Zinc in PDB 2wby: Crystal Structure of Human Insulin-Degrading Enzyme in Complex with Insulin

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

The structure of Crystal Structure of Human Insulin-Degrading Enzyme in Complex with Insulin, PDB code: 2wby was solved by M.Manolopoulou, Q.Guo, E.Malito, A.B.Schilling, W.J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.08 / 2.60
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	262.319, 262.319, 90.609, 90.00, 90.00, 120.00
R / Rfree (%)	16.4 / 21.8

The binding sites of Zinc atom in the Crystal Structure of Human Insulin-Degrading Enzyme in Complex with Insulin (pdb code 2wby). 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 Human Insulin-Degrading Enzyme in Complex with Insulin, PDB code: 2wby:
Jump to Zinc binding site number: 1; 2;

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


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 Human Insulin-Degrading Enzyme in Complex with Insulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3012 b:2.0 occ:1.00 OE1 A:GLU189 1.0 2.0 1.0 N D:PHE1 1.2 25.8 1.0 NE2 A:HIS112 1.7 16.6 1.0 NE2 A:HIS108 1.8 14.7 1.0 CD A:GLU189 2.3 15.9 1.0 CA D:PHE1 2.5 27.4 1.0 CE1 A:HIS112 2.6 20.9 1.0 CD2 A:HIS108 2.8 17.8 1.0 CE1 A:HIS108 2.9 17.7 1.0 CD2 A:HIS112 2.9 19.9 1.0 OE2 A:GLU189 3.0 22.4 1.0 C D:PHE1 3.5 28.3 1.0 CB D:PHE1 3.8 28.0 1.0 ND1 A:HIS112 3.8 16.1 1.0 CG A:GLU189 3.9 15.1 1.0 ND1 A:HIS108 3.9 15.2 1.0 NE2 A:GLN111 4.0 14.5 1.0 CG A:HIS112 4.0 16.8 1.0 CG A:HIS108 4.0 14.8 1.0 O A:HOH2055 4.0 26.6 1.0 N D:VAL2 4.0 28.9 1.0 O D:PHE1 4.2 27.2 1.0 O A:HOH2340 4.4 42.6 1.0 OE1 A:GLN111 4.4 26.6 1.0 CD A:GLN111 4.6 20.6 1.0 CB A:GLU189 4.8 20.5 1.0 CE1 A:TYR831 4.8 27.3 1.0 OH A:TYR831 4.9 27.6 1.0

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


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 Human Insulin-Degrading Enzyme in Complex with Insulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3012 b:2.0 occ:1.00 N F:PHE1 1.1 26.8 1.0 OE2 B:GLU189 1.1 13.5 1.0 NE2 B:HIS108 1.7 15.5 1.0 NE2 B:HIS112 1.8 16.5 1.0 CD B:GLU189 2.4 22.1 1.0 CA F:PHE1 2.5 28.5 1.0 CE1 B:HIS108 2.6 21.5 1.0 CE1 B:HIS112 2.7 20.5 1.0 CD2 B:HIS108 2.8 16.9 1.0 CD2 B:HIS112 2.9 18.7 1.0 OE1 B:GLU189 3.2 26.6 1.0 C F:PHE1 3.5 30.1 1.0 CB F:PHE1 3.7 29.4 1.0 ND1 B:HIS108 3.8 17.5 1.0 ND1 B:HIS112 3.8 14.1 1.0 CG B:HIS108 3.9 15.5 1.0 CG B:GLU189 3.9 18.6 1.0 O F:HOH2001 4.0 28.7 1.0 CG B:HIS112 4.0 17.0 1.0 NE2 B:GLN111 4.0 17.9 1.0 N F:VAL2 4.0 31.1 1.0 O F:PHE1 4.2 39.0 1.0 O B:HOH2241 4.5 48.6 1.0 OE1 B:GLN111 4.5 25.3 1.0 CD B:GLN111 4.7 23.7 1.0 CE1 B:TYR831 4.7 32.5 1.0 CB B:GLU189 4.7 22.2 1.0

M.Manolopoulou, Q.Guo, E.Malito, A.B.Schilling, W.J.Tang. Molecular Basis of Catalytic Chamber-Assisted Unfolding and Cleavage of Human Insulin By Human Insulin Degrading Enzyme. J.Biol.Chem. V. 284 14177 2009.
ISSN: ISSN 0021-9258
PubMed: 19321446
DOI: 10.1074/JBC.M900068200