Zinc in PDB 3u92: Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form

The structure of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form, PDB code: 3u92 was solved by J.Kumar, M.L.Mayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.53 / 1.90
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	129.537, 55.654, 90.052, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.2

The structure of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form (pdb code 3u92). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form, PDB code: 3u92:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


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 the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn259 b:32.9 occ:1.00 HE3 A:LYS246 1.9 68.9 1.0 OE2 A:GLU194 2.0 32.7 1.0 HE2 A:LYS246 2.3 68.9 1.0 OE1 A:GLU194 2.3 31.9 1.0 CE A:LYS246 2.5 57.5 1.0 CD A:GLU194 2.5 21.7 1.0 HZ1 A:LYS246 3.4 80.4 1.0 HD3 A:LYS246 3.5 35.6 1.0 NZ A:LYS246 3.5 67.0 1.0 CD A:LYS246 3.6 29.7 1.0 HG2 A:LYS246 3.8 31.6 1.0 HZ2 A:LYS246 4.0 80.4 1.0 O A:HOH350 4.0 46.4 1.0 CG A:GLU194 4.0 35.8 1.0 HD1 A:TRP250 4.1 39.4 1.0 HZ3 A:LYS246 4.1 80.4 1.0 CG A:LYS246 4.2 26.3 1.0 CD1 A:TRP250 4.2 32.8 1.0 HB3 A:TRP250 4.3 30.6 1.0 HD2 A:LYS246 4.3 35.6 1.0 HG2 A:GLU194 4.4 43.0 1.0 HG22 A:THR191 4.4 36.0 1.0 HG3 A:GLU194 4.4 43.0 1.0 CG A:TRP250 4.4 28.8 1.0 HB2 A:TRP250 4.5 30.6 1.0 O A:HOH461 4.5 55.2 1.0 HG3 A:LYS246 4.6 31.6 1.0 CB A:TRP250 4.6 25.5 1.0 NE1 A:TRP250 4.8 29.8 1.0 HB3 A:GLU194 4.8 27.4 1.0 O A:HOH404 4.9 34.8 1.0 O A:HOH368 4.9 31.7 1.0 CB A:GLU194 5.0 22.9 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


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 the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn260 b:53.0 occ:0.75 ND1 A:HIS80 2.0 44.1 1.0 O A:HOH356 2.1 61.2 1.0 HB3 A:HIS80 2.8 58.2 1.0 CE1 A:HIS80 2.9 53.1 1.0 CG A:HIS80 3.0 56.2 1.0 HE1 A:HIS80 3.1 63.8 1.0 CB A:HIS80 3.4 48.5 1.0 HB2 A:HIS80 4.0 58.2 1.0 NE2 A:HIS80 4.1 56.2 1.0 CD2 A:HIS80 4.1 62.6 1.0 HG2 A:PRO220 4.3 42.5 1.0 HA A:HIS80 4.3 59.1 1.0 O A:HOH316 4.3 44.1 1.0 CA A:HIS80 4.5 49.3 1.0 HB2 A:PRO220 4.8 40.0 1.0 O A:HIS80 4.9 42.7 1.0 HB3 A:PRO220 5.0 40.0 1.0 HD2 A:HIS80 5.0 75.2 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


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 the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn261 b:60.1 occ:0.79 O A:HOH460 2.1 53.1 1.0 NE2 A:HIS45 2.1 94.3 1.0 O A:HOH451 2.2 57.2 1.0 CD2 A:HIS45 2.9 78.0 1.0 HD2 A:HIS45 3.0 93.5 1.0 CE1 A:HIS45 3.2 90.4 1.0 HE1 A:HIS45 3.5 0.5 1.0 CG A:HIS45 4.1 57.0 1.0 ND1 A:HIS45 4.2 69.4 1.0 O A:HOH351 4.4 55.4 1.0 O A:HOH439 4.4 49.3 1.0 O A:HOH440 4.4 43.0 1.0 HZ1 A:LYS241 4.9 64.7 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


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 the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn259 b:24.4 occ:0.85 OD1 B:ASP240 2.0 30.8 1.0 ND1 A:HIS93 2.0 29.8 1.0 ND1 B:HIS243 2.0 27.9 1.0 OE1 A:GLU96 2.0 27.3 1.0 OD2 B:ASP240 2.2 44.1 1.0 CG B:ASP240 2.4 32.2 1.0 CE1 A:HIS93 2.8 37.6 1.0 HE1 A:HIS93 2.8 45.1 1.0 CD A:GLU96 2.9 29.8 1.0 CE1 B:HIS243 3.0 34.1 1.0 CG B:HIS243 3.0 28.0 1.0 HE1 B:HIS243 3.2 41.0 1.0 HB3 B:HIS243 3.2 33.4 1.0 OE2 A:GLU96 3.2 30.9 1.0 HA A:HIS93 3.2 38.6 1.0 CG A:HIS93 3.2 28.9 1.0 HB2 B:HIS243 3.3 33.4 1.0 CB B:HIS243 3.4 27.9 1.0 HB3 A:HIS93 3.5 40.8 1.0 CB A:HIS93 3.7 34.0 1.0 CA A:HIS93 3.9 32.2 1.0 CB B:ASP240 3.9 34.9 1.0 NE2 A:HIS93 4.0 39.5 1.0 O B:HOH337 4.1 47.5 1.0 NE2 B:HIS243 4.1 34.8 1.0 HB2 A:GLU96 4.1 30.6 1.0 CD2 B:HIS243 4.1 32.6 1.0 O A:HOH385 4.2 39.1 1.0 CD2 A:HIS93 4.2 37.9 1.0 HB2 B:ASP240 4.3 41.9 1.0 CG A:GLU96 4.3 25.8 1.0 HA B:ASP240 4.3 31.4 1.0 HB3 B:ASP240 4.4 41.9 1.0 HB3 A:GLU96 4.5 30.6 1.0 CB A:GLU96 4.6 25.5 1.0 HB2 A:HIS93 4.6 40.8 1.0 CA B:ASP240 4.7 26.2 1.0 N A:HIS93 4.7 26.9 1.0 HG3 A:GLU96 4.8 30.9 1.0 O B:ASP240 4.8 28.6 1.0 HG2 A:GLU96 4.8 30.9 1.0 CA B:HIS243 4.9 27.5 1.0 O A:HIS93 5.0 29.5 1.0 C A:HIS93 5.0 30.2 1.0 H A:HIS93 5.0 32.3 1.0 HD2 B:HIS243 5.0 39.1 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


