Iron in PDB 7r3v: Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.
Enzymatic activity of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.
All present enzymatic activity of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.:
7.1.1.8;
Protein crystallography data
The structure of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67., PDB code: 7r3v
was solved by
N.Pinthong,
K.Amporndanai,
P.M.O'neill,
S.S.Hasnain,
S.Antonyuk,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.86 /
3.20
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
209.589,
209.589,
342.429,
90,
90,
120
|
R / Rfree (%)
|
20.5 /
25.6
|
Other elements in 7r3v:
The structure of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67. 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 Inhibitor Ck-2-67.
(pdb code 7r3v). 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 Inhibitor Ck-2-67., PDB code: 7r3v:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 7r3v
Go back to
Iron Binding Sites List in 7r3v
Iron binding site 1 out
of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.
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 Inhibitor Ck-2-67. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:62.4
occ:1.00
|
FE
|
C:HEM401
|
0.0
|
62.4
|
1.0
|
ND
|
C:HEM401
|
1.9
|
60.5
|
1.0
|
NA
|
C:HEM401
|
2.0
|
70.5
|
1.0
|
NC
|
C:HEM401
|
2.0
|
65.2
|
1.0
|
NB
|
C:HEM401
|
2.1
|
63.9
|
1.0
|
NE2
|
C:HIS83
|
2.2
|
59.6
|
1.0
|
NE2
|
C:HIS182
|
2.2
|
50.9
|
1.0
|
C4D
|
C:HEM401
|
2.9
|
67.6
|
1.0
|
C1D
|
C:HEM401
|
2.9
|
57.0
|
1.0
|
C1A
|
C:HEM401
|
3.0
|
69.8
|
1.0
|
CE1
|
C:HIS83
|
3.0
|
65.1
|
1.0
|
C4C
|
C:HEM401
|
3.0
|
67.3
|
1.0
|
CE1
|
C:HIS182
|
3.0
|
58.0
|
1.0
|
C4B
|
C:HEM401
|
3.1
|
69.1
|
1.0
|
C4A
|
C:HEM401
|
3.1
|
72.3
|
1.0
|
C1B
|
C:HEM401
|
3.1
|
70.3
|
1.0
|
C1C
|
C:HEM401
|
3.1
|
67.8
|
1.0
|
CD2
|
C:HIS182
|
3.2
|
53.8
|
1.0
|
CD2
|
C:HIS83
|
3.2
|
60.3
|
1.0
|
CHA
|
C:HEM401
|
3.3
|
71.6
|
1.0
|
CHD
|
C:HEM401
|
3.4
|
62.0
|
1.0
|
CHC
|
C:HEM401
|
3.5
|
71.2
|
1.0
|
CHB
|
C:HEM401
|
3.5
|
71.7
|
1.0
|
ND1
|
C:HIS83
|
4.1
|
77.2
|
1.0
|
C2D
|
C:HEM401
|
4.2
|
63.5
|
1.0
|
C2A
|
C:HEM401
|
4.2
|
66.7
|
1.0
|
ND1
|
C:HIS182
|
4.2
|
65.1
|
1.0
|
C3D
|
C:HEM401
|
4.2
|
69.4
|
1.0
|
C3A
|
C:HEM401
|
4.2
|
68.6
|
1.0
|
C3C
|
C:HEM401
|
4.2
|
69.7
|
1.0
|
C2C
|
C:HEM401
|
4.3
|
73.4
|
1.0
|
CG
|
C:HIS83
|
4.3
|
67.7
|
1.0
|
C2B
|
C:HEM401
|
4.3
|
70.6
|
1.0
|
CG
|
C:HIS182
|
4.3
|
57.2
|
1.0
|
C3B
|
C:HEM401
|
4.3
|
72.3
|
1.0
|
NE2
|
C:GLN44
|
4.9
|
64.4
|
1.0
|
CA
|
C:GLY130
|
4.9
|
70.0
|
1.0
|
|
Iron binding site 2 out
of 5 in 7r3v
Go back to
Iron Binding Sites List in 7r3v
Iron binding site 2 out
of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.
