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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 2wby

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

Go back to Zinc Binding Sites List in 2wby
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

Reference:

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
Page generated: Thu Oct 17 04:51:37 2024

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