Iron in PDB 8ekt: CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1)
Enzymatic activity of CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1)
All present enzymatic activity of CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1):
1.14.13.70;
Protein crystallography data
The structure of CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1), PDB code: 8ekt
was solved by
T.Y.Hargrove,
Z.Wawrzak,
G.I.Lepesheva,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.89 /
2.29
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
99.453,
99.304,
107.915,
81.22,
84.08,
60.08
|
R / Rfree (%)
|
21.3 /
22.4
|
Other elements in 8ekt:
The structure of CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1) also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1)
(pdb code 8ekt). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1), PDB code: 8ekt:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 8ekt
Go back to
Iron Binding Sites List in 8ekt
Iron binding site 1 out
of 6 in the CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:8.8
occ:1.00
|
FE
|
A:HEM501
|
0.0
|
8.8
|
1.0
|
ND
|
A:HEM501
|
1.9
|
9.5
|
1.0
|
NA
|
A:HEM501
|
2.0
|
9.3
|
1.0
|
NC
|
A:HEM501
|
2.1
|
10.4
|
1.0
|
NB
|
A:HEM501
|
2.1
|
8.8
|
1.0
|
SG
|
A:CYS434
|
2.2
|
8.1
|
1.0
|
NAF
|
A:VT1502
|
2.2
|
10.0
|
1.0
|
C4D
|
A:HEM501
|
2.9
|
9.9
|
1.0
|
C1D
|
A:HEM501
|
2.9
|
10.4
|
1.0
|
C1A
|
A:HEM501
|
2.9
|
9.3
|
1.0
|
C4A
|
A:HEM501
|
3.0
|
8.8
|
1.0
|
C4C
|
A:HEM501
|
3.1
|
12.0
|
1.0
|
C1B
|
A:HEM501
|
3.1
|
9.7
|
1.0
|
C4B
|
A:HEM501
|
3.1
|
9.9
|
1.0
|
C1C
|
A:HEM501
|
3.1
|
10.8
|
1.0
|
CAE
|
A:VT1502
|
3.2
|
12.7
|
1.0
|
CB
|
A:CYS434
|
3.2
|
10.7
|
1.0
|
NAG
|
A:VT1502
|
3.2
|
12.8
|
1.0
|
CHA
|
A:HEM501
|
3.3
|
8.9
|
1.0
|
CHD
|
A:HEM501
|
3.4
|
11.3
|
1.0
|
CHB
|
A:HEM501
|
3.5
|
9.4
|
1.0
|
CHC
|
A:HEM501
|
3.5
|
10.9
|
1.0
|
CA
|
A:CYS434
|
4.0
|
11.1
|
1.0
|
C2D
|
A:HEM501
|
4.1
|
10.5
|
1.0
|
C3D
|
A:HEM501
|
4.1
|
11.0
|
1.0
|
C2A
|
A:HEM501
|
4.2
|
9.2
|
1.0
|
C3A
|
A:HEM501