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 the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn260 b:40.4 occ:0.37 O B:HOH336 2.1 45.8 1.0 O B:HOH361 2.2 42.6 1.0 O B:HOH335 2.8 68.0 1.0 HE2 B:MET221 3.2 0.2 1.0 O B:GLU96 3.9 50.8 1.0 OD1 B:ASP100 3.9 40.7 1.0 CE B:MET221 4.1 0.7 1.0 HB3 B:GLU96 4.2 48.4 1.0 HE1 B:MET221 4.3 0.2 1.0 HE3 B:MET221 4.3 0.2 1.0 O B:HOH283 4.4 32.0 1.0 HH22 B:ARG226 4.6 81.3 1.0 HH12 B:ARG226 4.8 60.0 1.0 C B:GLU96 4.9 48.2 1.0 HG2 B:MET221 4.9 74.2 1.0 HA B:ASP100 5.0 45.4 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn261 b:36.7 occ:0.52 HZ2 B:LYS241 1.4 78.3 1.0 OE1 B:GLU42 2.0 37.2 1.0 O B:HOH393 2.1 58.7 1.0 OE2 B:GLU42 2.1 47.8 1.0 NZ B:LYS241 2.2 65.3 1.0 CD B:GLU42 2.3 38.3 1.0 HE3 B:LYS241 2.6 76.8 1.0 HZ3 B:LYS241 2.6 78.3 1.0 CE B:LYS241 2.7 64.0 1.0 HE2 B:LYS241 2.8 76.8 1.0 HZ1 B:LYS241 2.8 78.3 1.0 CG B:GLU42 3.8 34.4 1.0 HD21 B:LEU236 3.8 32.1 1.0 HG3 B:GLU42 4.2 41.3 1.0 CD B:LYS241 4.2 59.6 1.0 HG2 B:GLU42 4.3 41.3 1.0 O B:HOH422 4.3 58.4 1.0 HD23 B:LEU236 4.3 32.1 1.0 HB3 B:GLU42 4.3 34.2 1.0 HA B:GLU42 4.4 35.8 1.0 CD2 B:LEU236 4.4 26.7 1.0 HD22 B:LEU236 4.4 32.1 1.0 HD2 B:LYS241 4.5 71.5 1.0 HD11 B:ILE46 4.5 44.8 1.0 HD3 B:LYS241 4.6 71.5 1.0 CB B:GLU42 4.6 28.5 1.0 HG3 B:LYS241 4.8 50.9 1.0 HG13 B:ILE46 4.9 43.2 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn262 b:39.7 occ:0.47 OE2 B:GLU238 2.0 98.0 1.0 OE1 B:GLU238 2.1 72.3 1.0 O B:HOH321 2.1 54.3 1.0 O B:HOH396 2.1 45.2 1.0 CD B:GLU238 2.3 84.6 1.0 O A:HOH437 3.3 43.4 1.0 CG B:GLU238 3.9 73.5 1.0 O A:HOH345 4.1 47.3 1.0 HG3 B:GLU238 4.3 88.2 1.0 HG2 B:GLU238 4.3 88.2 1.0 O B:HOH415 4.3 35.5 1.0 HA B:GLU238 4.4 53.5 1.0 HG A:SER212 4.4 44.6 1.0 OG A:SER212 4.7 37.1 1.0 HB2 B:GLU238 4.7 60.0 1.0 CB B:GLU238 4.8 50.0 1.0 HB3 A:SER212 4.9 42.6 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn263 b:53.0 occ:0.53 ND1 B:HIS80 2.0 0.6 1.0 CE1 B:HIS80 2.9 0.5 1.0 CG B:HIS80 3.0 89.8 1.0 HE1 B:HIS80 3.0 0.8 1.0 HB2 B:HIS80 3.2 94.2 1.0 CB B:HIS80 3.4 78.5 1.0 HB3 B:HIS80 3.5 94.2 1.0 NE2 B:HIS80 4.0 86.7 1.0 CD2 B:HIS80 4.0 83.4 1.0 HD2 B:HIS80 4.9 0.1 1.0 CA B:HIS80 4.9 51.3 1.0

J.Veran, J.Kumar, P.S.Pinheiro, A.Athane, M.L.Mayer, D.Perrais, C.Mulle. Zinc Potentiates GLUK3 Glutamate Receptor Function By Stabilizing the Ligand Binding Domain Dimer Interface. Neuron V. 76 565 2012.
ISSN: ISSN 0896-6273
PubMed: 23141068
DOI: 10.1016/J.NEURON.2012.08.027