Zinc in PDB 6gbx: Crystal Structure of Human Glutaminyl Cyclase Variant Y115E-Y117E in Complex with SEN177

All present enzymatic activity of Crystal Structure of Human Glutaminyl Cyclase Variant Y115E-Y117E in Complex with SEN177:
2.3.2.5;

The structure of Crystal Structure of Human Glutaminyl Cyclase Variant Y115E-Y117E in Complex with SEN177, PDB code: 6gbx was solved by C.Pozzi, F.Di Pisa, M.Benvenuti, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.23 / 1.72
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.140, 149.810, 95.980, 90.00, 97.18, 90.00
R / Rfree (%)	15.8 / 18.3

The structure of Crystal Structure of Human Glutaminyl Cyclase Variant Y115E-Y117E in Complex with SEN177 also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Human Glutaminyl Cyclase Variant Y115E-Y117E in Complex with SEN177 (pdb code 6gbx). 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 Human Glutaminyl Cyclase Variant Y115E-Y117E in Complex with SEN177, PDB code: 6gbx:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Human Glutaminyl Cyclase Variant Y115E-Y117E in Complex with SEN177


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 Glutaminyl Cyclase Variant Y115E-Y117E in Complex with SEN177 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:12.4 occ:1.00 OD2 A:ASP159 1.9 10.2 1.0 OE2 A:GLU202 2.0 11.0 1.0 N5 A:S77403 2.0 11.3 1.0 NE2 A:HIS330 2.1 11.7 1.0 CG A:ASP159 2.7 10.4 1.0 CD A:GLU202 2.8 9.8 1.0 N4 A:S77403 2.9 11.4 1.0 OD1 A:ASP159 2.9 10.3 1.0 OE1 A:GLU202 2.9 10.8 1.0 CD2 A:HIS330 3.0 11.4 1.0 C13 A:S77403 3.1 11.9 1.0 CE1 A:HIS330 3.2 12.1 1.0 O A:HOH555 4.0 10.8 1.0 C4 A:S77403 4.0 12.4 1.0 N2 A:S77403 4.1 12.5 1.0 NE1 A:TRP329 4.2 13.9 1.0 CG A:HIS330 4.2 11.9 1.0 CB A:ASP159 4.2 10.9 1.0 CG A:GLU202 4.2 9.8 1.0 ND1 A:HIS330 4.2 13.0 1.0 O A:HOH525 4.5 11.5 1.0 OE1 A:GLU201 4.5 13.2 1.0 CD1 A:TRP329 4.6 14.0 1.0 CD2 A:LEU249 4.6 13.3 1.0 NE2 A:HIS140 4.8 9.8 1.0 O A:ASP159 5.0 10.8 1.0 CD A:LYS144 5.0 13.9 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Human Glutaminyl Cyclase Variant Y115E-Y117E in Complex with SEN177


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 Glutaminyl Cyclase Variant Y115E-Y117E in Complex with SEN177 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:12.3 occ:1.00 OD2 B:ASP159 1.9 9.6 1.0 OE2 B:GLU202 2.0 9.1 1.0 N5 B:S77403 2.1 13.2 1.0 NE2 B:HIS330 2.1 10.9 1.0 CG B:ASP159 2.7 10.6 1.0 CD B:GLU202 2.8 9.9 1.0 OE1 B:GLU202 2.9 9.8 1.0 OD1 B:ASP159 2.9 11.6 1.0 N4 B:S77403 2.9 12.5 1.0 CD2 B:HIS330 3.0 11.8 1.0 CE1 B:HIS330 3.1 12.5 1.0 C13 B:S77403 3.2 12.4 1.0 O B:HOH592 4.0 11.4 1.0 C4 B:S77403 4.1 13.1 1.0 NE1 B:TRP329 4.1 13.3 1.0 CB B:ASP159 4.2 10.5 1.0 CG B:HIS330 4.2 11.9 1.0 CG B:GLU202 4.2 9.4 1.0 N2 B:S77403 4.2 12.8 1.0 ND1 B:HIS330 4.2 11.6 1.0 O B:HOH591 4.5 12.5 1.0 CD1 B:TRP329 4.6 13.3 1.0 OE1 B:GLU201 4.6 12.9 1.0 CD2 B:LEU249 4.7 11.1 1.0 NE2 B:HIS140 4.8 9.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Human Glutaminyl Cyclase Variant Y115E-Y117E in Complex with SEN177


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 Human Glutaminyl Cyclase Variant Y115E-Y117E in Complex with SEN177 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:12.1 occ:1.00 OD2 C:ASP159 1.9 9.8 1.0 OE2 C:GLU202 2.0 11.2 1.0 N5 C:S77403 2.1 10.9 1.0 NE2 C:HIS330 2.1 12.3 1.0 CG C:ASP159 2.7 10.3 1.0 CD C:GLU202 2.8 10.3 1.0 OD1 C:ASP159 2.9 10.1 1.0 OE1 C:GLU202 2.9 10.4 1.0 CD2 C:HIS330 3.0 11.7 1.0 N4 C:S77403 3.0 11.5 1.0 C13 C:S77403 3.1 11.2 1.0 CE1 C:HIS330 3.2 12.9 1.0 O C:HOH573 3.9 11.2 1.0 C4 C:S77403 4.1 11.5 1.0 NE1 C:TRP329 4.1 13.8 1.0 CB C:ASP159 4.1 10.6 1.0 N2 C:S77403 4.2 11.8 1.0 CG C:HIS330 4.2 12.1 1.0 CG C:GLU202 4.2 9.8 1.0 ND1 C:HIS330 4.2 12.8 1.0 O C:HOH624 4.4 11.4 1.0 CD1 C:TRP329 4.5 13.8 1.0 OE1 C:GLU201 4.5 12.7 1.0 CD2 C:LEU249 4.6 12.7 1.0 NE2 C:HIS140 4.8 9.0 1.0

C.Pozzi, F.Di Pisa, M.Benvenuti, S.Mangani. The Structure of the Human Glutaminyl Cyclase-SEN177 Complex Indicates Routes For Developing New Potent Inhibitors As Possible Agents For the Treatment of Neurological Disorders. J. Biol. Inorg. Chem. V. 23 1219 2018.
ISSN: ESSN 1432-1327
PubMed: 30132075
DOI: 10.1007/S00775-018-1605-1