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

Protein crystallography data

The structure of Crystal Structure of Human Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607, PDB code: 5tin 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 / 2.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 136.301, 136.787, 192.495, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 21.4

Other elements in 5tin:

The structure of Crystal Structure of Human Glycine Receptor Alpha-3 Mutant N38Q Bound to Am-3607 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 Mutant N38Q Bound to Am-3607 (pdb code 5tin). 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, PDB code: 5tin:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5tin

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:71.4
occ:0.50
OD1 A:ASP194 2.1 76.6 1.0
OE2 A:GLU192 2.4 92.7 1.0
NE2 A:HIS215 2.6 60.8 1.0
CG A:ASP194 2.8 68.5 1.0
OD2 A:ASP194 2.8 71.2 1.0
CD2 A:HIS215 3.2 60.4 1.0
CD A:GLU192 3.4 94.7 1.0
CE1 A:HIS215 3.6 61.6 1.0
OE1 A:GLU192 4.1 97.9 1.0
CB A:ASP194 4.2 61.2 1.0
CG A:HIS215 4.3 58.1 1.0
ND1 A:HIS215 4.5 60.9 1.0
CG A:GLU192 4.5 87.6 1.0
N A:ASP194 4.5 58.4 1.0
O A:GLU192 4.6 67.8 1.0
CA A:ASP194 4.8 56.6 1.0
CB A:GLU192 5.0 79.2 1.0

Zinc binding site 2 out of 5 in 5tin

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:72.3
occ:0.50
OE2 B:GLU192 2.3 92.3 1.0
OD1 B:ASP194 2.3 75.7 1.0
NE2 B:HIS215 2.6 65.3 1.0
CG B:ASP194 3.0 67.9 1.0
OD2 B:ASP194 3.0 71.4 1.0
CD2 B:HIS215 3.1 62.9 1.0
CD B:GLU192 3.4 95.6 1.0
CE1 B:HIS215 3.5 64.0 1.0
OE1 B:GLU192 4.0 0.2 1.0
CG B:HIS215 4.2 57.6 1.0
ND1 B:HIS215 4.4 62.2 1.0
CG B:GLU192 4.4 88.9 1.0
O B:GLU192 4.5 65.6 1.0
CB B:ASP194 4.5 60.7 1.0
N B:ASP194 4.6 54.9 1.0
CB B:GLU192 4.8 80.2 1.0
CA B:ASP194 5.0 55.6 1.0
C B:GLU192 5.0 66.6 1.0

Zinc binding site 3 out of 5 in 5tin

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:76.7
occ:0.50
OE2 C:GLU192 2.2 0.1 1.0
OD1 C:ASP194 2.2 74.0 1.0
NE2 C:HIS215 2.6 61.5 1.0
CG C:ASP194 3.0 67.4 1.0
OD2 C:ASP194 3.0 73.3 1.0
CD2 C:HIS215 3.1 59.2 1.0
CD C:GLU192 3.3 0.6 1.0
CE1 C:HIS215 3.6 61.8 1.0
OE1 C:GLU192 3.9 0.3 1.0
CG C:HIS215 4.2 55.2 1.0
CG C:GLU192 4.3 97.0 1.0
O C:GLU192 4.4 67.4 1.0
CB C:ASP194 4.4 61.1 1.0
ND1 C:HIS215 4.5 59.7 1.0
N C:ASP194 4.5 58.5 1.0
CB C:GLU192 4.8 84.6 1.0
C C:GLU192 4.9 69.7 1.0
CA C:ASP194 4.9 57.1 1.0

Zinc binding site 4 out of 5 in 5tin

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn403

b:73.2
occ:0.50
OE2 D:GLU192 2.1 98.6 1.0
OD1 D:ASP194 2.1 84.9 1.0
NE2 D:HIS215 2.6 65.4 1.0
CG D:ASP194 2.9 78.4 1.0
CD2 D:HIS215 3.1 65.0 1.0
OD2 D:ASP194 3.1 87.2 1.0
CD D:GLU192 3.2 98.3 1.0
CE1 D:HIS215 3.7 66.5 1.0
OE1 D:GLU192 3.9 0.4 1.0
CG D:GLU192 4.1 90.1 1.0
O D:GLU192 4.2 73.2 1.0
CG D:HIS215 4.2 61.3 1.0
CB D:ASP194 4.3 70.6 1.0
N D:ASP194 4.4 63.6 1.0
ND1 D:HIS215 4.5 64.1 1.0
CB D:GLU192 4.6 81.5 1.0
C D:GLU192 4.7 70.3 1.0
CA D:ASP194 4.7 64.1 1.0
C D:LYS193 4.8 62.0 1.0

Zinc binding site 5 out of 5 in 5tin

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn404

b:89.5
occ:0.50
OE2 E:GLU192 2.0 0.0 1.0
OD1 E:ASP194 2.3 78.7 1.0
O E:HOH532 2.3 60.8 1.0
NE2 E:HIS215 2.6 75.2 1.0
CD2 E:HIS215 3.0 73.3 1.0
CD E:GLU192 3.1 0.2 1.0
CG E:ASP194 3.1 77.4 1.0
OD2 E:ASP194 3.3 78.5 1.0
CE1 E:HIS215 3.7 73.7 1.0
OE1 E:GLU192 3.8 0.1 1.0
O E:GLU192 4.0 80.5 1.0
CG E:GLU192 4.0 98.4 1.0
CG E:HIS215 4.1 69.7 1.0
CB E:GLU192 4.4 92.2 1.0
N E:ASP194 4.4 70.3 1.0
ND1 E:HIS215 4.5 71.6 1.0
CB E:ASP194 4.5 72.4 1.0
C E:GLU192 4.5 81.4 1.0
CA E:ASP194 4.9 69.5 1.0
C E:LYS193 4.9 71.5 1.0

Reference:

X.Huang, P.L.Shaffer, S.Ayube, H.Bregman, H.Chen, S.G.Lehto, J.A.Luther, D.J.Matson, S.I.Mcdonough, K.Michelsen, M.M.Plant, S.Schneider, J.R.Simard, Y.Teffera, S.Yi, M.Zhang, E.F.Dimauro, J.Gingras. Crystal Structures of Human GLYRA3 Bound to A Novel Class of Potentiators with Efficacy in A Mouse Model of Neuropathic Pain To Be Published.
Page generated: Wed Dec 16 10:56:01 2020

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