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Iron in PDB 4g3j: Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]

Enzymatic activity of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]

All present enzymatic activity of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]:
1.14.13.70;

Protein crystallography data

The structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)], PDB code: 4g3j was solved by T.Y.Hargrove, Z.Wawrzak, M.R.Waterman, G.I.Lepesheva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.93 / 1.83
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.013, 79.480, 116.353, 74.59, 79.28, 68.48
R / Rfree (%) 16.9 / 22

Other elements in 4g3j:

The structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] (pdb code 4g3j). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)], PDB code: 4g3j:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4g3j

Go back to Iron Binding Sites List in 4g3j
Iron binding site 1 out of 4 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:21.2
occ:1.00
 FE A:HEM501 0.0 21.2 1.0
ND A:HEM501 2.0 19.0 1.0
NA A:HEM501 2.0 18.3 1.0
NC A:HEM501 2.1 18.3 1.0
NB A:HEM501 2.1 21.6 1.0
NAS A:VNT502 2.2 19.9 1.0
SG A:CYS422 2.4 21.0 1.0
CAP A:VNT502 2.9 20.7 1.0
C1D A:HEM501 3.0 21.0 1.0
C4D A:HEM501 3.0 18.1 1.0
C1A A:HEM501 3.0 18.1 1.0
C4A A:HEM501 3.0 19.7 1.0
C4C A:HEM501 3.0 20.8 1.0
C1B A:HEM501 3.1 20.6 1.0
C4B A:HEM501 3.1 19.6 1.0
C1C A:HEM501 3.1 18.4 1.0
CB A:CYS422 3.3 20.2 1.0
CAO A:VNT502 3.4 21.8 1.0
CHD A:HEM501 3.4 19.0 1.0
CHA A:HEM501 3.4 17.9 1.0
CHB A:HEM501 3.5 20.5 1.0
CHC A:HEM501 3.5 18.7 1.0
CA A:CYS422 4.1 22.6 1.0
NBI A:VNT502 4.1 22.4 1.0
C2A A:HEM501 4.2 20.8 1.0
C3A A:HEM501 4.2 21.7 1.0
C2D A:HEM501 4.3 19.9 1.0
C3D A:HEM501 4.3 20.0 1.0
C3C A:HEM501 4.3 19.6 1.0
NAT A:VNT502 4.3 22.8 1.0
C2C A:HEM501 4.3 19.4 1.0
C2B A:HEM501 4.3 21.1 1.0
C3B A:HEM501 4.4 22.0 1.0
N A:GLY424 4.7 21.2 1.0
C A:CYS422 4.8 21.6 1.0
N A:ILE423 4.8 22.4 1.0
CB A:ALA291 5.0 24.2 1.0

Iron binding site 2 out of 4 in 4g3j

Go back to Iron Binding Sites List in 4g3j
Iron binding site 2 out of 4 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:20.6
occ:1.00
 FE B:HEM501 0.0 20.6 1.0
ND B:HEM501 2.0 21.6 1.0
NA B:HEM501 2.0 20.0 1.0
NC B:HEM501 2.1 22.0 1.0
NAS B:VNT502 2.1 21.5 1.0
NB B:HEM501 2.1 19.6 1.0
SG B:CYS422 2.4 20.3 1.0
CAP B:VNT502 2.9 20.9 1.0
C4D B:HEM501 3.0 20.7 1.0
C1D B:HEM501 3.0 24.1 1.0
C1A B:HEM501 3.0 19.1 1.0
C4A B:HEM501 3.0 17.4 1.0
C4C B:HEM501 3.1 21.0 1.0
C1B B:HEM501 3.1 19.8 1.0
C4B B:HEM501 3.1 18.4 1.0
C1C B:HEM501 3.1 20.5 1.0
CAO B:VNT502 3.1 20.9 1.0
CB B:CYS422 3.4 19.2 1.0
CHA B:HEM501 3.4 20.6 1.0
CHD B:HEM501 3.4 20.8 1.0
CHB B:HEM501 3.5 18.7 1.0
CHC B:HEM501 3.5 18.6 1.0
CA B:CYS422 4.1 19.8 1.0
NBI B:VNT502 4.1 21.7 1.0
NAT B:VNT502 4.2 21.4 1.0
C2A B:HEM501 4.2 18.8 1.0
C3A B:HEM501 4.2 17.8 1.0
C3D B:HEM501 4.3 22.4 1.0
C2D B:HEM501 4.3 23.7 1.0
C3C B:HEM501 4.3 22.5 1.0
C2C B:HEM501 4.3 19.4 1.0
C2B B:HEM501 4.3 19.3 1.0
C3B B:HEM501 4.4 18.2 1.0
N B:GLY424 4.7 20.1 1.0
N B:ILE423 4.8 18.3 1.0
C B:CYS422 4.8 19.9 1.0
CB B:ALA291 5.0 18.0 1.0

