Zinc in PDB 2wk3: Crystal Structure of Human Insulin-Degrading Enzyme in Complex with Amyloid-Beta (1-42)

All present enzymatic activity of Crystal Structure of Human Insulin-Degrading Enzyme in Complex with Amyloid-Beta (1-42):
3.4.24.56;

The structure of Crystal Structure of Human Insulin-Degrading Enzyme in Complex with Amyloid-Beta (1-42), PDB code: 2wk3 was solved by Q.Guo, W.J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.44 / 2.59
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	261.628, 261.628, 90.675, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 23.2

The binding sites of Zinc atom in the Crystal Structure of Human Insulin-Degrading Enzyme in Complex with Amyloid-Beta (1-42) (pdb code 2wk3). 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 Amyloid-Beta (1-42), PDB code: 2wk3:
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 Amyloid-Beta (1-42)


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 Amyloid-Beta (1-42) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3013 b:50.5 occ:0.50 O C:PHE19 1.7 75.7 1.0 NE2 A:HIS108 2.1 30.1 1.0 OE1 A:GLU189 2.2 36.6 1.0 NE2 A:HIS112 2.5 30.8 1.0 C C:PHE19 2.6 75.8 1.0 OE2 A:GLU189 2.9 39.0 1.0 CD A:GLU189 2.9 36.1 1.0 CE1 A:HIS108 3.0 27.5 1.0 CD2 A:HIS108 3.2 28.3 1.0 CD2 A:HIS112 3.3 27.2 1.0 N C:PHE19 3.5 75.3 1.0 N C:PHE20 3.5 75.1 1.0 CE1 A:HIS112 3.5 29.0 1.0 CA C:PHE19 3.6 76.4 1.0 C C:VAL18 3.7 74.6 1.0 CA C:PHE20 3.8 74.7 1.0 O C:VAL18 3.9 74.1 1.0 ND1 A:HIS108 4.1 30.4 1.0 CG A:HIS108 4.2 28.2 1.0 NE2 A:GLN111 4.3 36.6 1.0 OH A:TYR831 4.4 34.5 1.0 CG A:GLU189 4.4 31.7 1.0 OE1 A:GLN111 4.5 33.3 1.0 CG A:HIS112 4.5 26.0 1.0 CE1 A:TYR831 4.6 30.5 1.0 ND1 A:HIS112 4.6 27.8 1.0 CB C:VAL18 4.6 73.7 1.0 CA C:VAL18 4.6 74.4 1.0 C C:PHE20 4.6 74.4 1.0 O C:PHE20 4.7 73.7 1.0 CD A:GLN111 4.8 33.0 1.0 CB C:PHE19 4.8 76.9 1.0 CB C:PHE20 4.9 74.5 1.0 CZ A:TYR831 5.0 31.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Insulin-Degrading Enzyme in Complex with Amyloid-Beta (1-42)


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 Amyloid-Beta (1-42) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3013 b:52.4 occ:0.50 O D:PHE19 1.8 77.4 1.0 NE2 B:HIS108 2.2 28.5 1.0 NE2 B:HIS112 2.3 35.0 1.0 OE1 B:GLU189 2.4 43.2 1.0 C D:PHE19 2.8 77.4 1.0 CE1 B:HIS108 2.8 30.4 1.0 CD2 B:HIS112 3.2 34.1 1.0 CD B:GLU189 3.2 40.0 1.0 CE1 B:HIS112 3.3 34.6 1.0 OE2 B:GLU189 3.4 42.4 1.0 CD2 B:HIS108 3.4 26.3 1.0 CA D:PHE20 3.5 77.0 1.0 N D:PHE20 3.5 77.0 1.0 N D:PHE19 3.9 78.0 1.0 CA D:PHE19 3.9 78.2 1.0 ND1 B:HIS108 4.1 28.1 1.0 C D:VAL18 4.2 77.9 1.0 CE1 B:TYR831 4.2 37.3 1.0 OH B:TYR831 4.3 41.7 1.0 O D:VAL18 4.3 77.3 1.0 CG B:HIS112 4.3 33.0 1.0 CG B:HIS108 4.4 25.7 1.0 ND1 B:HIS112 4.4 32.3 1.0 C D:PHE20 4.4 77.0 1.0 NE2 B:GLN111 4.4 33.4 1.0 O D:PHE20 4.5 76.1 1.0 OE1 B:GLN111 4.6 32.6 1.0 CB D:PHE20 4.6 76.7 1.0 CG B:GLU189 4.6 34.6 1.0 CZ B:TYR831 4.7 37.3 1.0 CB D:VAL18 4.9 77.2 1.0 CD B:GLN111 4.9 31.9 1.0

Q.Guo, M.Manolopoulou, Y.Bian, A.B.Schilling, W.J.Tang. Molecular Basis For the Recognition and Cleavages of Igf-II, Tgf-Alpha, and Amylin By Human Insulin Degrading Enzyme. J.Mol.Biol. V. 395 430 2010.
ISSN: ISSN 0022-2836
PubMed: 19896952
DOI: 10.1016/J.JMB.2009.10.072