|
4.2
|
8.4
|
1.0
|
C3C
|
A:HEM501
|
4.3
|
12.5
|
1.0
|
C2B
|
A:HEM501
|
4.3
|
9.7
|
1.0
|
NAD
|
A:VT1502
|
4.3
|
13.9
|
1.0
|
C2C
|
A:HEM501
|
4.3
|
12.2
|
1.0
|
C3B
|
A:HEM501
|
4.3
|
10.1
|
1.0
|
NAH
|
A:VT1502
|
4.4
|
13.5
|
1.0
|
N
|
A:GLY436
|
4.7
|
17.8
|
1.0
|
C
|
A:CYS434
|
4.8
|
11.9
|
1.0
|
N
|
A:MET435
|
4.9
|
13.4
|
1.0
|
|
Iron binding site 2 out
of 6 in 8ekt
Go back to
Iron Binding Sites List in 8ekt
Iron binding site 2 out
of 6 in the CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:14.1
occ:1.00
|
FE
|
B:HEM501
|
0.0
|
14.1
|
1.0
|
ND
|
B:HEM501
|
1.9
|
16.4
|
1.0
|
NA
|
B:HEM501
|
2.0
|
15.5
|
1.0
|
NC
|
B:HEM501
|
2.1
|
15.3
|
1.0
|
NB
|
B:HEM501
|
2.1
|
16.2
|
1.0
|
NAF
|
B:VT1502
|
2.2
|
12.2
|
1.0
|
SG
|
B:CYS434
|
2.3
|
15.0
|
1.0
|
C4D
|
B:HEM501
|
2.9
|
16.5
|
1.0
|
C1D
|
B:HEM501
|
2.9
|
16.2
|
1.0
|
C1A
|
B:HEM501
|
3.0
|
15.1
|
1.0
|
C4C
|
B:HEM501
|
3.0
|
14.8
|
1.0
|
C4A
|
B:HEM501
|
3.0
|
16.0
|
1.0
|
C4B
|
B:HEM501
|
3.1
|
16.8
|
1.0
|
C1B
|
B:HEM501
|
3.1
|
15.7
|
1.0
|
C1C
|
B:HEM501
|
3.1
|
15.1
|
1.0
|
CAE
|
B:VT1502
|
3.1
|
15.0
|
1.0
|
NAG
|
B:VT1502
|
3.2
|
17.6
|
1.0
|
CB
|
B:CYS434
|
3.3
|
16.6
|
1.0
|
CHA
|
B:HEM501
|
3.3
|
14.9
|
1.0
|
CHD
|
B:HEM501
|
3.4
|
15.2
|
1.0
|
CHB
|
B:HEM501
|
3.5
|
15.1
|
1.0
|
CHC
|
B:HEM501
|
3.5
|
15.7
|
1.0
|
CA
|
B:CYS434
|
3.9
|
15.8
|
1.0
|
C2D
|
B:HEM501
|
4.1
|
16.4
|
1.0
|
C3D
|
B:HEM501
|
4.1
|
17.0
|
1.0
|
C2A
|
B:HEM501
|
4.2
|
14.8
|
1.0
|
C3A
|
B:HEM501
|
4.2
|
16.0
|
1.0
|
C3C
|
B:HEM501
|
4.2
|
14.9
|
1.0
|
C2C
|
B:HEM501
|
4.3
|
14.7
|
1.0
|
NAD
|
B:VT1502
|
4.3
|
16.7
|
1.0
|
C2B
|
B:HEM501
|
4.3
|
15.3
|
1.0
|
C3B
|
B:HEM501
|
4.3
|
15.1
|
1.0
|
NAH
|
B:VT1502
|
4.3
|
16.9
|
1.0
|
N
|
B:GLY436
|
4.7
|
19.3
|
1.0
|
C
|
B:CYS434
|
4.7
|
16.0
|
1.0
|
N
|
B:MET435
|
4.8
|
16.6
|
1.0
|
|
Iron binding site 3 out
of 6 in 8ekt
Go back to
Iron Binding Sites List in 8ekt
Iron binding site 3 out
of 6 in the CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:17.2
occ:1.00
|
FE
|
C:HEM501
