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Zinc in PDB 4gsc: Structure Analysis of Insulin Degrading Enzyme with Compound BDM41559 ((S)-2-[2-(Carboxymethyl-Phenethyl-Amino)-Acetylamino]-3-(1H- Imidazol-4-Yl)-Propionic Acid Methyl Ester)

Enzymatic activity of Structure Analysis of Insulin Degrading Enzyme with Compound BDM41559 ((S)-2-[2-(Carboxymethyl-Phenethyl-Amino)-Acetylamino]-3-(1H- Imidazol-4-Yl)-Propionic Acid Methyl Ester)

All present enzymatic activity of Structure Analysis of Insulin Degrading Enzyme with Compound BDM41559 ((S)-2-[2-(Carboxymethyl-Phenethyl-Amino)-Acetylamino]-3-(1H- Imidazol-4-Yl)-Propionic Acid Methyl Ester):
3.4.24.56;

Protein crystallography data

The structure of Structure Analysis of Insulin Degrading Enzyme with Compound BDM41559 ((S)-2-[2-(Carboxymethyl-Phenethyl-Amino)-Acetylamino]-3-(1H- Imidazol-4-Yl)-Propionic Acid Methyl Ester), PDB code: 4gsc was solved by Q.Guo, R.Deprez-Poulain, B.Deprez, W.J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.85 / 2.81
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 263.759, 263.759, 91.260, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 25.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure Analysis of Insulin Degrading Enzyme with Compound BDM41559 ((S)-2-[2-(Carboxymethyl-Phenethyl-Amino)-Acetylamino]-3-(1H- Imidazol-4-Yl)-Propionic Acid Methyl Ester) (pdb code 4gsc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure Analysis of Insulin Degrading Enzyme with Compound BDM41559 ((S)-2-[2-(Carboxymethyl-Phenethyl-Amino)-Acetylamino]-3-(1H- Imidazol-4-Yl)-Propionic Acid Methyl Ester), PDB code: 4gsc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4gsc

Go back to Zinc Binding Sites List in 4gsc
Zinc binding site 1 out of 2 in the Structure Analysis of Insulin Degrading Enzyme with Compound BDM41559 ((S)-2-[2-(Carboxymethyl-Phenethyl-Amino)-Acetylamino]-3-(1H- Imidazol-4-Yl)-Propionic Acid Methyl Ester)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure Analysis of Insulin Degrading Enzyme with Compound BDM41559 ((S)-2-[2-(Carboxymethyl-Phenethyl-Amino)-Acetylamino]-3-(1H- Imidazol-4-Yl)-Propionic Acid Methyl Ester) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:2.0
occ:1.00
 OE1 A:GLU189 1.7 3.8 1.0
NE2 A:HIS108 2.0 23.1 1.0
NE2 A:HIS112 2.4 39.5 1.0
CD A:GLU189 2.5 20.7 1.0
OE2 A:GLU189 2.8 20.4 1.0
CD2 A:HIS108 2.9 31.4 1.0
CE1 A:HIS108 3.1 27.6 1.0
CE1 A:HIS112 3.4 41.0 1.0
CD2 A:HIS112 3.4 39.8 1.0
OE1 A:GLN111 3.6 41.8 1.0
OH A:TYR831 3.8 42.8 1.0
CG A:GLU189 3.9 28.0 1.0
CG A:HIS108 4.1 31.1 1.0
ND1 A:HIS108 4.1 28.9 1.0
CD A:GLN111 4.4 39.8 1.0
ND1 A:HIS112 4.5 40.3 1.0
NE2 A:GLN111 4.5 39.5 1.0
CG A:HIS112 4.5 37.9 1.0
CE1 A:TYR831 4.6 41.4 1.0
CZ A:TYR831 4.7 41.8 1.0
O A:ALA140 4.9 30.9 1.0

Zinc binding site 2 out of 2 in 4gsc

Go back to Zinc Binding Sites List in 4gsc
Zinc binding site 2 out of 2 in the Structure Analysis of Insulin Degrading Enzyme with Compound BDM41559 ((S)-2-[2-(Carboxymethyl-Phenethyl-Amino)-Acetylamino]-3-(1H- Imidazol-4-Yl)-Propionic Acid Methyl Ester)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure Analysis of Insulin Degrading Enzyme with Compound BDM41559 ((S)-2-[2-(Carboxymethyl-Phenethyl-Amino)-Acetylamino]-3-(1H- Imidazol-4-Yl)-Propionic Acid Methyl Ester) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1101

b:2.0
occ:1.00
 OE2 B:GLU189 1.8 34.0 1.0
OE1 B:GLU189 1.9 20.1 1.0
NE2 B:HIS112 1.9 36.7 1.0
NE2 B:HIS108 2.0 27.2 1.0
CD B:GLU189 2.2 32.2 1.0
CE1 B:HIS112 2.6 41.3 1.0
CE1 B:HIS108 2.9 31.7 1.0
CD2 B:HIS112 3.1 39.9 1.0
CD2 B:HIS108 3.1 34.7 1.0
OH B:TYR831 3.7 58.9 1.0
ND1 B:HIS112 3.7 39.9 1.0
OE1 B:GLN111 3.7 42.3 1.0
CG B:GLU189 3.8 35.9 1.0
CG B:HIS112 4.0 40.7 1.0
ND1 B:HIS108 4.0 33.7 1.0
CG B:HIS108 4.2 33.8 1.0
CE1 B:TYR831 4.3 56.4 1.0
CZ B:TYR831 4.3 57.4 1.0
NE2 B:GLN111 4.4 42.1 1.0
CD B:GLN111 4.4 39.9 1.0
CB B:GLU189 4.9 39.8 1.0

Reference:

J.Charton, M.Gauriot, Q.Guo, N.Hennuyer, X.Marechal, J.Dumont, M.Hamdane, V.Pottiez, V.Landry, O.Sperandio, M.Flipo, L.Buee, B.Staels, F.Leroux, W.J.Tang, B.Deprez, R.Deprez-Poulain. Imidazole-Derived 2-[N-Carbamoylmethyl-Alkylamino]Acetic Acids, Substrate-Dependent Modulators of Insulin-Degrading Enzyme in Amyloid-Beta Hydrolysis. Eur.J.Med.Chem. V. 79 184 2014.
ISSN: ISSN 0223-5234
PubMed: 24735644
DOI: 10.1016/J.EJMECH.2014.04.009
Page generated: Sat Oct 26 23:29:01 2024

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