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 Inhibitor Ck-2-67. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe402
b:51.8
occ:1.00
|
FE
|
C:HEM402
|
0.0
|
51.8
|
1.0
|
ND
|
C:HEM402
|
1.9
|
56.8
|
1.0
|
NA
|
C:HEM402
|
2.0
|
64.3
|
1.0
|
NB
|
C:HEM402
|
2.0
|
55.8
|
1.0
|
NC
|
C:HEM402
|
2.0
|
56.3
|
1.0
|
NE2
|
C:HIS196
|
2.2
|
43.8
|
1.0
|
NE2
|
C:HIS97
|
2.2
|
55.5
|
1.0
|
C4D
|
C:HEM402
|
2.9
|
57.1
|
1.0
|
C1D
|
C:HEM402
|
2.9
|
56.5
|
1.0
|
C1A
|
C:HEM402
|
3.0
|
63.9
|
1.0
|
C4C
|
C:HEM402
|
3.0
|
56.0
|
1.0
|
C4B
|
C:HEM402
|
3.0
|
67.3
|
1.0
|
CE1
|
C:HIS97
|
3.0
|
60.5
|
1.0
|
C1B
|
C:HEM402
|
3.0
|
58.6
|
1.0
|
C1C
|
C:HEM402
|
3.1
|
59.5
|
1.0
|
C4A
|
C:HEM402
|
3.1
|
63.9
|
1.0
|
CD2
|
C:HIS196
|
3.1
|
46.1
|
1.0
|
CE1
|
C:HIS196
|
3.2
|
52.9
|
1.0
|
CD2
|
C:HIS97
|
3.2
|
52.6
|
1.0
|
CHD
|
C:HEM402
|
3.3
|
54.1
|
1.0
|
CHA
|
C:HEM402
|
3.4
|
56.6
|
1.0
|
CHC
|
C:HEM402
|
3.4
|
64.2
|
1.0
|
CHB
|
C:HEM402
|
3.5
|
66.8
|
1.0
|
ND1
|
C:HIS97
|
4.1
|
63.3
|
1.0
|
C3D
|
C:HEM402
|
4.2
|
63.3
|
1.0
|
C2A
|
C:HEM402
|
4.2
|
56.6
|
1.0
|
C2D
|
C:HEM402
|
4.2
|
62.5
|
1.0
|
C3C
|
C:HEM402
|
4.2
|
60.8
|
1.0
|
CG
|
C:HIS196
|
4.2
|
51.1
|
1.0
|
C2C
|
C:HEM402
|
4.2
|
62.3
|
1.0
|
ND1
|
C:HIS196
|
4.2
|
55.0
|
1.0
|
CG
|
C:HIS97
|
4.3
|
56.7
|
1.0
|
C3A
|
C:HEM402
|
4.3
|
54.9
|
1.0
|
C3B
|
C:HEM402
|
4.3
|
67.7
|
1.0
|
C2B
|
C:HEM402
|
4.3
|
59.0
|
1.0
|
NH2
|
C:ARG100
|
5.0
|
68.0
|
1.0
|
|
Iron binding site 3 out
of 5 in 7r3v
Go back to
Iron Binding Sites List in 7r3v
Iron binding site 3 out
of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.