|
0.0
|
17.2
|
1.0
|
ND
|
C:HEM501
|
1.9
|
19.1
|
1.0
|
NA
|
C:HEM501
|
2.0
|
19.6
|
1.0
|
NC
|
C:HEM501
|
2.1
|
19.6
|
1.0
|
NB
|
C:HEM501
|
2.1
|
21.6
|
1.0
|
NAF
|
C:VT1502
|
2.2
|
16.0
|
1.0
|
SG
|
C:CYS434
|
2.3
|
21.6
|
1.0
|
C1D
|
C:HEM501
|
2.9
|
17.7
|
1.0
|
C4D
|
C:HEM501
|
2.9
|
19.9
|
1.0
|
C1A
|
C:HEM501
|
3.0
|
20.6
|
1.0
|
C4A
|
C:HEM501
|
3.0
|
20.9
|
1.0
|
C4C
|
C:HEM501
|
3.1
|
18.7
|
1.0
|
C1B
|
C:HEM501
|
3.1
|
21.9
|
1.0
|
C4B
|
C:HEM501
|
3.1
|
26.1
|
1.0
|
CAE
|
C:VT1502
|
3.1
|
18.5
|
1.0
|
C1C
|
C:HEM501
|
3.1
|
22.2
|
1.0
|
NAG
|
C:VT1502
|
3.3
|
18.3
|
1.0
|
CHA
|
C:HEM501
|
3.3
|
20.8
|
1.0
|
CB
|
C:CYS434
|
3.4
|
23.4
|
1.0
|
CHD
|
C:HEM501
|
3.4
|
17.7
|
1.0
|
CHB
|
C:HEM501
|
3.4
|
19.4
|
1.0
|
CHC
|
C:HEM501
|
3.5
|
24.6
|
1.0
|
CA
|
C:CYS434
|
4.0
|
22.8
|
1.0
|
C2D
|
C:HEM501
|
4.1
|
18.6
|
1.0
|
C3D
|
C:HEM501
|
4.1
|
19.3
|
1.0
|
C2A
|
C:HEM501
|
4.1
|
20.8
|
1.0
|
C3A
|
C:HEM501
|
4.2
|
23.0
|
1.0
|
NAD
|
C:VT1502
|
4.3
|
17.5
|
1.0
|
C3C
|
C:HEM501
|
4.3
|
18.6
|
1.0
|
C2B
|
C:HEM501
|
4.3
|
24.2
|
1.0
|
C2C
|
C:HEM501
|
4.3
|
18.9
|
1.0
|
C3B
|
C:HEM501
|
4.3
|
24.4
|
1.0
|
NAH
|
C:VT1502
|
4.4
|
17.2
|
1.0
|
N
|
C:GLY436
|
4.8
|
22.1
|
1.0
|
C
|
C:CYS434
|
4.8
|
22.2
|
1.0
|
N
|
C:MET435
|
4.9
|
20.7
|
1.0
|
|
Iron binding site 4 out
of 6 in 8ekt
Go back to
Iron Binding Sites List in 8ekt
Iron binding site 4 out
of 6 in the CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:18.5
occ:1.00
|
FE
|
D:HEM501
|
0.0
|
18.5
|
1.0
|
ND
|
D:HEM501
|
1.9
|
18.6
|
1.0
|
NA
|
D:HEM501
|
2.0
|
18.8
|
1.0
|
NC
|
D:HEM501
|
2.1
|
16.8
|
1.0
|
NB
|
D:HEM501
|
2.1
|
18.0
|
1.0
|
NAF
|
D:VT1502
|
2.3
|
22.1
|
1.0
|
SG
|
D:CYS434
|
2.3
|
20.1
|
1.0
|
C1D
|
D:HEM501
|
2.9
|
18.3
|
1.0
|
C4D
|
D:HEM501
|
2.9
|
19.5
|
1.0
|
C1A
|
D:HEM501
|
3.0
|
20.4
|
1.0
|
C4C
|
D:HEM501
|
3.0
|
17.0
|
1.0
|
C4A
|
D:HEM501
|
3.0
|
20.3
|
1.0
|
C1B
|
D:HEM501
|
3.1
|
19.9
|
1.0
|
C4B
|
D:HEM501
|
3.1
|
20.5
|
1.0
|
C1C
|
D:HEM501
|
3.1
|
18.7
|
1.0
|
CB
|
D:CYS434
