Zinc in PDB 4nxo: Crystal Structure of Insulin Degrading Enzyme in Complex with BDM44768

All present enzymatic activity of Crystal Structure of Insulin Degrading Enzyme in Complex with BDM44768:
3.4.24.56;

The structure of Crystal Structure of Insulin Degrading Enzyme in Complex with BDM44768, PDB code: 4nxo was solved by W.G.Liang, R.Deprez, B.Deprez, W.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.82 / 2.73
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	262.909, 262.909, 86.337, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 21.9

The structure of Crystal Structure of Insulin Degrading Enzyme in Complex with BDM44768 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Insulin Degrading Enzyme in Complex with BDM44768 (pdb code 4nxo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Insulin Degrading Enzyme in Complex with BDM44768, PDB code: 4nxo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Insulin Degrading Enzyme in Complex with BDM44768


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Insulin Degrading Enzyme in Complex with BDM44768 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:58.4 occ:1.00 O32 A:2H71102 1.9 92.8 1.0 OE1 A:GLU189 2.0 72.7 1.0 NE2 A:HIS112 2.1 52.5 1.0 NE2 A:HIS108 2.3 71.8 1.0 O33 A:2H71102 2.5 98.4 1.0 CD A:GLU189 2.8 66.6 1.0 N31 A:2H71102 2.8 69.7 1.0 OE2 A:GLU189 2.8 67.7 1.0 CE1 A:HIS112 2.9 67.6 1.0 C30 A:2H71102 3.0 68.0 1.0 CE1 A:HIS108 3.1 67.5 1.0 CD2 A:HIS112 3.1 69.0 1.0 CD2 A:HIS108 3.4 56.9 1.0 ND1 A:HIS112 4.1 69.0 1.0 CG A:HIS112 4.2 61.2 1.0 CE1 A:TYR831 4.2 50.8 1.0 CG A:GLU189 4.2 60.2 1.0 ND1 A:HIS108 4.3 71.3 1.0 CG A:HIS108 4.5 67.8 1.0 OH A:TYR831 4.5 64.3 1.0 C29 A:2H71102 4.5 79.2 0.2 CB A:GLU189 4.7 48.2 1.0 CZ A:TYR831 4.7 62.5 1.0 OE1 A:GLN111 5.0 70.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Insulin Degrading Enzyme in Complex with BDM44768


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Insulin Degrading Enzyme in Complex with BDM44768 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:55.2 occ:1.00 OE1 B:GLU189 1.9 65.6 1.0 O32 B:2H71102 2.1 73.4 1.0 NE2 B:HIS112 2.1 69.3 1.0 NE2 B:HIS108 2.2 43.5 1.0 O33 B:2H71102 2.6 85.4 1.0 CD B:GLU189 2.8 55.2 1.0 OE2 B:GLU189 2.9 62.6 1.0 N31 B:2H71102 3.0 68.6 1.0 CE1 B:HIS108 3.0 39.9 1.0 CE1 B:HIS112 3.1 61.0 1.0 CD2 B:HIS112 3.1 61.9 1.0 C30 B:2H71102 3.2 65.1 1.0 CD2 B:HIS108 3.2 48.3 1.0 ND1 B:HIS112 4.2 62.9 1.0 ND1 B:HIS108 4.2 49.7 1.0 CG B:GLU189 4.2 55.9 1.0 CG B:HIS112 4.2 53.0 1.0 O B:HOH1253 4.3 47.8 1.0 CG B:HIS108 4.3 51.4 1.0 CE1 B:TYR831 4.3 54.5 1.0 OH B:TYR831 4.5 63.3 1.0 CB B:GLU189 4.6 62.7 1.0 C29 B:2H71102 4.6 75.2 0.5 OE1 B:GLN111 4.8 65.9 1.0 CZ B:TYR831 4.8 68.9 1.0 C18 B:2H71102 4.9 70.9 0.9 CG2 B:VAL186 5.0 43.6 1.0 NE2 B:GLN111 5.0 52.1 1.0

R.Deprez-Poulain, N.Hennuyer, D.Bosc, W.G.Liang, E.Enee, X.Marechal, J.Charton, J.Totobenazara, G.Berte, J.Jahklal, T.Verdelet, J.Dumont, S.Dassonneville, E.Woitrain, M.Gauriot, C.Paquet, I.Duplan, P.Hermant, F.X.Cantrelle, E.Sevin, M.Culot, V.Landry, A.Herledan, C.Piveteau, G.Lippens, F.Leroux, W.J.Tang, P.Van Endert, B.Staels, B.Deprez. Catalytic Site Inhibition of Insulin-Degrading Enzyme By A Small Molecule Induces Glucose Intolerance in Mice. Nat Commun V. 6 8250 2015.
ISSN: ESSN 2041-1723
PubMed: 26394692
DOI: 10.1038/NCOMMS9250