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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 2wk3

Go back to Zinc Binding Sites List in 2wk3
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 2wk3

Go back to Zinc Binding Sites List in 2wk3
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

Reference:

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
Page generated: Sat Sep 26 04:24:20 2020
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