|
3.2
|
19.5
|
1.0
|
CAE
|
D:VT1502
|
3.2
|
25.5
|
1.0
|
NAG
|
D:VT1502
|
3.3
|
24.6
|
1.0
|
CHA
|
D:HEM501
|
3.3
|
19.2
|
1.0
|
CHD
|
D:HEM501
|
3.4
|
16.1
|
1.0
|
CHB
|
D:HEM501
|
3.5
|
20.9
|
1.0
|
CHC
|
D:HEM501
|
3.5
|
20.8
|
1.0
|
CA
|
D:CYS434
|
4.0
|
19.5
|
1.0
|
C2D
|
D:HEM501
|
4.1
|
19.2
|
1.0
|
C3D
|
D:HEM501
|
4.1
|
20.4
|
1.0
|
C2A
|
D:HEM501
|
4.2
|
19.7
|
1.0
|
C3A
|
D:HEM501
|
4.2
|
20.1
|
1.0
|
C3C
|
D:HEM501
|
4.3
|
17.2
|
1.0
|
C2C
|
D:HEM501
|
4.3
|
17.7
|
1.0
|
C2B
|
D:HEM501
|
4.3
|
21.4
|
1.0
|
NAD
|
D:VT1502
|
4.4
|
23.3
|
1.0
|
C3B
|
D:HEM501
|
4.4
|
22.6
|
1.0
|
NAH
|
D:VT1502
|
4.4
|
23.8
|
1.0
|
N
|
D:GLY436
|
4.7
|
20.9
|
1.0
|
C
|
D:CYS434
|
4.8
|
18.4
|
1.0
|
N
|
D:MET435
|
4.8
|
19.4
|
1.0
|
|
Iron binding site 5 out
of 6 in 8ekt
Go back to
Iron Binding Sites List in 8ekt
Iron binding site 5 out
of 6 in the CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe501
b:18.5
occ:1.00
|
FE
|
E:HEM501
|
0.0
|
18.5
|
1.0
|
ND
|
E:HEM501
|
1.9
|
21.1
|
1.0
|
NA
|
E:HEM501
|
2.0
|
19.7
|
1.0
|
NC
|
E:HEM501
|
2.1
|
23.3
|
1.0
|
NB
|
E:HEM501
|
2.1
|
19.5
|
1.0
|
NAF
|
E:VT1502
|
2.2
|
12.6
|
1.0
|
SG
|
E:CYS434
|
2.2
|
17.4
|
1.0
|
C4D
|
E:HEM501
|
2.9
|
19.8
|
1.0
|
C1D
|
E:HEM501
|
2.9
|
19.8
|
1.0
|
C1A
|
E:HEM501
|
3.0
|
18.8
|
1.0
|
C4A
|
E:HEM501
|
3.0
|
21.0
|
1.0
|
C4C
|
E:HEM501
|
3.0
|
23.0
|
1.0
|
C1B
|
E:HEM501
|
3.1
|
21.0
|
1.0
|
C4B
|
E:HEM501
|
3.1
|
20.3
|
1.0
|
C1C
|
E:HEM501
|
3.1
|
21.3
|
1.0
|
CAE
|
E:VT1502
|
3.1
|
17.2
|
1.0
|
NAG
|
E:VT1502
|
3.3
|
16.7
|
1.0
|
CHA
|
E:HEM501
|
3.3
|
18.3
|
1.0
|
CHD
|
E:HEM501
|
3.4
|
21.3
|
1.0
|
CB
|
E:CYS434
|
3.5
|
16.7
|
1.0
|
CHB
|
E:HEM501
|
3.5
|
21.2
|
1.0
|
CHC
|
E:HEM501
|
3.5
|
21.0
|
1.0
|
CA
|
E:CYS434
|
4.0
|
18.1
|
1.0
|
C2D
|
E:HEM501
|
4.1
|
21.6
|
1.0
|
C3D
|
E:HEM501
|
4.1
|
22.1
|
1.0
|
C2A
|
E:HEM501
|
4.2
|
18.0
|
1.0
|
C3A
|
E:HEM501
|
4.2
|
19.8
|
1.0
|
C3C
|
E:HEM501
|
4.3
|
23.1
|
1.0
|
C2C
|
E:HEM501
|
4.3
|
24.6
|
1.0
|
NAD
|
E:VT1502
|
4.3
|
17.4
|
1.0
|
C2B
|
