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Zinc in PDB 4ywy: Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase in Complex with Inhibitor Pbd-150

Enzymatic activity of Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase in Complex with Inhibitor Pbd-150

All present enzymatic activity of Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase in Complex with Inhibitor Pbd-150:
2.3.2.5;

Protein crystallography data

The structure of Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase in Complex with Inhibitor Pbd-150, PDB code: 4ywy was solved by F.Di Pisa, C.Pozzi, M.Benvenuti, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.99 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 86.429, 149.540, 96.210, 90.00, 96.82, 90.00
R / Rfree (%) 16.4 / 21.1

Other elements in 4ywy:

The structure of Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase in Complex with Inhibitor Pbd-150 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase in Complex with Inhibitor Pbd-150 (pdb code 4ywy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase in Complex with Inhibitor Pbd-150, PDB code: 4ywy:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4ywy

Go back to Zinc Binding Sites List in 4ywy
Zinc binding site 1 out of 3 in the Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase in Complex with Inhibitor Pbd-150


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 Double Mutant Y115E Y117E Human Glutaminyl Cyclase in Complex with Inhibitor Pbd-150 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:8.1
occ:1.00
 OE2 A:GLU202 1.9 8.7 1.0
OD2 A:ASP159 1.9 6.8 1.0
NAM A:PBD402 2.0 7.1 1.0
NE2 A:HIS330 2.2 9.4 1.0
CD A:GLU202 2.7 8.1 1.0
CG A:ASP159 2.8 7.8 1.0
OE1 A:GLU202 2.8 8.0 1.0
OD1 A:ASP159 2.9 8.2 1.0
CAH A:PBD402 2.9 7.1 1.0
CAD A:PBD402 3.0 7.6 1.0
CD2 A:HIS330 3.1 9.2 1.0
CE1 A:HIS330 3.2 9.3 1.0
NE1 A:TRP329 3.9 8.4 1.0
O A:HOH592 4.0 4.6 1.0
NAV A:PBD402 4.1 7.5 1.0
CAG A:PBD402 4.1 7.4 1.0
CG A:GLU202 4.1 8.0 1.0
CG A:HIS330 4.2 9.4 1.0
CB A:ASP159 4.2 7.9 1.0
ND1 A:HIS330 4.3 9.5 1.0
OE1 A:GLU201 4.4 8.8 1.0
O A:HOH555 4.6 7.0 1.0
CD1 A:TRP329 4.6 8.3 1.0
NE2 A:HIS140 4.6 5.3 1.0
CE2 A:TRP329 4.7 8.7 1.0
CD2 A:LEU249 4.8 6.9 1.0
CZ2 A:TRP329 4.9 8.4 1.0
CE1 A:HIS140 4.9 5.2 1.0
CD A:LYS144 4.9 9.3 1.0
O A:ASP159 5.0 8.6 1.0

Zinc binding site 2 out of 3 in 4ywy

Go back to Zinc Binding Sites List in 4ywy
Zinc binding site 2 out of 3 in the Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase in Complex with Inhibitor Pbd-150


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 Double Mutant Y115E Y117E Human Glutaminyl Cyclase in Complex with Inhibitor Pbd-150 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:8.6
occ:1.00
 OD2 B:ASP159 1.9 6.1 1.0
OE2 B:GLU202 1.9 7.4 1.0
NAM B:PBD402 2.0 8.3 1.0
NE2 B:HIS330 2.1 9.2 1.0
CG B:ASP159 2.7 6.4 1.0
CD B:GLU202 2.8 7.5 1.0
OD1 B:ASP159 2.8 7.0 1.0
OE1 B:GLU202 2.9 7.2 1.0
CD2 B:HIS330 3.0 9.7 1.0
CAH B:PBD402 3.0 8.0 1.0
CAD B:PBD402 3.0 8.5 1.0
CE1 B:HIS330 3.2 9.6 1.0
O B:HOH566 3.9 4.2 1.0
NE1 B:TRP329 3.9 8.7 1.0
CG B:GLU202 4.2 7.6 1.0
NAV B:PBD402 4.2 8.8 1.0
CAG B:PBD402 4.2 8.5 1.0
CG B:HIS330 4.2 9.3 1.0
CB B:ASP159 4.2 6.9 1.0
ND1 B:HIS330 4.2 9.7 1.0
OE1 B:GLU201 4.5 7.2 1.0
O B:HOH658 4.5 7.8 1.0
CE2 B:TRP329 4.6 9.4 1.0
NE2 B:HIS140 4.7 7.3 1.0
CD1 B:TRP329 4.7 9.1 1.0
CD2 B:LEU249 4.7 6.5 1.0
CZ2 B:TRP329 4.9 9.5 1.0
CD B:LYS144 4.9 8.6 1.0
CE1 B:HIS140 4.9 7.3 1.0
O B:ASP159 5.0 8.5 1.0

Zinc binding site 3 out of 3 in 4ywy

Go back to Zinc Binding Sites List in 4ywy
Zinc binding site 3 out of 3 in the Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase in Complex with Inhibitor Pbd-150


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase in Complex with Inhibitor Pbd-150 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:8.4
occ:1.00
 OD2 C:ASP159 1.9 7.1 1.0
OE2 C:GLU202 2.0 8.5 1.0
NAM C:PBD402 2.1 9.3 1.0
NE2 C:HIS330 2.1 10.7 1.0
CG C:ASP159 2.7 7.5 1.0
CD C:GLU202 2.7 7.8 1.0
OD1 C:ASP159 2.9 8.0 1.0
OE1 C:GLU202 2.9 8.2 1.0
CAD C:PBD402 3.0 8.9 1.0
CD2 C:HIS330 3.0 10.9 1.0
CE1 C:HIS330 3.1 10.7 1.0
CAH C:PBD402 3.1 8.6 1.0
NE1 C:TRP329 3.8 10.3 1.0
O C:HOH567 3.9 5.2 1.0
CB C:ASP159 4.2 7.8 1.0
CG C:GLU202 4.2 7.9 1.0
CAG C:PBD402 4.2 9.1 1.0
NAV C:PBD402 4.2 8.6 1.0
CG C:HIS330 4.2 10.2 1.0
ND1 C:HIS330 4.2 10.7 1.0
CD1 C:TRP329 4.6 10.3 1.0
OE1 C:GLU201 4.6 8.9 1.0
CE2 C:TRP329 4.6 10.0 1.0
O C:HOH529 4.6 8.4 1.0
NE2 C:HIS140 4.7 6.9 1.0
CD2 C:LEU249 4.8 8.8 1.0
CZ2 C:TRP329 4.9 9.6 1.0
O C:ASP159 5.0 8.9 1.0

Reference:

F.Dipisa, C.Pozzi, M.Benvenuti, M.Andreini, G.Marconi, S.Mangani. The Soluble Y115E-Y117E Variant of Human Glutaminyl Cyclase Is A Valid Target For X-Ray and uc(Nmr) Screening of Inhibitors Against Alzheimer Disease. Acta Crystallogr.,Sect.F V. 71 986 2015.
ISSN: ESSN 2053-230X
PubMed: 26249687
DOI: 10.1107/S2053230X15010389
Page generated: Sun Oct 27 11:29:44 2024

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