Zinc in PDB 3ofi: Crystal Structure of Human Insulin-Degrading Enzyme in Complex with Ubiquitin

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

The structure of Crystal Structure of Human Insulin-Degrading Enzyme in Complex with Ubiquitin, PDB code: 3ofi was solved by V.Kalas, L.A.Ralat, W.-J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.35
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	262.943, 262.943, 90.968, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 24

The binding sites of Zinc atom in the Crystal Structure of Human Insulin-Degrading Enzyme in Complex with Ubiquitin (pdb code 3ofi). 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 Ubiquitin, PDB code: 3ofi:
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 Ubiquitin


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 Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2012 b:34.3 occ:1.00 OE1 A:GLU189 2.1 28.5 1.0 NE2 A:HIS108 2.1 22.5 1.0 NE2 A:HIS112 2.2 22.9 1.0 OE2 A:GLU189 2.7 26.2 1.0 CD A:GLU189 2.7 27.3 1.0 CE1 A:HIS108 3.1 23.3 1.0 CE1 A:HIS112 3.1 23.6 1.0 CD2 A:HIS108 3.1 22.6 1.0 CD2 A:HIS112 3.2 21.0 1.0 ND1 A:HIS108 4.2 26.7 1.0 ND1 A:HIS112 4.2 24.6 1.0 CG A:HIS108 4.3 24.6 1.0 CG A:GLU189 4.3 27.4 1.0 CG A:HIS112 4.3 21.5 1.0 NE2 A:GLN111 4.4 24.9 1.0 CE1 A:TYR831 4.5 25.1 1.0 OE1 A:GLN111 4.6 34.6 1.0 OH A:TYR831 4.8 29.2 1.0 CB A:GLU189 4.9 24.4 1.0 CD A:GLN111 4.9 29.0 1.0

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


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 Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2012 b:36.2 occ:1.00 NE2 B:HIS108 2.0 22.3 1.0 OE1 B:GLU189 2.1 30.8 1.0 NE2 B:HIS112 2.2 21.4 1.0 CD B:GLU189 2.8 26.1 1.0 OE2 B:GLU189 2.9 24.3 1.0 CE1 B:HIS108 2.9 23.3 1.0 CE1 B:HIS112 3.1 27.0 1.0 CD2 B:HIS112 3.1 23.6 1.0 CD2 B:HIS108 3.2 15.9 1.0 ND1 B:HIS108 4.0 25.3 1.0 CG B:HIS108 4.2 23.8 1.0 ND1 B:HIS112 4.3 23.8 1.0 CG B:HIS112 4.3 25.9 1.0 CG B:GLU189 4.3 26.9 1.0 OE1 B:GLN111 4.4 32.9 1.0 CE1 B:TYR831 4.4 29.6 1.0 NE2 B:GLN111 4.7 28.5 1.0 OH B:TYR831 4.7 35.0 1.0 CB B:GLU189 4.9 25.5 1.0 CD B:GLN111 4.9 28.7 1.0 CZ B:TYR831 5.0 32.4 1.0

L.A.Ralat, V.Kalas, Z.Zheng, R.D.Goldman, T.R.Sosnick, W.J.Tang. Ubiquitin Is A Novel Substrate For Human Insulin-Degrading Enzyme. J.Mol.Biol. V. 406 454 2011.
ISSN: ISSN 0022-2836
PubMed: 21185309
DOI: 10.1016/J.JMB.2010.12.026