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 Inhibitor Ck-2-67. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:90.7
occ:1.00
|
FE
|
D:HEC501
|
0.0
|
90.7
|
1.0
|
NE2
|
D:HIS41
|
1.8
|
120.0
|
1.0
|
NB
|
D:HEC501
|
2.1
|
78.6
|
1.0
|
NA
|
D:HEC501
|
2.1
|
86.1
|
1.0
|
ND
|
D:HEC501
|
2.1
|
84.8
|
1.0
|
NC
|
D:HEC501
|
2.1
|
102.7
|
1.0
|
SD
|
D:MET160
|
2.3
|
107.1
|
1.0
|
CE1
|
D:HIS41
|
2.8
|
119.3
|
1.0
|
CD2
|
D:HIS41
|
2.9
|
120.0
|
1.0
|
C4B
|
D:HEC501
|
3.0
|
85.4
|
1.0
|
C1B
|
D:HEC501
|
3.1
|
78.4
|
1.0
|
C4A
|
D:HEC501
|
3.1
|
92.2
|
1.0
|
C4D
|
D:HEC501
|
3.1
|
91.3
|
1.0
|
C1A
|
D:HEC501
|
3.1
|
83.8
|
1.0
|
C1C
|
D:HEC501
|
3.1
|
108.2
|
1.0
|
C1D
|
D:HEC501
|
3.1
|
79.8
|
1.0
|
C4C
|
D:HEC501
|
3.1
|
108.5
|
1.0
|
CHC
|
D:HEC501
|
3.4
|
100.3
|
1.0
|
CHB
|
D:HEC501
|
3.4
|
81.2
|
1.0
|
CHA
|
D:HEC501
|
3.4
|
93.1
|
1.0
|
CHD
|
D:HEC501
|
3.5
|
94.3
|
1.0
|
CE
|
D:MET160
|
3.6
|
101.7
|
1.0
|
CG
|
D:MET160
|
3.7
|
109.9
|
1.0
|
ND1
|
D:HIS41
|
3.9
|
124.4
|
1.0
|
CG
|
D:HIS41
|
4.0
|
116.8
|
1.0
|
C3B
|
D:HEC501
|
4.3
|
85.6
|
1.0
|
C2B
|
D:HEC501
|
4.4
|
82.1
|
1.0
|
C3A
|
D:HEC501
|
4.4
|
94.2
|
1.0
|
C3D
|
D:HEC501
|
4.4
|
94.6
|
1.0
|
C2D
|
D:HEC501
|
4.4
|
89.8
|
1.0
|
C2A
|
D:HEC501
|
4.5
|
82.4
|
1.0
|
CB
|
D:MET160
|
4.5
|
103.8
|
1.0
|
C3C
|
D:HEC501
|
4.5
|
107.9
|
1.0
|
C2C
|
D:HEC501
|
4.5
|
111.1
|
1.0
|
|
Iron binding site 4 out
of 5 in 7r3v
Go back to
Iron Binding Sites List in 7r3v
Iron binding site 4 out
of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.
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 Inhibitor Ck-2-67. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:144.8
occ:0.50
|
FE1
|
E:FES201
|
0.0
|
144.8
|
0.5
|
S2
|
E:FES201
|
2.2
|
185.9
|
0.5
|
S1
|
E:FES201
|
2.2
|
211.0
|
1.0
|
SG
|
E:CYS158
|
2.6
|
144.5
|
0.5
|
SG
|
E:CYS139
|
2.6
|
192.7
|
1.0
|
CB
|
E:CYS158
|
2.9
|
155.0
|
1.0
|
FE2
|
E:FES201
|
3.0
|
205.8
|
1.0
|
CB
|
E:CYS139
|
3.3
|
149.9
|
1.0
|
CB
|
E:CYS144
|
3.9
|
176.2
|
1.0
|
CB
|
E:CYS160
|
4.0
|
153.7
|
1.0
|
CB
|
E:SER163
|
4.2
|
251.9
|
1.0
|
OG
|
E:SER163
|
4.2
|
173.0
|
1.0
|
SG
|
E:CYS144
|
4.3
|
168.8
|
1.0
|
SG
|
E:CYS160
|
4.3
|
162.2
|
1.0
|
CA
|
E:CYS158
|
4.3
|
164.9
|
0.5
|
O
|
E:CYS158
|
4.4
|
150.8
|
1.0
|
C
|
E:CYS158
|
4.5
|
150.9
|
1.0
|
N
|
E:HIS161
|
4.6
|
245.8
|
1.0
|
N
|
E:CYS160
|
4.6
|
207.5
|
1.0
|
N
|
E:CYS144
|
4.7
|
184.4
|
1.0
|
CA
|
E:CYS139
|
4.7
|
159.3
|
1.0
|
CB
|
E:HIS141
|
4.8
|
172.3
|
1.0
|
CA
|
E:CYS160
|
4.8
|
188.5
|
1.0
|
CA
|
E:CYS144
|
4.9
|
175.8
|
1.0
|
|
Iron binding site 5 out
of 5 in 7r3v
Go back to
Iron Binding Sites List in 7r3v
Iron binding site 5 out
of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.
