Zinc in PDB 7cp0: Crystal Structure of Double Mutant Y115E Y117E Human Secretory Glutaminyl Cyclase

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

The structure of Crystal Structure of Double Mutant Y115E Y117E Human Secretory Glutaminyl Cyclase, PDB code: 7cp0 was solved by K.V.Dileep, K.Ihara, N.Sakai, M.Shirozu, K.Y.J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.05 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.277, 149.383, 96.032, 90, 96.91, 90
R / Rfree (%)	20.5 / 22.3

The binding sites of Zinc atom in the Crystal Structure of Double Mutant Y115E Y117E Human Secretory Glutaminyl Cyclase (pdb code 7cp0). 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 Secretory Glutaminyl Cyclase, PDB code: 7cp0:
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 Secretory 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 Secretory Glutaminyl Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:14.2 occ:1.00 OD2 A:ASP159 1.9 10.3 1.0 O A:HOH668 1.9 15.0 1.0 OE2 A:GLU202 2.0 10.9 1.0 NE2 A:HIS330 2.1 16.3 1.0 CG A:ASP159 2.7 11.3 1.0 CD A:GLU202 2.8 12.7 1.0 CD2 A:HIS330 2.9 15.0 1.0 OD1 A:ASP159 2.9 14.7 1.0 OE1 A:GLU202 3.0 14.8 1.0 CE1 A:HIS330 3.2 18.6 1.0 O A:HOH587 3.8 19.7 1.0 O A:HOH522 3.9 13.3 1.0 NE1 A:TRP329 4.0 14.1 1.0 CG A:HIS330 4.1 15.2 1.0 CB A:ASP159 4.1 10.3 1.0 ND1 A:HIS330 4.2 17.4 1.0 CG A:GLU202 4.2 12.5 1.0 O A:HOH514 4.5 16.2 1.0 CE2 A:TRP329 4.7 16.5 1.0 CD1 A:TRP329 4.7 13.9 1.0 OE1 A:GLU201 4.7 16.4 1.0 CD2 A:LEU249 4.8 12.4 1.0 NE2 A:HIS140 4.8 12.8 1.0 CD A:LYS144 4.9 16.2 1.0 CB A:LYS144 4.9 14.3 1.0 O A:ASP159 4.9 14.1 1.0 CZ2 A:TRP329 4.9 18.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Double Mutant Y115E Y117E Human Secretory 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 Secretory Glutaminyl Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:14.7 occ:1.00 OD2 B:ASP159 1.9 12.2 1.0 OE2 B:GLU202 2.0 12.2 1.0 O B:HOH670 2.0 17.7 1.0 NE2 B:HIS330 2.1 16.7 1.0 CD B:GLU202 2.8 12.8 1.0 CG B:ASP159 2.8 14.3 1.0 OE1 B:GLU202 2.9 16.0 1.0 OD1 B:ASP159 3.0 13.0 1.0 CD2 B:HIS330 3.0 15.6 1.0 CE1 B:HIS330 3.1 15.1 1.0 O B:HOH590 3.7 21.1 1.0 O B:HOH529 4.0 15.0 1.0 NE1 B:TRP329 4.0 16.1 1.0 CG B:HIS330 4.1 13.0 1.0 CB B:ASP159 4.2 12.7 1.0 ND1 B:HIS330 4.2 17.9 1.0 CG B:GLU202 4.2 13.3 1.0 O B:HOH562 4.5 15.8 1.0 OE1 B:GLU201 4.7 15.7 1.0 CD1 B:TRP329 4.7 13.9 1.0 CE2 B:TRP329 4.7 20.7 1.0 NE2 B:HIS140 4.7 13.8 1.0 CD2 B:LEU249 4.8 14.4 1.0 CD B:LYS144 4.8 18.1 1.0 CB B:LYS144 4.9 14.0 1.0 O B:ASP159 4.9 14.2 1.0 CZ2 B:TRP329 5.0 20.1 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Double Mutant Y115E Y117E Human Secretory 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 Secretory Glutaminyl Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:15.1 occ:1.00 OD2 C:ASP159 1.9 14.7 1.0 OE2 C:GLU202 1.9 11.5 1.0 O C:HOH675 2.0 17.0 1.0 NE2 C:HIS330 2.1 17.7 1.0 CG C:ASP159 2.8 13.7 1.0 CD C:GLU202 2.8 14.3 1.0 CD2 C:HIS330 2.9 17.3 1.0 OD1 C:ASP159 3.0 14.9 1.0 OE1 C:GLU202 3.0 14.3 1.0 CE1 C:HIS330 3.1 17.6 1.0 O C:HOH605 3.8 20.7 1.0 O C:HOH553 3.9 13.8 1.0 NE1 C:TRP329 4.0 16.9 1.0 CG C:HIS330 4.1 15.6 1.0 CB C:ASP159 4.2 12.6 1.0 ND1 C:HIS330 4.2 17.3 1.0 CG C:GLU202 4.2 14.2 1.0 O C:HOH582 4.4 19.2 1.0 OE1 C:GLU201 4.7 16.5 1.0 CE2 C:TRP329 4.7 16.9 1.0 CD2 C:LEU249 4.7 12.4 1.0 CD1 C:TRP329 4.7 16.1 1.0 NE2 C:HIS140 4.8 14.7 1.0 CD C:LYS144 4.8 14.7 1.0 CB C:LYS144 4.9 15.8 1.0 CZ2 C:TRP329 4.9 18.3 1.0 O C:ASP159 5.0 15.6 1.0

K.V.Dileep, N.Sakai, K.Ihara, M.Kato-Murayama, A.Nakata, A.Ito, D.M.Sivaraman, J.W.Shin, M.Yoshida, M.Shirouzu, K.Y.J.Zhang. Piperidine-4-Carboxamide As A New Scaffold For Designing Secretory Glutaminyl Cyclase Inhibitors. Int.J.Biol.Macromol. V. 170 415 2020.
ISSN: ISSN 0141-8130
PubMed: 33373636
DOI: 10.1016/J.IJBIOMAC.2020.12.118