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Iron in PDB 4g7g: Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]

Enzymatic activity of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]

All present enzymatic activity of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]:
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-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)], PDB code: 4g7g 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) 29.82 / 2.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.947, 79.706, 117.868, 74.64, 81.20, 68.96
R / Rfree (%) 16.3 / 22.6

Other elements in 4g7g:

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

Fluorine (F) 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-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)] (pdb code 4g7g). 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-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)], PDB code: 4g7g:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4g7g

Go back to Iron Binding Sites List in 4g7g
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-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]


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-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:25.1
occ:1.00
 FE A:HEM501 0.0 25.1 1.0
NC A:HEM501 2.0 25.5 1.0
NA A:HEM501 2.0 22.0 1.0
NAX A:VFV502 2.0 25.3 1.0
ND A:HEM501 2.1 24.3 1.0
NB A:HEM501 2.1 24.0 1.0
SG A:CYS422 2.4 25.5 1.0
CAG A:VFV502 2.9 23.8 1.0
C4C A:HEM501 3.0 25.4 1.0
CAU A:VFV502 3.0 25.4 1.0
C1D A:HEM501 3.0 29.1 1.0
C1C A:HEM501 3.1 21.5 1.0
C4B A:HEM501 3.1 23.3 1.0
C4A A:HEM501 3.1 21.3 1.0
C1A A:HEM501 3.1 20.6 1.0
C4D A:HEM501 3.2 26.5 1.0
C1B A:HEM501 3.2 22.3 1.0
CHD A:HEM501 3.3 25.5 1.0
CB A:CYS422 3.4 23.9 1.0
CHC A:HEM501 3.5 22.7 1.0
CHB A:HEM501 3.5 20.4 1.0
CHA A:HEM501 3.6 24.1 1.0
CAT A:VFV502 4.1 21.8 1.0
NBO A:VFV502 4.1 26.6 1.0
CA A:CYS422 4.1 25.2 1.0
C3C A:HEM501 4.3 26.4 1.0
C2C A:HEM501 4.4 24.1 1.0
C2A A:HEM501 4.4 22.2 1.0
C2D A:HEM501 4.4 27.8 1.0
C3B A:HEM501 4.4 22.0 1.0
C3A A:HEM501 4.4 23.3 1.0
C3D A:HEM501 4.4 29.2 1.0
C2B A:HEM501 4.5 23.0 1.0
N A:GLY424 4.7 26.2 1.0
CB A:ALA291 4.9 24.7 1.0
C A:CYS422 4.9 31.4 1.0
N A:ILE423 4.9 31.1 1.0

Iron binding site 2 out of 4 in 4g7g

Go back to Iron Binding Sites List in 4g7g
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-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]


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-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:26.1
occ:1.00
 FE B:HEM501 0.0 26.1 1.0
NC B:HEM501 1.9 25.3 1.0
NA B:HEM501 2.0 27.7 1.0
NAX B:VFV502 2.1 25.2 1.0
ND B:HEM501 2.1 27.6 1.0
NB B:HEM501 2.1 23.9 1.0
SG B:CYS422 2.2 24.3 1.0
C4C B:HEM501 3.0 22.8 1.0
CAU B:VFV502 3.0 24.2 1.0
C1A B:HEM501 3.0 26.5 1.0
C1C B:HEM501 3.1 24.0 1.0
CAG B:VFV502 3.1 25.6 1.0
C1D B:HEM501 3.1 30.7 1.0
C4A B:HEM501 3.1 26.3 1.0
C4D B:HEM501 3.1 28.5 1.0
C4B B:HEM501 3.1 26.3 1.0
C1B B:HEM501 3.2 24.9 1.0
CB B:CYS422 3.3 26.2 1.0
CHD B:HEM501 3.4 24.1 1.0
CHA B:HEM501 3.4 26.0 1.0
CHC B:HEM501 3.5 23.0 1.0
CHB B:HEM501 3.6 24.5 1.0
CA B:CYS422 4.0 28.4 1.0
NBO B:VFV502 4.1 25.1 1.0
CAT B:VFV502 4.2 25.6 1.0
C3C B:HEM501 4.2 23.6 1.0
C2A B:HEM501 4.3 26.7 1.0
C2C B:HEM501 4.3 24.3 1.0
C3A B:HEM501 4.4 29.4 1.0
C2D B:HEM501 4.4 30.5 1.0
C3D B:HEM501 4.4 30.4 1.0
C3B B:HEM501 4.5 26.7 1.0
C2B B:HEM501 4.5 22.8 1.0
N B:GLY424 4.6 20.3 1.0
C B:CYS422 4.7 28.4 1.0
N B:ILE423 4.8 25.4 1.0

