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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:

Chlorine (Cl) 8 atoms

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

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
Page generated: Sun Aug 4 10:55:45 2024

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