Iron in PDB 3gw9: Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei Bound to An Inhibitor N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3, 4-Oxaziazol-2-Yl)Benzamide
Enzymatic activity of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei Bound to An Inhibitor N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3, 4-Oxaziazol-2-Yl)Benzamide
All present enzymatic activity of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei Bound to An Inhibitor N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3, 4-Oxaziazol-2-Yl)Benzamide:
1.14.13.70;
Protein crystallography data
The structure of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei Bound to An Inhibitor N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3, 4-Oxaziazol-2-Yl)Benzamide, PDB code: 3gw9
was solved by
G.I.Lepesheva,
T.Y.Hargrove,
J.Harp,
Z.Wawrzak,
M.R.Waterman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.48 /
1.87
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.078,
79.113,
115.998,
74.74,
79.13,
68.57
|
R / Rfree (%)
|
18.9 /
23.8
|
Other elements in 3gw9:
The structure of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei Bound to An Inhibitor N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3, 4-Oxaziazol-2-Yl)Benzamide also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei Bound to An Inhibitor N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3, 4-Oxaziazol-2-Yl)Benzamide
(pdb code 3gw9). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei Bound to An Inhibitor N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3, 4-Oxaziazol-2-Yl)Benzamide, PDB code: 3gw9:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3gw9
Go back to
Iron Binding Sites List in 3gw9
Iron binding site 1 out
of 4 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei Bound to An Inhibitor N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3, 4-Oxaziazol-2-Yl)Benzamide
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 Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei Bound to An Inhibitor N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3, 4-Oxaziazol-2-Yl)Benzamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe480
b:22.9
occ:1.00
|
FE
|
A:HEM480
|
0.0
|
22.9
|
1.0
|
NB
|
A:HEM480
|
1.9
|
21.8
|
1.0
|
ND
|
A:HEM480
|
2.0
|
21.2
|
1.0
|
NC
|
A:HEM480
|
2.0
|
18.0
|
1.0
|
N3
|
A:VNI490
|
2.0
|
27.3
|
1.0
|
NA
|
A:HEM480
|
2.0
|
17.4
|
1.0
|
SG
|
A:CYS422
|
2.4
|
24.0
|
1.0
|
C4B
|
A:HEM480
|
2.9
|
22.8
|
1.0
|
C1D
|
A:HEM480
|
3.0
|
22.3
|
1.0
|
C1C
|
A:HEM480
|
3.0
|
22.1
|
1.0
|
C6
|
A:VNI490
|
3.0
|
21.4
|
1.0
|
C1B
|
A:HEM480
|
3.0
|
22.7
|
1.0
|
C4C
|
A:HEM480
|
3.0
|
21.9
|
1.0
|
C4D
|
A:HEM480
|
3.0
|
21.8
|
1.0
|
C5
|
A:VNI490
|
3.0
|
21.8
|
1.0
|
C1A
|
A:HEM480
|
3.1
|
19.4
|
1.0
|
C4A
|
A:HEM480
|
3.1
|
20.1
|
1.0
|
CHC
|
A:HEM480
|
3.3
|
23.4
|
1.0
|
CHD
|
A:HEM480
|
3.4
|
24.0
|
1.0
|
CB
|
A:CYS422
|
3.4
|
23.5
|
1.0
|
CHB
|
A:HEM480
|
3.4
|
21.1
|
1.0
|
CHA
|
A:HEM480
|
3.4
|
20.7
|
1.0
|
CA
|
A:CYS422
|
4.0
|
23.4
|
1.0
|
N2
|
A:VNI490
|
4.1
|
25.1
|
1.0
|
C3B
|
A:HEM480
|
4.1
|
24.9
|
1.0
|
C4
|
A:VNI490
|
4.2
|
24.5
|
1.0
|
C2B
|
A:HEM480
|
4.2
|
22.3
|
1.0
|
C2D
|
A:HEM480
|
4.2
|
23.5
|
1.0
|
C3C
|
A:HEM480
|
4.2
|
23.6
|
1.0
|
C2C
|
A:HEM480
|
4.2
|
20.4
|
1.0
|
C3D
|
A:HEM480
|
4.2
|
23.4
|
1.0
|
C2A
|
A:HEM480
|
4.3
|
18.8
|
1.0
|
C3A
|
A:HEM480
|
4.3
|
17.0
|
1.0
|
N
|
A:GLY424
|
4.6
|
24.5
|
1.0
|
N
|
A:ILE423
|
4.7
|
22.8
|
1.0
|
C
|
A:CYS422
|
4.8
|
23.0
|
1.0
|
|
Iron binding site 2 out
of 4 in 3gw9
Go back to
Iron Binding Sites List in 3gw9
Iron binding site 2 out
of 4 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei Bound to An Inhibitor N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3, 4-Oxaziazol-2-Yl)Benzamide
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 Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei Bound to An Inhibitor N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3, 4-Oxaziazol-2-Yl)Benzamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe480
b:21.1
occ:1.00
|
FE
|
B:HEM480
|
0.0
|
21.1
|
1.0
|
NB
|
B:HEM480
|
2.0
|
19.1
|
1.0
|
NA
|
B:HEM480
|
2.0
|
20.2
|
1.0
|
N3
|
B:VNI490
|
2.0
|
24.9
|
1.0
|
ND
|
B:HEM480
|
2.0
|
19.5
|
1.0
|
NC
|
B:HEM480
|
2.0
|
21.3
|
1.0
|
SG
|
B:CYS422
|
2.4
|
24.2
|
1.0
|
C5
|
B:VNI490
|
3.0
|
23.9
|
1.0
|
C4B
|
B:HEM480
|
3.0
|
23.0
|
1.0
|
C1B
|
B:HEM480
|
3.0
|
19.7
|
1.0
|
C4C
|
B:HEM480
|
3.0
|
22.0
|
1.0
|
C1A
|
B:HEM480
|
3.0
|
22.1
|
1.0
|
C1D
|
B:HEM480
|
3.0
|
22.5
|
1.0
|
C4A
|
B:HEM480
|
3.0
|
19.3
|
1.0
|
C4D
|
B:HEM480
|
3.0
|
24.5
|
1.0
|
C6
|
B:VNI490
|
3.0
|
24.9
|
1.0
|
C1C
|
B:HEM480
|
3.1
|
24.2
|
1.0
|
CB
|
B:CYS422
|
3.4
|
22.1
|
1.0
|
CHA
|
B:HEM480
|
3.4
|
24.9
|
1.0
|
CHD
|
B:HEM480
|
3.4
|
21.1
|
1.0
|
CHC
|
B:HEM480
|
3.4
|
24.1
|
1.0
|
CHB
|
B:HEM480
|
3.4
|
19.2
|
1.0
|
CA
|
B:CYS422
|
4.0
|
22.9
|
1.0
|
N2
|
B:VNI490
|
4.1
|
25.7
|
1.0
|
C4
|
B:VNI490
|
4.1
|
26.2
|
1.0
|
C3B
|
B:HEM480
|
4.2
|
22.3
|
1.0
|
C2B
|
B:HEM480
|
4.2
|
20.4
|
1.0
|
C3A
|
B:HEM480
|
4.2
|
20.0
|
1.0
|
C2A
|
B:HEM480
|
4.2
|
20.5
|
1.0
|
C3C
|
B:HEM480
|
4.2
|
22.6
|
1.0
|
C2D
|
B:HEM480
|
4.3
|
23.0
|
1.0
|
C3D
|
B:HEM480
|
4.3
|
22.9
|
1.0
|
C2C
|
B:HEM480
|
4.3
|
23.1
|
1.0
|
N
|
B:GLY424
|
4.7
|
22.6
|
1.0
|
N
|
B:ILE423
|
4.8
|
22.5
|
1.0
|
C
|
B:CYS422
|
4.8
|
22.6
|
1.0
|
CB
|
B:ALA291
|
4.9
|
23.8
|
1.0
|
|
Iron binding site 3 out
of 4 in 3gw9
Go back to
Iron Binding Sites List in 3gw9
Iron binding site 3 out
of 4 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei Bound to An Inhibitor N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3, 4-Oxaziazol-2-Yl)Benzamide
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 Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei Bound to An Inhibitor N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3, 4-Oxaziazol-2-Yl)Benzamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe480
b:20.1
occ:1.00
|
FE
|
C:HEM480
|
0.0
|
20.1
|
1.0
|
NB
|
C:HEM480
|
1.9
|
20.5
|
1.0
|
N3
|
C:VNI490
|
2.0
|
20.4
|
1.0
|
ND
|
C:HEM480
|
2.0
|
17.4
|
1.0
|
NA
|
C:HEM480
|
2.0
|
17.5
|
1.0
|
NC
|
C:HEM480
|
2.0
|
19.1
|
1.0
|
SG
|
C:CYS422
|
2.4
|
19.9
|
1.0
|
C4B
|
C:HEM480
|
2.9
|
21.6
|
1.0
|
C5
|
C:VNI490
|
3.0
|
20.4
|
1.0
|
C1B
|
C:HEM480
|
3.0
|
21.2
|
1.0
|
C4D
|
C:HEM480
|
3.0
|
20.4
|
1.0
|
C6
|
C:VNI490
|
3.0
|
23.6
|
1.0
|
C4A
|
C:HEM480
|
3.0
|
19.1
|
1.0
