Zinc in PDB 4yu9: Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase

All present enzymatic activity of Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase:
2.3.2.5;

The structure of Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase, PDB code: 4yu9 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)	95.65 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.380, 149.630, 96.300, 90.00, 96.68, 90.00
R / Rfree (%)	21.1 / 25.4

The binding sites of Zinc atom in the Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase (pdb code 4yu9). 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, PDB code: 4yu9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:13.4 occ:1.00 OE2 A:GLU202 1.8 8.1 1.0 OD2 A:ASP159 2.0 6.7 1.0 NE2 A:HIS330 2.1 15.0 1.0 O A:HOH816 2.1 14.0 1.0 CD A:GLU202 2.7 8.3 1.0 CG A:ASP159 2.7 6.7 1.0 OD1 A:ASP159 2.8 6.5 1.0 CD2 A:HIS330 2.9 14.7 1.0 OE1 A:GLU202 3.0 7.9 1.0 CE1 A:HIS330 3.1 14.0 1.0 O A:HOH571 4.0 7.7 1.0 NE1 A:TRP329 4.1 11.0 1.0 CG A:GLU202 4.1 8.7 1.0 CG A:HIS330 4.1 14.0 1.0 CB A:ASP159 4.2 6.9 1.0 ND1 A:HIS330 4.2 15.0 1.0 OE1 A:GLU201 4.5 11.8 1.0 O A:HOH585 4.6 6.5 1.0 CD2 A:LEU249 4.7 7.2 1.0 NE2 A:HIS140 4.7 8.5 1.0 O A:HOH823 4.7 18.1 1.0 CD1 A:TRP329 4.8 11.3 1.0 CD A:LYS144 4.8 11.5 1.0 CE2 A:TRP329 4.8 11.7 1.0 O A:ASP159 5.0 7.6 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:12.7 occ:1.00 O B:HOH812 1.8 29.5 1.0 OE2 B:GLU202 1.9 8.6 1.0 OD2 B:ASP159 2.1 7.6 1.0 NE2 B:HIS330 2.1 12.2 1.0 CD B:GLU202 2.7 8.5 1.0 OE1 B:GLU202 2.8 8.3 1.0 CG B:ASP159 2.8 8.1 1.0 OD1 B:ASP159 2.9 7.7 1.0 CD2 B:HIS330 3.0 11.9 1.0 CE1 B:HIS330 3.1 11.9 1.0 O B:HOH543 4.0 6.2 1.0 NE1 B:TRP329 4.1 12.2 1.0 CG B:GLU202 4.1 8.9 1.0 CG B:HIS330 4.2 12.0 1.0 ND1 B:HIS330 4.2 12.3 1.0 CB B:ASP159 4.3 8.5 1.0 O B:HOH565 4.5 6.5 1.0 OE1 B:GLU201 4.5 10.9 1.0 CD2 B:LEU249 4.5 8.6 1.0 NE2 B:HIS140 4.7 9.1 1.0 CD1 B:TRP329 4.7 11.9 1.0 O B:HOH774 4.8 19.4 1.0 CE2 B:TRP329 4.8 12.2 1.0 CD B:LYS144 4.9 12.2 1.0 CE1 B:HIS140 5.0 8.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Double Mutant Y115E Y117E Human Glutaminyl Cyclase


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:13.8 occ:1.00 OE2 C:GLU202 1.8 11.8 1.0 OD2 C:ASP159 1.9 8.0 1.0 O C:HOH790 2.1 21.0 1.0 NE2 C:HIS330 2.1 13.0 1.0 CD C:GLU202 2.7 10.9 1.0 CG C:ASP159 2.7 8.5 1.0 OD1 C:ASP159 2.8 8.1 1.0 OE1 C:GLU202 2.9 11.7 1.0 CD2 C:HIS330 3.0 13.1 1.0 CE1 C:HIS330 3.2 12.9 1.0 O C:HOH577 3.8 6.7 1.0 CG C:GLU202 4.1 10.8 1.0 NE1 C:TRP329 4.1 10.3 1.0 CB C:ASP159 4.2 8.7 1.0 CG C:HIS330 4.2 12.8 1.0 ND1 C:HIS330 4.3 13.0 1.0 O C:HOH579 4.4 10.8 1.0 OE1 C:GLU201 4.5 12.6 1.0 CD2 C:LEU249 4.6 11.2 1.0 CD C:LYS144 4.7 13.5 1.0 NE2 C:HIS140 4.7 10.3 1.0 CE2 C:TRP329 4.8 11.1 1.0 CD1 C:TRP329 4.8 11.0 1.0 CE1 C:HIS140 4.9 10.4 1.0 O C:ASP159 4.9 8.6 1.0

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