Atomistry » Iron » PDB 4g39-4gl5 » 4g3j
Atomistry »
  Iron »
    PDB 4g39-4gl5 »
      4g3j »

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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy