Zinc in PDB 3u94: Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 Form

The structure of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 Form, PDB code: 3u94 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)	38.94 / 1.96
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.155, 111.374, 129.851, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.7

The structure of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 Form also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 Form (pdb code 3u94). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 Form, PDB code: 3u94:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 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 Glutamate and Zinc: P21212 Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn259 b:33.3 occ:1.00 OE2 A:GLU247 1.7 28.3 1.0 OE2 B:GLU194 2.0 37.7 1.0 NE2 A:HIS243 2.1 34.6 1.0 OE1 B:GLU194 2.3 30.0 1.0 CD B:GLU194 2.4 28.5 1.0 CD2 A:HIS243 2.9 38.7 1.0 HD3 B:LYS246 3.0 66.9 1.0 HD2 A:HIS243 3.0 46.5 1.0 CD A:GLU247 3.0 48.8 1.0 HE2 B:LYS246 3.1 69.6 1.0 CE1 A:HIS243 3.2 41.3 1.0 HE1 A:HIS243 3.5 49.5 1.0 HG3 A:GLU247 3.6 51.8 1.0 HZ3 B:LYS246 3.7 77.0 1.0 CD B:LYS246 3.7 55.8 1.0 CE B:LYS246 3.8 58.0 1.0 OE1 A:GLU247 3.9 69.3 1.0 CG A:GLU247 3.9 43.2 1.0 HD13 A:ILE244 4.0 67.8 1.0 CG B:GLU194 4.0 41.9 1.0 O B:HOH411 4.1 50.0 1.0 CG A:HIS243 4.1 40.5 1.0 NZ B:LYS246 4.2 64.2 1.0 HG2 B:LYS246 4.2 44.3 1.0 ND1 A:HIS243 4.2 36.7 1.0 HG2 A:GLU247 4.3 51.8 1.0 HD1 B:TRP250 4.3 43.5 1.0 HG2 B:GLU194 4.4 50.2 1.0 HG3 B:GLU194 4.4 50.2 1.0 HD11 A:ILE244 4.4 67.8 1.0 HD2 B:LYS246 4.4 66.9 1.0 CD1 B:TRP250 4.5 36.2 1.0 CG B:LYS246 4.5 36.9 1.0 HZ1 B:LYS246 4.5 77.0 1.0 O A:HOH648 4.6 39.0 1.0 HE3 B:LYS246 4.6 69.6 1.0 HB3 B:TRP250 4.6 39.0 1.0 CD1 A:ILE244 4.7 56.5 1.0 HG3 B:LYS246 4.8 44.3 1.0 CG B:TRP250 4.8 35.2 1.0 HB3 B:GLU194 4.9 44.4 1.0 HZ2 B:LYS246 4.9 77.0 1.0 HB2 B:TRP250 4.9 39.0 1.0 CB B:GLU194 5.0 37.0 1.0

Zinc binding site 2 out of 13 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 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 Glutamate and Zinc: P21212 Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn260 b:58.3 occ:0.95 ND1 A:HIS80 1.8 22.3 1.0 HB3 A:HIS80 2.7 39.7 1.0 CG A:HIS80 2.7 38.0 1.0 CE1 A:HIS80 2.7 49.3 1.0 HE1 A:HIS80 3.0 59.1 1.0 CB A:HIS80 3.2 33.1 1.0 NE2 A:HIS80 3.7 46.9 1.0 CD2 A:HIS80 3.7 46.8 1.0 HB2 A:HIS80 3.8 39.7 1.0 HA A:HIS80 4.0 28.6 1.0 HG2 A:PRO220 4.1 29.0 1.0 CA A:HIS80 4.3 23.8 1.0 HD2 A:HIS80 4.5 56.2 1.0 HB2 A:PRO220 4.7 33.0 1.0 HB3 A:PRO220 4.9 33.0 1.0 CG A:PRO220 4.9 24.1 1.0 O A:HIS80 5.0 32.3 1.0 O A:HOH419 5.0 40.9 1.0

Zinc binding site 3 out of 13 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 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 Glutamate and Zinc: P21212 Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn261 b:52.7 occ:0.84 O A:HOH688 2.1 50.4 1.0 O A:HOH689 2.1 54.2 1.0 NE2 A:HIS45 2.2 55.0 1.0 CD2 A:HIS45 3.1 45.8 1.0 HD2 A:HIS45 3.1 55.0 1.0 CE1 A:HIS45 3.3 51.8 1.0 HE1 A:HIS45 3.6 62.1 1.0 O A:HOH346 4.1 43.6 1.0 CG A:HIS45 4.3 37.1 1.0 ND1 A:HIS45 4.4 42.2 1.0 HZ1 A:LYS241 4.6 59.2 1.0 HZ2 A:LYS241 4.7 59.2 1.0 O A:HOH610 4.7 52.8 1.0 O A:HOH637 4.9 32.4 1.0

Zinc binding site 4 out of 13 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 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 Glutamate and Zinc: P21212 Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn259 b:35.9 occ:0.95 OE2 B:GLU247 1.7 24.5 1.0 OE2 A:GLU194 2.0 39.1 1.0 NE2 B:HIS243 2.1 51.5 1.0 OE1 A:GLU194 2.2 28.3 1.0 O B:HOH297 2.2 41.1 1.0 CD A:GLU194 2.4 31.7 1.0 HE2 A:LYS246 2.5 70.5 1.0 CD B:GLU247 2.9 43.1 1.0 CE1 B:HIS243 3.0 40.0 1.0 CD2 B:HIS243 3.1 52.3 1.0 HE1 B:HIS243 3.1 48.0 1.0 HD2 B:HIS243 3.3 62.8 1.0 CE A:LYS246 3.3 58.7 1.0 HZ1 A:LYS246 3.4 61.6 1.0 OE1 B:GLU247 3.5 36.9 1.0 HZ3 A:LYS246 3.6 61.6 1.0 NZ A:LYS246 3.6 51.4 1.0 HE3 A:LYS246 3.8 70.5 1.0 CG A:GLU194 3.9 48.3 1.0 HG2 A:LYS246 4.1 46.0 1.0 ND1 B:HIS243 4.1 40.5 1.0 CG B:GLU247 4.1 34.6 1.0 CG B:HIS243 4.2 47.1 1.0 HG2 A:GLU194 4.2 58.0 1.0 HG2 B:GLU247 4.3 41.5 1.0 HG3 A:LYS246 4.3 46.0 1.0 O A:HOH537 4.3 38.5 1.0 HG3 A:GLU194 4.3 58.0 1.0 HG3 B:GLU247 4.3 41.5 1.0 HD12 B:ILE244 4.4 67.3 1.0 HD1 A:TRP250 4.4 35.1 1.0 CD A:LYS246 4.4 48.3 1.0 CG A:LYS246 4.5 38.3 1.0 HZ2 A:LYS246 4.5 61.6 1.0 CD1 A:TRP250 4.5 29.3 1.0 HB3 A:TRP250 4.6 34.8 1.0 HD2 A:LYS246 4.7 58.0 1.0 O A:HOH279 4.7 38.1 1.0 HB2 A:TRP250 4.7 34.8 1.0 CG A:TRP250 4.8 28.5 1.0 HB3 A:GLU194 4.9 49.7 1.0 HD11 B:ILE244 4.9 67.3 1.0 CB A:GLU194 4.9 41.4 1.0 HB2 A:GLU194 4.9 49.7 1.0 O A:HOH500 5.0 37.3 1.0 CB A:TRP250 5.0 29.0 1.0

Zinc binding site 5 out of 13 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 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 Glutamate and Zinc: P21212 Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn260 b:50.0 occ:0.65 ND1 B:HIS80 1.9 32.7 1.0 O B:HOH651 2.2 46.8 1.0 O B:HOH298 2.2 38.5 1.0 CE1 B:HIS80 2.7 33.8 1.0 HE1 B:HIS80 2.8 40.6 1.0 CG B:HIS80 3.0 41.0 1.0 HB3 B:HIS80 3.2 54.2 1.0 HG2 B:PRO220 3.3 39.6 1.0 CB B:HIS80 3.5 45.2 1.0 HA B:HIS80 3.7 48.4 1.0 NE2 B:HIS80 3.8 44.7 1.0 CD2 B:HIS80 3.9 41.5 1.0 CA B:HIS80 4.2 40.3 1.0 CG B:PRO220 4.2 33.0 1.0 HB2 B:HIS80 4.4 54.2 1.0 OD1 B:ASP83 4.4 46.7 1.0 HB2 B:PRO220 4.4 47.8 1.0 HG3 B:PRO220 4.6 39.6 1.0 HB3 B:PRO220 4.7 47.8 1.0 HA B:ASP83 4.7 47.1 1.0 CB B:PRO220 4.7 39.8 1.0 O B:HIS80 4.7 53.8 1.0 HD2 B:HIS80 4.8 49.8 1.0 C B:HIS80 4.9 48.2 1.0 O B:ALA82 4.9 41.0 1.0

Zinc binding site 6 out of 13 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 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 Glutamate and Zinc: P21212 Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn259 b:18.2 occ:0.83 ND1 C:HIS243 1.9 21.4 1.0 OE1 B:GLU96 1.9 25.6 1.0 ND1 B:HIS93 2.0 23.0 1.0 OD1 C:ASP240 2.0 24.2 1.0 OD2 C:ASP240 2.4 31.2 1.0 CG C:ASP240 2.5 29.8 1.0 CE1 B:HIS93 2.7 31.7 1.0 HE1 B:HIS93 2.8 38.0 1.0 CE1 C:HIS243 2.9 29.6 1.0 CD B:GLU96 2.9 26.3 1.0 CG C:HIS243 3.0 23.6 1.0 HE1 C:HIS243 3.1 35.5 1.0 HA B:HIS93 3.1 33.5 1.0 HB3 C:HIS243 3.1 28.7 1.0 CG B:HIS93 3.1 23.7 1.0 OE2 B:GLU96 3.3 24.1 1.0 HB2 C:HIS243 3.3 28.7 1.0 CB C:HIS243 3.4 23.9 1.0 HB3 B:HIS93 3.5 32.5 1.0 CB B:HIS93 3.7 27.1 1.0 CA B:HIS93 3.8 27.9 1.0 O B:HOH645 3.9 38.3 1.0 NE2 B:HIS93 3.9 29.4 1.0 NE2 C:HIS243 4.0 33.4 1.0 O C:HOH649 4.0 43.5 1.0 CB C:ASP240 4.1 27.2 1.0 HB2 B:GLU96 4.1 26.5 1.0 CD2 C:HIS243 4.1 30.6 1.0 CD2 B:HIS93 4.1 28.4 1.0 CG B:GLU96 4.3 21.2 1.0 HA C:ASP240 4.4 25.6 1.0 HB2 C:ASP240 4.4 32.6 1.0 HB3 C:ASP240 4.5 32.6 1.0 CB B:GLU96 4.5 22.1 1.0 HB3 B:GLU96 4.6 26.5 1.0 HB2 B:HIS93 4.6 32.5 1.0 N B:HIS93 4.7 17.4 1.0 HG3 B:GLU96 4.7 25.4 1.0 CA C:ASP240 4.8 21.4 1.0 HG2 B:GLU96 4.9 25.4 1.0 O B:HIS93 4.9 21.6 1.0 O C:ASP240 4.9 19.2 1.0 C B:HIS93 4.9 26.5 1.0 CA C:HIS243 4.9 19.8 1.0 HD2 C:HIS243 4.9 36.7 1.0 H B:HIS93 5.0 20.9 1.0

Zinc binding site 7 out of 13 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 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 Glutamate and Zinc: P21212 Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn260 b:37.5 occ:0.87 OE1 C:GLU238 2.2 41.2 1.0 CD C:GLU238 3.0 42.2 1.0 OE2 C:GLU238 3.1 47.7 1.0 OE2 A:GLU238 3.4 45.8 1.0 O C:HOH647 3.9 48.4 1.0 HA C:GLU238 4.0 30.1 1.0 OE1 A:GLU238 4.0 43.1 1.0 CD A:GLU238 4.1 35.7 1.0 O C:HOH329 4.3 25.1 1.0 O C:HOH646 4.4 36.0 1.0 CG C:GLU238 4.4 41.2 1.0 HB2 C:GLU238 4.6 27.8 1.0 CA C:GLU238 4.8 25.1 1.0 CB C:GLU238 4.9 23.2 1.0 HG2 C:GLU238 4.9 49.5 1.0 HG3 C:GLU238 4.9 49.5 1.0 HG B:SER212 5.0 39.1 1.0

Zinc binding site 8 out of 13 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 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 Glutamate and Zinc: P21212 Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn261 b:33.4 occ:0.87 HE1 D:HIS45 1.2 32.0 1.0 HZ2 C:LYS241 1.4 43.8 1.0 HZ1 C:LYS241 1.7 43.8 1.0 NZ C:LYS241 1.8 36.5 1.0 OE1 C:GLU42 2.0 23.6 1.0 CE1 D:HIS45 2.1 26.6 1.0 OE2 C:GLU42 2.3 42.4 1.0 HZ3 C:LYS241 2.3 43.8 1.0 CD C:GLU42 2.5 19.3 1.0 NE2 D:HIS45 2.9 25.4 1.0 O C:HOH652 3.0 47.9 1.0 ND1 D:HIS45 3.1 29.3 1.0 CE C:LYS241 3.2 53.1 1.0 HE3 C:LYS241 3.2 63.8 1.0 HD21 C:LEU236 3.6 20.2 1.0 HE2 C:LYS241 3.8 63.8 1.0 HD2 C:HIS45 3.9 32.7 1.0 HD2 C:LYS241 4.0 62.3 1.0 HD11 C:ILE46 4.0 33.3 1.0 CG C:GLU42 4.0 16.8 1.0 CD2 D:HIS45 4.1 23.5 1.0 CD C:LYS241 4.2 51.9 1.0 CG D:HIS45 4.2 24.5 1.0 HA C:GLU42 4.2 27.9 1.0 HD23 C:LEU236 4.3 20.2 1.0 CD2 C:LEU236 4.3 16.8 1.0 HB3 C:GLU42 4.4 24.9 1.0 HG13 C:ILE46 4.4 23.1 1.0 CD2 C:HIS45 4.4 27.3 1.0 HG3 C:GLU42 4.5 20.2 1.0 HG2 C:GLU42 4.5 20.2 1.0 O C:HOH653 4.5 26.1 1.0 HD22 C:LEU236 4.6 20.2 1.0 CB C:GLU42 4.7 20.8 1.0 HD3 C:LYS241 4.8 62.3 1.0 CD1 C:ILE46 4.8 27.8 1.0 HG12 C:ILE46 4.8 23.1 1.0 HA D:ILE46 4.8 33.4 1.0 OE1 C:GLU239 4.8 48.1 1.0 CG1 C:ILE46 4.9 19.2 1.0 HB3 C:HIS45 4.9 24.6 1.0 HD2 D:HIS45 4.9 28.2 1.0 CA C:GLU42 4.9 23.3 1.0 NE2 C:HIS45 5.0 25.8 1.0

Zinc binding site 9 out of 13 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn262 b:32.6 occ:0.62 ND1 C:HIS80 1.9 38.0 1.0 HE1 C:HIS80 2.5 0.0 0.0 CE1 C:HIS80 2.8 48.9 1.0 HB3 C:HIS80 2.9 38.8 1.0 CG C:HIS80 3.0 36.0 1.0 CB C:HIS80 3.4 32.3 1.0 HB2 C:HIS80 3.6 38.8 1.0 NE2 C:HIS80 3.9 41.5 1.0 CD2 C:HIS80 4.0 34.1 1.0 O C:HOH415 4.4 49.2 1.0 CA C:HIS80 4.8 23.5 1.0 O C:HOH364 4.8 25.2 1.0 HD2 C:HIS80 4.9 41.0 1.0 HA C:HIS80 4.9 28.2 1.0 O C:HIS80 5.0 26.4 1.0

Zinc binding site 10 out of 13 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Glutamate and Zinc: P21212 Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn259 b:20.8 occ:0.94 ND1 D:HIS243 1.9 21.8 1.0 ND1 A:HIS93 2.0 22.9 1.0 OE1 A:GLU96 2.0 25.8 1.0 OD1 D:ASP240 2.0 26.1 1.0 OD2 D:ASP240 2.4 32.4 1.0 CG D:ASP240 2.5 21.8 1.0 CE1 A:HIS93 2.8 30.5 1.0 CE1 D:HIS243 2.9 30.2 1.0 CG D:HIS243 2.9 23.5 1.0 CD A:GLU96 2.9 21.4 1.0 HE1 A:HIS93 2.9 36.6 1.0 HE1 D:HIS243 3.1 36.2 1.0 HB3 D:HIS243 3.1 31.1 1.0 CG A:HIS93 3.1 27.6 1.0 HA A:HIS93 3.2 32.4 1.0 HB2 D:HIS243 3.2 31.1 1.0 OE2 A:GLU96 3.2 21.3 1.0 CB D:HIS243 3.3 25.9 1.0 HB3 A:HIS93 3.4 35.2 1.0 CB A:HIS93 3.6 29.3 1.0 O A:HOH351 3.8 36.9 1.0 CA A:HIS93 3.9 27.0 1.0 NE2 D:HIS243 4.0 29.3 1.0 NE2 A:HIS93 4.0 29.3 1.0 CD2 D:HIS243 4.0 29.9 1.0 O D:HOH640 4.0 38.0 1.0 CB D:ASP240 4.1 24.9 1.0 HB2 A:GLU96 4.1 25.2 1.0 CD2 A:HIS93 4.2 25.9 1.0 CG A:GLU96 4.3 18.5 1.0 HA D:ASP240 4.4 31.3 1.0 HB2 D:ASP240 4.4 29.9 1.0 HB2 A:HIS93 4.5 35.2 1.0 HB3 A:GLU96 4.6 25.2 1.0 HB3 D:ASP240 4.6 29.9 1.0 CB A:GLU96 4.6 21.0 1.0 N A:HIS93 4.7 18.5 1.0 HG3 A:GLU96 4.8 22.2 1.0 CA D:ASP240 4.8 26.1 1.0 CA D:HIS243 4.8 27.5 1.0 HG2 A:GLU96 4.9 22.2 1.0 O D:ASP240 4.9 22.7 1.0 HD2 D:HIS243 4.9 35.9 1.0 C A:HIS93 5.0 27.5 1.0 H A:HIS93 5.0 22.1 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