Zinc in PDB 7d8e: Crystal Structure of Double Mutant Y115E Y117E Human Secretory Glutaminyl Cyclase in Complex with Lsb-09

All present enzymatic activity of Crystal Structure of Double Mutant Y115E Y117E Human Secretory Glutaminyl Cyclase in Complex with Lsb-09:
2.3.2.5;

The structure of Crystal Structure of Double Mutant Y115E Y117E Human Secretory Glutaminyl Cyclase in Complex with Lsb-09, PDB code: 7d8e 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)	46.85 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.181, 149.303, 94.539, 90, 97.64, 90
R / Rfree (%)	20.9 / 25.2

The binding sites of Zinc atom in the Crystal Structure of Double Mutant Y115E Y117E Human Secretory Glutaminyl Cyclase in Complex with Lsb-09 (pdb code 7d8e). 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-09, PDB code: 7d8e:
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-09


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-09 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1000 b:15.3 occ:1.00 OE2 A:GLU202 1.9 15.6 1.0 OD2 A:ASP159 1.9 12.8 1.0 NE2 A:HIS330 2.0 18.4 1.0 N03 A:GYO1008 2.0 13.4 1.0 CD A:GLU202 2.6 12.7 1.0 OE1 A:GLU202 2.7 12.9 1.0 CG A:ASP159 2.8 14.0 1.0 CD2 A:HIS330 2.9 15.8 1.0 OD1 A:ASP159 2.9 14.8 1.0 C02 A:GYO1008 3.0 14.0 1.0 CE1 A:HIS330 3.0 16.4 1.0 C04 A:GYO1008 3.0 11.7 1.0 C09 A:GYO1008 3.5 21.0 1.0 O A:HOH1124 3.9 12.1 1.0 NE1 A:TRP329 4.0 14.7 1.0 CG A:HIS330 4.1 18.5 1.0 ND1 A:HIS330 4.1 17.3 1.0 CG A:GLU202 4.1 11.4 1.0 C01 A:GYO1008 4.1 15.7 1.0 CB A:ASP159 4.2 17.2 1.0 N05 A:GYO1008 4.2 16.2 1.0 OE1 A:GLU201 4.2 23.7 1.0 O A:HOH1138 4.6 11.9 1.0 CD1 A:TRP329 4.7 12.8 1.0 CD2 A:LEU249 4.7 10.4 1.0 CE2 A:TRP329 4.8 17.1 1.0 NE2 A:HIS140 4.8 13.4 1.0 OE2 A:GLU201 4.8 31.3 1.0 O A:HOH1109 4.9 17.9 1.0 CD A:LYS144 4.9 14.6 1.0 CD A:GLU201 5.0 13.7 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-09


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-09 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1000 b:14.3 occ:1.00 OE2 B:GLU202 1.9 12.6 1.0 OD2 B:ASP159 2.0 10.9 1.0 N03 B:GYO1006 2.0 19.9 1.0 NE2 B:HIS330 2.0 15.0 1.0 CD B:GLU202 2.6 12.1 1.0 OE1 B:GLU202 2.7 10.7 1.0 CG B:ASP159 2.8 16.0 1.0 C02 B:GYO1006 2.9 22.6 1.0 OD1 B:ASP159 3.0 14.7 1.0 CD2 B:HIS330 3.0 16.5 1.0 CE1 B:HIS330 3.0 18.3 1.0 C04 B:GYO1006 3.0 20.4 1.0 C09 B:GYO1006 3.5 21.3 1.0 NE1 B:TRP329 4.0 14.3 1.0 O B:HOH1112 4.0 11.6 1.0 ND1 B:HIS330 4.1 19.3 1.0 C01 B:GYO1006 4.1 24.0 1.0 CG B:HIS330 4.1 17.7 1.0 CG B:GLU202 4.1 13.8 1.0 N05 B:GYO1006 4.2 21.1 1.0 CB B:ASP159 4.2 13.9 1.0 OE1 B:GLU201 4.2 19.0 1.0 O B:HOH1141 4.6 15.0 1.0 CD1 B:TRP329 4.6 14.1 1.0 CD2 B:LEU249 4.7 12.7 1.0 OE2 B:GLU201 4.7 26.8 1.0 CE2 B:TRP329 4.8 20.7 1.0 NE2 B:HIS140 4.9 17.4 1.0 CD B:LYS144 4.9 12.0 1.0 CD B:GLU201 4.9 14.0 1.0 C08 B:GYO1006 5.0 28.0 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-09


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-09 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1000 b:16.9 occ:1.00 OE2 C:GLU202 1.9 13.5 1.0 OD2 C:ASP159 2.0 10.2 1.0 NE2 C:HIS330 2.0 13.8 1.0 N03 C:GYO1005 2.0 17.0 1.0 CD C:GLU202 2.6 11.6 1.0 OE1 C:GLU202 2.7 10.9 1.0 CG C:ASP159 2.8 12.7 1.0 OD1 C:ASP159 2.9 13.1 1.0 CD2 C:HIS330 2.9 17.6 1.0 C02 C:GYO1005 3.0 17.9 1.0 CE1 C:HIS330 3.0 16.6 1.0 C04 C:GYO1005 3.0 14.3 1.0 C09 C:GYO1005 3.6 21.9 1.0 O C:HOH1118 4.0 11.1 1.0 NE1 C:TRP329 4.0 17.5 1.0 ND1 C:HIS330 4.1 18.8 1.0 CG C:HIS330 4.1 18.4 1.0 CG C:GLU202 4.1 13.8 1.0 C01 C:GYO1005 4.2 19.9 1.0 N05 C:GYO1005 4.2 16.2 1.0 CB C:ASP159 4.2 14.6 1.0 OE1 C:GLU201 4.3 23.4 1.0 O C:HOH1135 4.6 11.9 1.0 CD2 C:LEU249 4.6 10.6 1.0 CD1 C:TRP329 4.7 14.9 1.0 CE2 C:TRP329 4.8 18.2 1.0 OE2 C:GLU201 4.8 33.9 1.0 NE2 C:HIS140 4.9 14.9 1.0 CD C:LYS144 4.9 12.0 1.0 O C:HOH1126 5.0 19.0 1.0 CD C:GLU201 5.0 18.2 1.0

K.V.Dileep, K.Ihara, N.Sakai, M.Shirozu, K.Y.J.Zhang. Crystal Structure of Double Mutant Y115E Y117E Human Secretory Glutaminyl Cyclase in Complex with Lsb-09 To Be Published.