108.0
|
1.0
|
CG
|
C:HIS182
|
4.3
|
108.4
|
1.0
|
C3B
|
C:HEM401
|
4.4
|
107.7
|
1.0
|
CA
|
C:GLY130
|
4.9
|
117.0
|
1.0
|
|
Iron binding site 2 out
of 5 in 6zfs
Go back to
Iron Binding Sites List in 6zfs
Iron binding site 2 out
of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4
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 Wdh-1U-4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe402
b:95.9
occ:1.00
|
FE
|
C:HEM402
|
0.0
|
95.9
|
1.0
|
ND
|
C:HEM402
|
1.9
|
96.6
|
1.0
|
NA
|
C:HEM402
|
2.0
|
96.6
|
1.0
|
NC
|
C:HEM402
|
2.1
|
96.6
|
1.0
|
NB
|
C:HEM402
|
2.1
|
96.3
|
1.0
|
NE2
|
C:HIS196
|
2.2
|
96.8
|
1.0
|
NE2
|
C:HIS97
|
2.2
|
97.7
|
1.0
|
C4D
|
C:HEM402
|
2.9
|
96.8
|
1.0
|
C1D
|
C:HEM402
|
2.9
|
96.8
|
1.0
|
C1A
|
C:HEM402
|
3.0
|
96.7
|
1.0
|
CD2
|
C:HIS196
|
3.0
|
97.2
|
1.0
|
C4C
|
C:HEM402
|
3.0
|
96.9
|
1.0
|
C4A
|
C:HEM402
|
3.1
|
96.7
|
1.0
|
CE1
|
C:HIS97
|
3.1
|
98.3
|
1.0
|
C4B
|
C:HEM402
|
3.1
|
96.5
|
1.0
|
C1B
|
C:HEM402
|
3.1
|
96.6
|
1.0
|
C1C
|
C:HEM402
|
3.1
|
96.9
|
1.0
|
CD2
|
C:HIS97
|
3.2
|
98.7
|
1.0
|
CE1
|
C:HIS196
|
3.2
|
98.1
|
1.0
|
CHA
|
C:HEM402
|
3.3
|
96.7
|
1.0
|
CHD
|
C:HEM402
|
3.4
|
96.9
|
1.0
|
CHB
|
C:HEM402
|
3.5
|
96.9
|
1.0
|
CHC
|
C:HEM402
|
3.5
|
96.9
|
1.0
|
C2D
|
C:HEM402
|
4.2
|
96.9
|
1.0
|
C3D
|
C:HEM402
|
4.2
|
97.1
|
1.0
|
CG
|
C:HIS196
|
4.2
|
98.1
|
1.0
|
C2A
|
C:HEM402
|
4.2
|
96.9
|
1.0
|
ND1
|
C:HIS97
|
4.2
|
98.9
|
1.0
|
ND1
|
C:HIS196
|
4.2
|
98.5
|
1.0
|
C3A
|
C:HEM402
|
4.2
|
96.6
|
1.0
|
C3C
|
C:HEM402
|
4.3
|
97.5
|
1.0
|
C2C
|
C:HEM402
|
4.3
|
97.1
|
1.0
|
CG
|
C:HIS97
|
4.3
|
99.1
|
1.0
|
C2B
|
C:HEM402
|
4.3
|
96.5
|
1.0
|
C3B
|
C:HEM402
|
4.4
|
96.5
|
1.0
|
|
Iron binding site 3 out
of 5 in 6zfs
Go back to
Iron Binding Sites List in 6zfs
Iron binding site 3 out
of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4
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 Wdh-1U-4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:151.6
occ:1.00
|
FE
|
D:HEC501
|
0.0
|
151.6
|
1.0
|
NE2
|
D:HIS41
|
2.1
|
150.8
|
1.0
|
NB
|
D:HEC501
|
2.1
|
150.0
|
1.0
|
NA
|
D:HEC501
|
2.1
|
149.5
|
1.0
|
NC
|
D:HEC501
|
2.1
|
155.8
|
1.0
|
ND
|
D:HEC501
|
2.1
|
152.9
|
1.0
|
SD
|
D:MET160
|
2.4
|
163.4
|
1.0
|
CE1
|
D:HIS41
|
2.8
|
149.1
|
1.0
|
C1B
|
D:HEC501
|
3.1
|
148.5
|
1.0
|
C4A
|
D:HEC501
|
3.1
|
148.8
|
1.0
|
C4B
|
D:HEC501
|
3.1
|
151.8
|
1.0
|
C4C
|
D:HEC501
|
3.1
|
157.8
|
1.0
|
C1C
|
D:HEC501
|
3.1
|
157.9
|
1.0
|
C1D
|
D:HEC501
|
3.1
|
155.3
|
1.0
|
C1A
|
D:HEC501
|
3.1
|
149.1
|
1.0
|
C4D
|
D:HEC501
|
3.1
|
152.1
|
1.0
|
CD2
|
D:HIS41
|
3.2
|
150.0
|
1.0
|
CHB
|
D:HEC501
|
3.4
|
147.9
|
1.0
|
CHC
|
D:HEC501
|
3.5
|
155.2
|
1.0
|
CHD
|
D:HEC501
|
3.5
|
156.6
|
1.0
|
CHA
|
D:HEC501
|
3.5
|
150.0
|
1.0
|
CE
|
D:MET160
|
3.7
|
167.8
|
1.0
|
CG
|
D:MET160
|
3.7
|
167.1
|
1.0
|
ND1
|
D:HIS41
|
4.0
|
148.0
|
1.0
|
CG
|
D:HIS41
|
4.2
|
148.1
|
1.0
|
CB
|
D:MET160
|
4.4
|
166.5
|
1.0
|
C3B
|
D:HEC501
|
4.4
|
151.3
|
1.0
|
C3C
|
D:HEC501
|
4.4
|
160.7
|
1.0
|
C2B
|
D:HEC501
|
4.4
|
149.4
|
1.0
|
C3A
|
D:HEC501
|
4.4
|
147.9
|
1.0
|
C2A
|
D:HEC501
|
4.5
|
147.5
|
1.0
|
C2C
|
D:HEC501
|
4.5
|
161.0
|
1.0
|
C2D
|
D:HEC501
|
4.5
|
156.0
|
1.0
|
C3D
|
D:HEC501
|
4.5
|
153.3
|
1.0
|
|
Iron binding site 4 out
of 5 in 6zfs
Go back to
Iron Binding Sites List in 6zfs
Iron binding site 4 out
of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4
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 Wdh-1U-4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:254.2
occ:1.00
|
FE1
|
E:FES201
|
0.0
|
254.2
|
1.0
|
S1
|
E:FES201
|
2.2
|
258.3
|
1.0
|
S2
|
E:FES201
|
2.2
|
263.4
|
1.0
|
SG
|
E:CYS158
|
2.7
|
200.3
|
1.0
|
SG
|
E:CYS139
|
3.0
|
218.7
|
1.0
|
FE2
|
E:FES201
|
3.1
|
267.9
|
1.0
|
CB
|
E:CYS160
|
3.6
|
218.2
|
1.0
|
CB
|
E:CYS139
|
3.6
|
214.8
|
1.0
|
CB
|
E:CYS158
|
3.8
|
199.5
|
1.0
|
SG
|
E:CYS144
|
3.9
|
223.3
|
1.0
|
N
|
E:HIS161
|
4.1
|
215.7
|
1.0
|
SG
|
E:CYS160
|
4.4
|
221.7
|
1.0
|
CB
|
E:CYS144
|
4.4
|
219.8
|
1.0
|
CA
|
E:CYS160
|
4.6
|
215.5
|
1.0
|
CB
|
E:HIS161
|
4.6
|
216.7
|
1.0
|
ND1
|
E:HIS161
|
4.6
|
214.5
|
1.0
|
OG
|
E:SER163
|
4.7
|
205.2
|
1.0
|
N
|
E:CYS160
|
4.8
|
211.9
|
1.0
|
C
|
E:CYS160
|
4.8
|
216.6
|
1.0
|
CB
|
E:HIS141
|
4.9
|
241.5
|
1.0
|
CB
|
E:SER163
|
4.9
|
202.7
|
1.0
|
CA
|
E:HIS161
|
4.9
|
215.3
|
1.0
|
|
Iron binding site 5 out
of 5 in 6zfs
Go back to
Iron Binding Sites List in 6zfs
Iron binding site 5 out
of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4
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 Wdh-1U-4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:267.9
occ:1.00
|
FE2
|
E:FES201
|
0.0
|
267.9
|
1.0
|
S1
|
E:FES201
|
2.2
|
258.3
|
1.0
|
S2
|
E:FES201
|
2.2
|
263.4
|
1.0
|
ND1
|
E:HIS141
|
2.8
|
251.9
|
1.0
|
CB
|
E:HIS161
|
2.9
|
216.7
|
1.0
|
CG
|
E:HIS161
|
3.1
|
216.8
|
1.0
|
FE1
|
E:FES201
|
3.1
|
254.2
|
1.0
|
ND1
|
E:HIS161
|
3.2
|
214.5
|
1.0
|
CB
|
E:HIS141
|
3.3
|
241.5
|
1.0
|
CG
|
E:HIS141
|
3.4
|
248.9
|
1.0
|
CD2
|
E:HIS161
|
3.9
|
216.9
|
1.0
|
CE1
|
E:HIS141
|
3.9
|
254.1
|
1.0
|
CG
|
E:PRO175
|
4.0
|
199.7
|
1.0
|
CE1
|
E:HIS161
|
4.1
|
213.8
|
1.0
|
CA
|
E:HIS161
|
4.2
|
215.3
|
1.0
|
N
|
E:LEU142
|
4.3
|
225.2
|
1.0
|
N
|
E:HIS161
|
4.3
|
215.7
|
1.0
|
NE2
|
E:HIS161
|
4.4
|
215.5
|
1.0
|
CB
|
E:LEU142
|
4.6
|
220.4
|
1.0
|
CD2
|
E:HIS141
|
4.6
|
252.5
|
1.0
|
CA
|
E:HIS141
|
4.6
|
232.8
|
1.0
|
CB
|
E:PRO175
|
4.7
|
199.8
|
1.0
|
NE2
|
E:HIS141
|
4.8
|
255.0
|
1.0
|
C
|
E:HIS141
|
4.8
|
230.0
|
1.0
|
OG
|
E:SER163
|
4.9
|
205.2
|
1.0
|
N
|
E:GLY162
|
4.9
|
206.2
|
1.0
|
C
|
E:HIS161
|
5.0
|
211.4
|
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 18:24:23 2024
|