Zinc in PDB 7coz: Crystal Structure of Double Mutant Y115E Y117E Human Secretory Glutaminyl Cyclase in Complex with Lsb-41

All present enzymatic activity of Crystal Structure of Double Mutant Y115E Y117E Human Secretory Glutaminyl Cyclase in Complex with Lsb-41:
2.3.2.5;

The structure of Crystal Structure of Double Mutant Y115E Y117E Human Secretory Glutaminyl Cyclase in Complex with Lsb-41, PDB code: 7coz 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)	43.03 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.229, 149.366, 95.377, 90, 97.34, 90
R / Rfree (%)	19.6 / 23.6

The binding sites of Zinc atom in the Crystal Structure of Double Mutant Y115E Y117E Human Secretory Glutaminyl Cyclase in Complex with Lsb-41 (pdb code 7coz). 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 in Complex with Lsb-41, PDB code: 7coz:
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 in Complex with Lsb-41


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 in Complex with Lsb-41 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:14.3 occ:1.00 OD2 A:ASP159 1.9 11.4 1.0 OE2 A:GLU202 2.0 13.2 1.0 NE2 A:HIS330 2.1 16.4 1.0 O1 A:Q39402 2.2 16.1 1.0 CD A:GLU202 2.7 13.4 1.0 CG A:ASP159 2.8 16.9 1.0 OE1 A:GLU202 2.8 14.7 1.0 CD2 A:HIS330 2.9 19.6 1.0 OD1 A:ASP159 3.0 12.1 1.0 CE1 A:HIS330 3.2 15.8 1.0 C1 A:Q39402 3.2 17.9 1.0 N1 A:Q39402 3.6 15.8 1.0 NE1 A:TRP329 3.8 13.5 1.0 O A:HOH578 3.9 11.7 1.0 CG A:HIS330 4.1 19.6 1.0 CB A:ASP159 4.2 15.8 1.0 CG A:GLU202 4.2 16.4 1.0 ND1 A:HIS330 4.2 21.5 1.0 O A:HOH611 4.4 14.2 1.0 C3 A:Q39402 4.4 19.6 1.0 C2 A:Q39402 4.5 15.5 1.0 CE2 A:TRP329 4.5 18.1 1.0 CD1 A:TRP329 4.6 15.6 1.0 CD2 A:LEU249 4.7 10.2 1.0 OE1 A:GLU201 4.8 15.9 1.0 CD A:LYS144 4.8 16.1 1.0 CZ2 A:TRP329 4.8 20.2 1.0 NE2 A:HIS140 4.9 13.9 1.0 CB A:LYS144 4.9 16.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Double Mutant Y115E Y117E Human Secretory Glutaminyl Cyclase in Complex with Lsb-41


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 in Complex with Lsb-41 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:13.6 occ:1.00 OD2 B:ASP159 1.9 13.1 1.0 OE2 B:GLU202 1.9 12.2 1.0 NE2 B:HIS330 2.0 16.0 1.0 O1 B:Q39402 2.1 11.3 1.0 CD B:GLU202 2.7 12.3 1.0 CG B:ASP159 2.8 13.4 1.0 OE1 B:GLU202 2.8 14.3 1.0 CD2 B:HIS330 2.9 17.0 1.0 C1 B:Q39402 3.0 16.4 1.0 OD1 B:ASP159 3.0 11.9 1.0 CE1 B:HIS330 3.1 16.5 1.0 N1 B:Q39402 3.3 13.5 1.0 NE1 B:TRP329 3.8 14.0 1.0 O B:HOH594 3.9 9.7 1.0 CG B:HIS330 4.1 15.9 1.0 CB B:ASP159 4.1 11.7 1.0 CG B:GLU202 4.2 13.0 1.0 ND1 B:HIS330 4.2 17.1 1.0 C2 B:Q39402 4.3 14.5 1.0 C3 B:Q39402 4.4 14.5 1.0 O B:HOH573 4.5 15.3 1.0 CD1 B:TRP329 4.5 13.7 1.0 CE2 B:TRP329 4.5 15.3 1.0 CD2 B:LEU249 4.7 13.3 1.0 CD B:LYS144 4.7 15.2 1.0 OE1 B:GLU201 4.8 15.9 1.0 CZ2 B:TRP329 4.8 22.3 1.0 CB B:LYS144 4.8 18.5 1.0 NE2 B:HIS140 4.9 14.0 1.0 C6 B:Q39402 5.0 19.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Double Mutant Y115E Y117E Human Secretory Glutaminyl Cyclase in Complex with Lsb-41


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 in Complex with Lsb-41 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:12.7 occ:1.00 OE2 C:GLU202 1.9 11.8 1.0 OD2 C:ASP159 2.0 10.2 1.0 NE2 C:HIS330 2.1 16.4 1.0 O1 C:Q39404 2.2 13.4 1.0 CD C:GLU202 2.7 11.9 1.0 OE1 C:GLU202 2.8 13.8 1.0 CG C:ASP159 2.8 15.1 1.0 CD2 C:HIS330 3.0 16.3 1.0 OD1 C:ASP159 3.0 12.5 1.0 C1 C:Q39404 3.1 17.8 1.0 CE1 C:HIS330 3.2 13.4 1.0 N1 C:Q39404 3.4 10.8 1.0 NE1 C:TRP329 3.8 15.8 1.0 O C:HOH593 4.0 11.2 1.0 CG C:GLU202 4.1 12.5 1.0 CG C:HIS330 4.2 16.8 1.0 CB C:ASP159 4.2 13.4 1.0 ND1 C:HIS330 4.3 17.4 1.0 O C:HOH633 4.4 15.0 1.0 C2 C:Q39404 4.4 18.8 1.0 CE2 C:TRP329 4.5 15.2 1.0 C3 C:Q39404 4.5 17.8 1.0 CD1 C:TRP329 4.6 16.3 1.0 CD2 C:LEU249 4.7 10.6 1.0 CZ2 C:TRP329 4.7 20.7 1.0 CD C:LYS144 4.8 17.0 1.0 OE1 C:GLU201 4.8 15.2 1.0 NE2 C:HIS140 4.9 15.4 1.0 CB C:LYS144 4.9 19.4 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