|
C1D
|
C:HEM480
|
3.0
|
19.0
|
1.0
|
C1C
|
C:HEM480
|
3.0
|
23.1
|
1.0
|
C1A
|
C:HEM480
|
3.0
|
20.3
|
1.0
|
C4C
|
C:HEM480
|
3.1
|
20.2
|
1.0
|
CB
|
C:CYS422
|
3.2
|
21.8
|
1.0
|
CHC
|
C:HEM480
|
3.3
|
25.0
|
1.0
|
CHA
|
C:HEM480
|
3.4
|
20.3
|
1.0
|
CHB
|
C:HEM480
|
3.4
|
19.9
|
1.0
|
CHD
|
C:HEM480
|
3.4
|
18.9
|
1.0
|
CA
|
C:CYS422
|
4.1
|
21.8
|
1.0
|
C3B
|
C:HEM480
|
4.1
|
23.4
|
1.0
|
N2
|
C:VNI490
|
4.1
|
22.7
|
1.0
|
C4
|
C:VNI490
|
4.1
|
22.3
|
1.0
|
C2B
|
C:HEM480
|
4.2
|
21.9
|
1.0
|
C3D
|
C:HEM480
|
4.2
|
19.3
|
1.0
|
C2D
|
C:HEM480
|
4.2
|
19.7
|
1.0
|
C3A
|
C:HEM480
|
4.3
|
20.7
|
1.0
|
C2A
|
C:HEM480
|
4.3
|
18.1
|
1.0
|
C3C
|
C:HEM480
|
4.3
|
20.8
|
1.0
|
C2C
|
C:HEM480
|
4.3
|
21.5
|
1.0
|
N
|
C:GLY424
|
4.7
|
21.4
|
1.0
|
N
|
C:ILE423
|
4.8
|
21.9
|
1.0
|
C
|
C:CYS422
|
4.8
|
22.2
|
1.0
|
|
Iron binding site 4 out
of 4 in 3gw9
Go back to
Iron Binding Sites List in 3gw9
Iron binding site 4 out
of 4 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei Bound to An Inhibitor N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3, 4-Oxaziazol-2-Yl)Benzamide
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 Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei Bound to An Inhibitor N-(1-(2,4- Dichlorophenyl)-2-(1H-Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3, 4-Oxaziazol-2-Yl)Benzamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe480
b:26.9
occ:1.00
|
FE
|
D:HEM480
|
0.0
|
26.9
|
1.0
|
NB
|
D:HEM480
|
1.8
|
27.6
|
1.0
|
ND
|
D:HEM480
|
1.9
|
30.4
|
1.0
|
NC
|
D:HEM480
|
2.0
|
24.2
|
1.0
|
NA
|
D:HEM480
|
2.0
|
25.5
|
1.0
|
N3
|
D:VNI490
|
2.0
|
25.1
|
1.0
|
SG
|
D:CYS422
|
2.4
|
30.2
|
1.0
|
C4B
|
D:HEM480
|
2.9
|
26.6
|
1.0
|
C1B
|
D:HEM480
|
2.9
|
28.0
|
1.0
|
C4D
|
D:HEM480
|
2.9
|
32.4
|
1.0
|
C1D
|
D:HEM480
|
2.9
|
32.1
|
1.0
|
C1C
|
D:HEM480
|
3.0
|
24.9
|
1.0
|
C6
|
D:VNI490
|
3.0
|
23.8
|
1.0
|
C1A
|
D:HEM480
|
3.0
|
29.3
|
1.0
|
C4C
|
D:HEM480
|
3.0
|
27.1
|
1.0
|
C4A
|
D:HEM480
|
3.0
|
27.6
|
1.0
|
C5
|
D:VNI490
|
3.1
|
23.6
|
1.0
|
CHC
|
D:HEM480
|
3.3
|
26.7
|
1.0
|
CHA
|
D:HEM480
|
3.3
|
30.7
|
1.0
|
CHD
|
D:HEM480
|
3.3
|
28.5
|
1.0
|
CHB
|
D:HEM480
|
3.3
|
27.7
|
1.0
|
CB
|
D:CYS422
|
3.5
|
32.2
|
1.0
|
C3B
|
D:HEM480
|
4.1
|
27.8
|
1.0
|
N2
|
D:VNI490
|
4.1
|
27.1
|
1.0
|
C2B
|
D:HEM480
|
4.1
|
28.3
|
1.0
|
CA
|
D:CYS422
|
4.1
|
33.0
|
1.0
|
C2D
|
D:HEM480
|
4.2
|
34.3
|
1.0
|
C4
|
D:VNI490
|
4.2
|
24.2
|
1.0
|
C3D
|
D:HEM480
|
4.2
|
35.0
|
1.0
|
C3C
|
D:HEM480
|
4.2
|
25.4
|
1.0
|
C2C
|
D:HEM480
|
4.2
|
25.2
|
1.0
|
C2A
|
D:HEM480
|
4.2
|
28.4
|
1.0
|
C3A
|
D:HEM480
|
4.2
|
26.5
|
1.0
|
N
|
D:GLY424
|
4.7
|
29.9
|
1.0
|
N
|
D:ILE423
|
4.8
|
31.4
|
1.0
|
C
|
D:CYS422
|
4.8
|
32.5
|
1.0
|
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Reference:
G.I.Lepesheva,
H.W.Park,
T.Y.Hargrove,
B.Vanhollebeke,
Z.Wawrzak,
J.M.Harp,
M.Sundaramoorthy,
W.D.Nes,
E.Pays,
M.Chaudhuri,
F.Villalta,
M.R.Waterman.
Crystal Structures of Trypanosoma Brucei Sterol 14ALPHA-Demethylase and Implications For Selective Treatment of Human Infections. J.Biol.Chem. V. 285 1773 2010.
ISSN: ISSN 0021-9258
PubMed: 19923211
DOI: 10.1074/JBC.M109.067470
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