Iron binding site 3 out of 4 in 4g3j

Go back to Iron Binding Sites List in 4g3j
Iron binding site 3 out of 4 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:26.9
occ:1.00
 FE C:HEM501 0.0 26.9 1.0
ND C:HEM501 2.0 27.3 1.0
NA C:HEM501 2.0 28.1 1.0
NC C:HEM501 2.0 26.1 1.0
NB C:HEM501 2.1 26.4 1.0
NAS C:VNT502 2.1 22.6 1.0
SG C:CYS422 2.4 28.5 1.0
CAP C:VNT502 2.9 21.7 1.0
C1D C:HEM501 3.0 29.2 1.0
C4D C:HEM501 3.0 28.5 1.0
C1A C:HEM501 3.0 28.6 1.0
C4C C:HEM501 3.0 25.8 1.0
C4A C:HEM501 3.0 26.3 1.0
C1C C:HEM501 3.1 23.9 1.0
C1B C:HEM501 3.1 25.9 1.0
C4B C:HEM501 3.1 25.6 1.0
CAO C:VNT502 3.3 22.2 1.0
CB C:CYS422 3.3 30.5 1.0
CHD C:HEM501 3.4 25.8 1.0
CHA C:HEM501 3.4 28.0 1.0
CHB C:HEM501 3.5 25.6 1.0
CHC C:HEM501 3.5 24.0 1.0
CA C:CYS422 4.0 32.0 1.0
NBI C:VNT502 4.1 21.9 1.0
C2A C:HEM501 4.2 30.0 1.0
C3C C:HEM501 4.2 25.9 1.0
C3A C:HEM501 4.2 27.6 1.0
NAT C:VNT502 4.3 22.7 1.0
C2D C:HEM501 4.3 30.3 1.0
C3D C:HEM501 4.3 33.0 1.0
C2C C:HEM501 4.3 28.3 1.0
C2B C:HEM501 4.4 28.1 1.0
C3B C:HEM501 4.4 24.8 1.0
N C:GLY424 4.7 29.6 1.0
C C:CYS422 4.8 33.9 1.0
N C:ILE423 4.8 30.1 1.0
CB C:ALA291 5.0 25.9 1.0

Iron binding site 4 out of 4 in 4g3j

Go back to Iron Binding Sites List in 4g3j
Iron binding site 4 out of 4 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:22.4
occ:1.00
 FE D:HEM501 0.0 22.4 1.0
ND D:HEM501 1.9 20.0 1.0
NA D:HEM501 2.0 21.2 1.0
NC D:HEM501 2.1 22.8 1.0
NB D:HEM501 2.1 20.0 1.0
NAS D:VNT502 2.1 21.6 1.0
SG D:CYS422 2.4 22.8 1.0
CAP D:VNT502 2.9 21.8 1.0
C1D D:HEM501 3.0 22.5 1.0
C4D D:HEM501 3.0 25.7 1.0
C1A D:HEM501 3.0 22.4 1.0
C4C D:HEM501 3.0 21.7 1.0
C4A D:HEM501 3.0 18.7 1.0
C1B D:HEM501 3.1 20.5 1.0
C4B D:HEM501 3.1 22.0 1.0
C1C D:HEM501 3.1 21.6 1.0
CAO D:VNT502 3.3 22.2 1.0
CB D:CYS422 3.4 25.1 1.0
CHD D:HEM501 3.4 23.2 1.0
CHA D:HEM501 3.4 23.1 1.0
CHB D:HEM501 3.5 20.8 1.0
CHC D:HEM501 3.5 25.2 1.0
CA D:CYS422 4.0 20.4 1.0
NBI D:VNT502 4.1 22.7 1.0
NAT D:VNT502 4.2 23.6 1.0
C3D D:HEM501 4.2 23.9 1.0
C2D D:HEM501 4.2 24.9 1.0
C3A D:HEM501 4.2 19.8 1.0
C2A D:HEM501 4.3 22.3 1.0
C3C D:HEM501 4.3 23.4 1.0
C2B D:HEM501 4.3 20.2 1.0
C2C D:HEM501 4.3 23.9 1.0
C3B D:HEM501 4.4 22.4 1.0
N D:GLY424 4.7 24.5 1.0
N D:ILE423 4.8 21.6 1.0
C D:CYS422 4.8 22.8 1.0
CB D:ALA291 4.9 25.6 1.0

Reference:

G.I.Lepesheva, T.Y.Hargrove, G.Rachakonda, Z.Wawrzak, S.Pomel, S.Cojean, P.N.Nde, W.D.Nes, C.W.Locuson, M.W.Calcutt, M.R.Waterman, J.S.Daniels, P.M.Loiseau, F.Villalta. Vfv As A New Effective CYP51 Structure-Derived Drug Candidate For Chagas Disease and Visceral Leishmaniasis. J Infect Dis V. 212 1439 2015.
ISSN: ISSN 1537-6613
PubMed: 25883390
DOI: 10.1093/INFDIS/JIV228
Page generated: Mon Aug 5 02:36:13 2024

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