Iron binding site 3 out of 4 in 4g7g

Go back to Iron Binding Sites List in 4g7g
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-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]


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-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)] within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:33.8
occ:1.00
 FE C:HEM501 0.0 33.8 1.0
NC C:HEM501 2.0 29.9 1.0
NA C:HEM501 2.0 35.3 1.0
NAX C:VFV502 2.0 27.0 1.0
ND C:HEM501 2.1 35.2 1.0
NB C:HEM501 2.1 32.4 1.0
SG C:CYS422 2.3 36.1 1.0
CAU C:VFV502 3.0 27.6 1.0
C4C C:HEM501 3.0 35.0 1.0
CAG C:VFV502 3.0 27.6 1.0
C1A C:HEM501 3.0 35.5 1.0
C1D C:HEM501 3.1 38.3 1.0
C4A C:HEM501 3.1 31.4 1.0
C4D C:HEM501 3.1 38.5 1.0
C1C C:HEM501 3.2 33.0 1.0
C4B C:HEM501 3.2 30.2 1.0
C1B C:HEM501 3.2 34.8 1.0
CB C:CYS422 3.3 33.4 1.0
CHD C:HEM501 3.3 31.1 1.0
CHA C:HEM501 3.5 35.6 1.0
CHB C:HEM501 3.5 29.7 1.0
CHC C:HEM501 3.6 29.8 1.0
NBO C:VFV502 4.1 25.0 1.0
CA C:CYS422 4.1 34.1 1.0
CAT C:VFV502 4.1 25.6 1.0
C3C C:HEM501 4.3 34.7 1.0
C2A C:HEM501 4.3 35.4 1.0
C3A C:HEM501 4.3 34.9 1.0
C2C C:HEM501 4.4 32.9 1.0
C2D C:HEM501 4.4 43.8 1.0
C3D C:HEM501 4.5 42.8 1.0
C3B C:HEM501 4.5 29.9 1.0
C2B C:HEM501 4.5 34.2 1.0
N C:GLY424 4.8 37.5 1.0
C C:CYS422 4.8 35.2 1.0
N C:ILE423 4.9 37.7 1.0
CB C:ALA291 5.0 34.0 1.0

Iron binding site 4 out of 4 in 4g7g

Go back to Iron Binding Sites List in 4g7g
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-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)]


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-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [Vni/Vnf (Vfv)] within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:27.6
occ:1.00
 FE D:HEM501 0.0 27.6 1.0
NAX D:VFV502 1.9 31.0 1.0
NC D:HEM501 2.0 26.9 1.0
NA D:HEM501 2.0 23.0 1.0
ND D:HEM501 2.1 24.7 1.0
NB D:HEM501 2.1 25.1 1.0
SG D:CYS422 2.4 28.6 1.0
CAG D:VFV502 2.6 33.5 1.0
C4C D:HEM501 3.0 27.9 1.0
C1A D:HEM501 3.0 23.4 1.0
C1D D:HEM501 3.1 28.9 1.0
C4D D:HEM501 3.1 27.7 1.0
CAU D:VFV502 3.1 28.1 1.0
C1C D:HEM501 3.1 25.5 1.0
C4B D:HEM501 3.1 22.5 1.0
C4A D:HEM501 3.2 23.3 1.0
C1B D:HEM501 3.2 25.8 1.0
CHD D:HEM501 3.3 30.4 1.0
CB D:CYS422 3.3 28.1 1.0
CHA D:HEM501 3.4 27.6 1.0
CHC D:HEM501 3.6 26.0 1.0
CHB D:HEM501 3.6 22.6 1.0
CAT D:VFV502 3.8 35.3 1.0
CA D:CYS422 4.0 29.9 1.0
NBO D:VFV502 4.1 30.2 1.0
C3C D:HEM501 4.3 30.6 1.0
C2A D:HEM501 4.3 25.2 1.0
C2C D:HEM501 4.4 30.1 1.0
C3A D:HEM501 4.4 25.0 1.0
C2D D:HEM501 4.4 31.7 1.0
C3D D:HEM501 4.4 30.6 1.0
C3B D:HEM501 4.5 24.1 1.0
C2B D:HEM501 4.5 25.5 1.0
N D:GLY424 4.7 35.1 1.0
C D:CYS422 4.8 31.6 1.0
N D:ILE423 4.8 33.1 1.0
CB D:ALA291 5.0 34.5 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 02:37:48 2024

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