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 Inhibitor Ck-2-67. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:205.8
occ:1.00
|
FE2
|
E:FES201
|
0.0
|
205.8
|
1.0
|
S2
|
E:FES201
|
2.2
|
185.9
|
0.5
|
S1
|
E:FES201
|
2.2
|
211.0
|
1.0
|
ND1
|
E:HIS161
|
2.7
|
187.5
|
1.0
|
ND1
|
E:HIS141
|
2.7
|
194.8
|
1.0
|
FE1
|
E:FES201
|
3.0
|
144.8
|
0.5
|
CB
|
E:HIS161
|
3.2
|
236.7
|
1.0
|
CG
|
E:HIS161
|
3.3
|
211.2
|
1.0
|
CG
|
E:HIS141
|
3.5
|
167.4
|
1.0
|
CB
|
E:HIS141
|
3.5
|
172.3
|
1.0
|
N
|
E:HIS161
|
3.5
|
245.8
|
1.0
|
CE1
|
E:HIS141
|
3.7
|
201.4
|
1.0
|
CB
|
E:CYS160
|
3.8
|
153.7
|
1.0
|
CE1
|
E:HIS161
|
3.8
|
172.4
|
1.0
|
CA
|
E:HIS161
|
3.9
|
242.6
|
1.0
|
N
|
E:LEU142
|
4.1
|
185.6
|
1.0
|
C
|
E:CYS160
|
4.2
|
208.0
|
1.0
|
CB
|
E:LEU142
|
4.3
|
150.0
|
1.0
|
SG
|
E:CYS139
|
4.5
|
192.7
|
1.0
|
CG
|
E:LEU142
|
4.5
|
126.9
|
1.0
|
CD2
|
E:HIS161
|
4.6
|
198.0
|
1.0
|
CA
|
E:CYS160
|
4.6
|
188.5
|
1.0
|
C
|
E:HIS161
|
4.7
|
221.6
|
1.0
|
OG
|
E:SER163
|
4.7
|
173.0
|
1.0
|
CD2
|
E:HIS141
|
4.7
|
171.6
|
1.0
|
CA
|
E:HIS141
|
4.7
|
168.1
|
1.0
|
CA
|
E:LEU142
|
4.8
|
177.9
|
1.0
|
NE2
|
E:HIS161
|
4.8
|
189.0
|
1.0
|
NE2
|
E:HIS141
|
4.8
|
201.2
|
1.0
|
C
|
E:HIS141
|
4.8
|
164.7
|
1.0
|
CD1
|
E:LEU142
|
4.9
|
107.5
|
1.0
|
O
|
E:CYS160
|
5.0
|
191.8
|
1.0
|
|
Reference:
K.Amporndanai,
N.Pinthong,
P.M.O'neill,
W.D.Hong,
R.K.Amewu,
C.Pidathala,
N.G.Berry,
S.C.Leung,
S.A.Ward,
G.A.Biagini,
S.S.Hasnain,
S.V.Antonyuk.
Targeting the Ubiquinol-Reduction (Q I ) Site of the Mitochondrial Cytochrome Bc 1 Complex For the Development of Next Generation Quinolone Antimalarials. Biology (Basel) V. 11 2022.
ISSN: ESSN 2079-7737
PubMed: 35892964
DOI: 10.3390/BIOLOGY11081109
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