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

Protein crystallography data

The structure of Crystal Structure of Human Glycine Receptor Alpha-3 Bound to Am-3607, Glycine, and Ivermectin, PDB code: 5vdh 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 / 2.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 119.065, 119.065, 429.934, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 23.6

Other elements in 5vdh:

The structure of Crystal Structure of Human Glycine Receptor Alpha-3 Bound to Am-3607, Glycine, and Ivermectin also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Glycine Receptor Alpha-3 Bound to Am-3607, Glycine, and Ivermectin (pdb code 5vdh). 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 Bound to Am-3607, Glycine, and Ivermectin, PDB code: 5vdh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5vdh

Go back to Zinc Binding Sites List in 5vdh
Zinc binding site 1 out of 5 in the Crystal Structure of Human Glycine Receptor Alpha-3 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 Bound to Am-3607, Glycine, and Ivermectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:85.8
occ:0.50
OD1 A:ASP194 2.6 91.7 1.0
OD2 A:ASP194 2.6 86.9 1.0
NE2 A:HIS215 2.9 81.5 1.0
OE2 A:GLU192 2.9 0.1 1.0
CG A:ASP194 2.9 85.2 1.0
CD2 A:HIS215 3.6 80.2 1.0
CE1 A:HIS215 3.7 81.2 1.0
CD A:GLU192 4.1 0.5 1.0
CB A:ASP194 4.5 80.0 1.0
CG A:HIS215 4.6 77.5 1.0
ND1 A:HIS215 4.6 79.5 1.0
OE1 A:GLU192 4.8 1.0 1.0

Zinc binding site 2 out of 5 in 5vdh

Go back to Zinc Binding Sites List in 5vdh
Zinc binding site 2 out of 5 in the Crystal Structure of Human Glycine Receptor Alpha-3 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 Bound to Am-3607, Glycine, and Ivermectin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:0.6
occ:0.50
OE2 B:GLU192 2.0 0.8 1.0
OD1 B:ASP194 2.5 95.6 1.0
NE2 B:HIS215 2.7 84.7 1.0
CD2 B:HIS215 3.0 83.2 1.0
CG B:ASP194 3.1 91.5 1.0
OD2 B:ASP194 3.1 92.3 1.0
CD B:GLU192 3.2 0.8 1.0
CE1 B:HIS215 3.9 84.6 1.0
CG B:GLU192 4.0 0.8 1.0
O B:GLU192 4.0 92.0 1.0
OE1 B:GLU192 4.1 0.5 1.0
CG B:HIS215 4.2 81.4 1.0
CB B:GLU192 4.2 0.6 1.0
N B:ASP194 4.4 85.6 1.0
CB B:ASP194 4.4 87.6 1.0
C B:GLU192 4.5 93.7 1.0
ND1 B:HIS215 4.6 83.5 1.0
CA B:ASP194 4.8 85.2 1.0
C B:LYS193 4.9 87.5 1.0

Zinc binding site 3 out of 5 in 5vdh

Go back to Zinc Binding Sites List in 5vdh
Zinc binding site 3 out of 5 in the Crystal Structure of Human Glycine Receptor Alpha-3 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 Bound to Am-3607, Glycine, and Ivermectin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn404

b:0.7
occ:0.50
NE2 C:HIS215 2.8 0.6 1.0
OE2 C:GLU192 2.9 0.4 1.0
OD2 C:ASP194 3.2 0.2 1.0
OD1 C:ASP194 3.3 0.9 1.0
CD2 C:HIS215 3.4 0.6 1.0
CE1 C:HIS215 3.6 1.0 1.0
CG C:ASP194 3.6 0.9 1.0
CD C:GLU192 4.1 0.6 1.0
CG C:HIS215 4.3 99.8 1.0
ND1 C:HIS215 4.4 0.5 1.0
OE1 C:GLU192 4.8 0.5 1.0

Zinc binding site 4 out of 5 in 5vdh

Go back to Zinc Binding Sites List in 5vdh
Zinc binding site 4 out of 5 in the Crystal Structure of Human Glycine Receptor Alpha-3 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 Bound to Am-3607, Glycine, and Ivermectin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn404

b:0.8
occ:0.50
OE2 D:GLU192 2.0 0.0 1.0
OD1 D:ASP194 2.7 0.2 1.0
NE2 D:HIS215 2.8 0.1 1.0
CD2 D:HIS215 3.1 0.0 1.0
OD2 D:ASP194 3.2 0.5 1.0
CD D:GLU192 3.3 0.2 1.0
CG D:ASP194 3.3 0.2 1.0
CE1 D:HIS215 3.9 0.3 1.0
OE1 D:GLU192 4.1 0.8 1.0
CG D:GLU192 4.2 0.2 1.0
CG D:HIS215 4.3 1.0 1.0
O D:GLU192 4.3 0.2 1.0
CB D:GLU192 4.4 0.4 1.0
ND1 D:HIS215 4.6 0.6 1.0
CB D:ASP194 4.7 0.1 1.0
N D:ASP194 4.8 0.3 1.0
C D:GLU192 4.8 0.6 1.0

Zinc binding site 5 out of 5 in 5vdh

Go back to Zinc Binding Sites List in 5vdh
Zinc binding site 5 out of 5 in the Crystal Structure of Human Glycine Receptor Alpha-3 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 Bound to Am-3607, Glycine, and Ivermectin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn404

b:0.4
occ:0.50
OE2 E:GLU192 2.6 0.1 1.0
NE2 E:HIS215 2.8 89.5 1.0
OD1 E:ASP194 2.8 99.4 1.0
OD2 E:ASP194 3.0 97.0 1.0
CG E:ASP194 3.3 96.4 1.0
CD2 E:HIS215 3.4 89.3 1.0
CE1 E:HIS215 3.7 88.6 1.0
CD E:GLU192 3.8 0.8 1.0
CG E:HIS215 4.4 87.9 1.0
OE1 E:GLU192 4.5 0.1 1.0
ND1 E:HIS215 4.5 87.7 1.0
CB E:ASP194 4.8 92.8 1.0
CG E:GLU192 4.8 0.8 1.0

Reference:

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
Page generated: Wed Dec 16 11:08:35 2020

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