E:HEM501
|
4.3
|
22.3
|
1.0
|
C3B
|
E:HEM501
|
4.3
|
22.7
|
1.0
|
NAH
|
E:VT1502
|
4.4
|
16.5
|
1.0
|
N
|
E:GLY436
|
4.6
|
27.2
|
1.0
|
C
|
E:CYS434
|
4.8
|
17.0
|
1.0
|
N
|
E:MET435
|
4.9
|
18.9
|
1.0
|
CA
|
E:GLY436
|
4.9
|
25.6
|
1.0
|
|
Iron binding site 6 out
of 6 in 8ekt
Go back to
Iron Binding Sites List in 8ekt
Iron binding site 6 out
of 6 in the CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole- Based Ind Inhibitor Vt-1161(VT1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe501
b:22.2
occ:1.00
|
FE
|
F:HEM501
|
0.0
|
22.2
|
1.0
|
ND
|
F:HEM501
|
1.9
|
23.5
|
1.0
|
NA
|
F:HEM501
|
2.0
|
22.3
|
1.0
|
NC
|
F:HEM501
|
2.1
|
21.1
|
1.0
|
NB
|
F:HEM501
|
2.1
|
19.5
|
1.0
|
NAF
|
F:VT1502
|
2.2
|
20.2
|
1.0
|
SG
|
F:CYS434
|
2.3
|
20.6
|
1.0
|
C1D
|
F:HEM501
|
2.9
|
24.4
|
1.0
|
C4D
|
F:HEM501
|
2.9
|
25.1
|
1.0
|
C1A
|
F:HEM501
|
3.0
|
23.3
|
1.0
|
C4C
|
F:HEM501
|
3.0
|
24.2
|
1.0
|
C4A
|
F:HEM501
|
3.0
|
20.4
|
1.0
|
C1B
|
F:HEM501
|
3.1
|
19.6
|
1.0
|
C4B
|
F:HEM501
|
3.1
|
19.5
|
1.0
|
C1C
|
F:HEM501
|
3.1
|
21.1
|
1.0
|
CAE
|
F:VT1502
|
3.2
|
24.0
|
1.0
|
NAG
|
F:VT1502
|
3.2
|
24.1
|
1.0
|
CB
|
F:CYS434
|
3.3
|
21.6
|
1.0
|
CHA
|
F:HEM501
|
3.3
|
23.4
|
1.0
|
CHD
|
F:HEM501
|
3.4
|
23.2
|
1.0
|
CHB
|
F:HEM501
|
3.4
|
20.6
|
1.0
|
CHC
|
F:HEM501
|
3.5
|
20.5
|
1.0
|
CA
|
F:CYS434
|
3.9
|
23.7
|
1.0
|
C2D
|
F:HEM501
|
4.1
|
24.9
|
1.0
|
C3D
|
F:HEM501
|
4.1
|
24.6
|
1.0
|
C2A
|
F:HEM501
|
4.2
|
20.7
|
1.0
|
C3A
|
F:HEM501
|
4.2
|
20.0
|
1.0
|
C3C
|
F:HEM501
|
4.2
|
23.4
|
1.0
|
C2B
|
F:HEM501
|
4.3
|
19.9
|
1.0
|
C2C
|
F:HEM501
|
4.3
|
22.2
|
1.0
|
NAD
|
F:VT1502
|
4.3
|
22.9
|
1.0
|
NAH
|
F:VT1502
|
4.3
|
24.4
|
1.0
|
C3B
|
F:HEM501
|
4.3
|
19.3
|
1.0
|
N
|
F:GLY436
|
4.7
|
26.6
|
1.0
|
N
|
F:MET435
|
4.8
|
22.8
|
1.0
|
C
|
F:CYS434
|
4.8
|
23.4
|
1.0
|
|
Reference:
T.Y.Hargrove,
Z.Wawrzak,
G.I.Lepesheva.
CYP51 From Acanthamoeba Castellanii in Complex with the Tetrazole-Based Inhibitor Vt-1161 To Be Published.
Page generated: Sat Aug 10 01:32:25 2024
|