Zinc in PDB 5vdi: Crystal Structure of Human Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607, Glycine, and Ivermectin

The structure of Crystal Structure of Human Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607, Glycine, and Ivermectin, PDB code: 5vdi was solved by P.L.Shaffer, X.Huang, H.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	136.006, 136.000, 191.635, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 25.6

The binding sites of Zinc atom in the Crystal Structure of Human Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607, Glycine, and Ivermectin (pdb code 5vdi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Human Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607, Glycine, and Ivermectin, PDB code: 5vdi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Human Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607, Glycine, and Ivermectin


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 Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607, Glycine, and Ivermectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:66.0 occ:0.50 OD1 A:ASP194 2.9 76.0 1.0 NE2 A:HIS215 2.9 66.4 1.0 OD2 A:ASP194 2.9 76.7 1.0 OE2 A:GLU192 3.1 0.8 1.0 CG A:ASP194 3.3 75.5 1.0 CE1 A:HIS215 3.6 65.9 1.0 CD2 A:HIS215 3.8 66.3 1.0 CD A:GLU192 4.1 0.4 1.0 ND1 A:HIS215 4.6 65.5 1.0 OE1 A:GLU192 4.6 0.6 1.0 CG A:HIS215 4.7 65.2 1.0 CB A:ASP194 4.8 73.8 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Human Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607, Glycine, and Ivermectin


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 Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607, Glycine, and Ivermectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:71.1 occ:0.50 OE2 B:GLU192 2.8 92.2 1.0 OD1 B:ASP194 2.8 67.1 1.0 NE2 B:HIS215 3.0 64.0 1.0 OD2 B:ASP194 3.1 64.4 1.0 CG B:ASP194 3.3 64.9 1.0 CD B:GLU192 3.8 92.2 1.0 CD2 B:HIS215 3.8 63.4 1.0 CE1 B:HIS215 3.8 63.4 1.0 OE1 B:GLU192 4.3 96.0 1.0 ND1 B:HIS215 4.7 62.5 1.0 CG B:HIS215 4.7 62.1 1.0 CB B:ASP194 4.8 63.4 1.0 CG B:GLU192 4.9 87.9 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Human Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607, Glycine, and Ivermectin


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 Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607, Glycine, and Ivermectin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn404 b:79.1 occ:0.50 OE2 C:GLU192 2.3 0.5 1.0 NE2 C:HIS215 2.7 60.2 1.0 OD1 C:ASP194 2.7 66.0 1.0 CD2 C:HIS215 3.1 60.1 1.0 OD2 C:ASP194 3.3 67.0 1.0 CG C:ASP194 3.4 65.3 1.0 CD C:GLU192 3.4 99.9 1.0 CE1 C:HIS215 3.6 59.7 1.0 OE1 C:GLU192 4.1 0.2 1.0 CG C:HIS215 4.2 59.5 1.0 CG C:GLU192 4.3 94.3 1.0 ND1 C:HIS215 4.4 59.6 1.0 O C:GLU192 4.5 81.9 1.0 CB C:GLU192 4.7 88.5 1.0 CB C:ASP194 4.9 63.9 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Human Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607, Glycine, and Ivermectin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607, Glycine, and Ivermectin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn404 b:0.0 occ:0.50 OE2 D:GLU192 2.7 94.8 1.0 OD1 D:ASP194 2.7 81.5 1.0 OD2 D:ASP194 3.1 82.9 1.0 NE2 D:HIS215 3.1 68.2 1.0 CG D:ASP194 3.3 79.9 1.0 CD D:GLU192 3.7 94.4 1.0 CD2 D:HIS215 3.9 67.1 1.0 CE1 D:HIS215 3.9 68.3 1.0 OE1 D:GLU192 4.2 95.7 1.0 CB D:ASP194 4.8 76.9 1.0 CG D:GLU192 4.8 90.9 1.0 ND1 D:HIS215 4.8 67.0 1.0 CG D:HIS215 4.9 66.1 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Human Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607, Glycine, and Ivermectin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607, Glycine, and Ivermectin within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn404 b:88.2 occ:0.50 OE2 E:GLU192 2.2 0.8 1.0 OD1 E:ASP194 2.6 88.3 1.0 NE2 E:HIS215 2.9 76.4 1.0 CD E:GLU192 3.2 0.3 1.0 OD2 E:ASP194 3.3 86.7 1.0 CG E:ASP194 3.3 85.3 1.0 CD2 E:HIS215 3.4 75.5 1.0 CE1 E:HIS215 3.9 75.8 1.0 OE1 E:GLU192 3.9 0.3 1.0 CG E:GLU192 4.2 0.4 1.0 CG E:HIS215 4.5 74.5 1.0 O E:GLU192 4.6 88.7 1.0 ND1 E:HIS215 4.7 75.0 1.0 CB E:GLU192 4.7 98.0 1.0 CB E:ASP194 4.8 82.3 1.0

X.Huang, H.Chen, P.L.Shaffer. Crystal Structures of Human Glyr Alpha 3 Bound to Ivermectin. Structure V. 25 945 2017.
ISSN: ISSN 1878-4186
PubMed: 28479061
DOI: 10.1016/J.STR.2017.04.007