Zinc in PDB 4gxs: Ligand Binding Domain of GLUA2 (Ampa/Glutamate Receptor) Bound to (-)- Kaitocephalin

The structure of Ligand Binding Domain of GLUA2 (Ampa/Glutamate Receptor) Bound to (-)- Kaitocephalin, PDB code: 4gxs was solved by A.H.Ahmed, R.E.Oswald, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.39 / 1.96
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.741, 121.466, 48.899, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.5

The structure of Ligand Binding Domain of GLUA2 (Ampa/Glutamate Receptor) Bound to (-)- Kaitocephalin also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Ligand Binding Domain of GLUA2 (Ampa/Glutamate Receptor) Bound to (-)- Kaitocephalin (pdb code 4gxs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Ligand Binding Domain of GLUA2 (Ampa/Glutamate Receptor) Bound to (-)- Kaitocephalin, PDB code: 4gxs:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Ligand Binding Domain of GLUA2 (Ampa/Glutamate Receptor) Bound to (-)- Kaitocephalin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ligand Binding Domain of GLUA2 (Ampa/Glutamate Receptor) Bound to (-)- Kaitocephalin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:68.5 occ:1.00 NE2 B:HIS46 2.2 50.8 1.0 OE1 B:GLU42 2.3 50.0 1.0 CD2 B:HIS46 3.0 46.7 1.0 CD B:GLU42 3.2 48.1 1.0 CE1 B:HIS46 3.3 53.1 1.0 OE2 B:GLU42 3.4 54.8 1.0 CG B:HIS46 4.2 47.1 1.0 ND1 B:HIS46 4.3 51.5 1.0 CD B:LYS45 4.3 55.3 1.0 CD2 B:LEU241 4.4 30.7 1.0 OE1 B:GLN244 4.4 41.8 1.0 CE B:LYS45 4.5 65.0 1.0 CG B:GLU42 4.6 37.9 1.0 CB B:GLU42 4.9 30.8 1.0

Zinc binding site 2 out of 3 in the Ligand Binding Domain of GLUA2 (Ampa/Glutamate Receptor) Bound to (-)- Kaitocephalin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ligand Binding Domain of GLUA2 (Ampa/Glutamate Receptor) Bound to (-)- Kaitocephalin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:79.0 occ:1.00 NE2 D:HIS46 2.3 52.1 1.0 OE1 D:GLU42 2.4 49.9 1.0 CD2 D:HIS46 3.2 46.7 1.0 CE1 D:HIS46 3.4 51.6 1.0 CD D:GLU42 3.5 47.4 1.0 OE2 D:GLU42 3.9 53.5 1.0 OE1 D:GLN244 4.1 46.7 1.0 CD2 D:LEU241 4.3 35.1 1.0 CG D:HIS46 4.4 49.9 1.0 ND1 D:HIS46 4.5 50.2 1.0 CD D:LYS45 4.6 60.5 1.0 CG D:GLU42 4.8 37.0 1.0 CE D:LYS45 4.8 71.9 1.0 NE2 D:GLN244 4.9 56.0 1.0 CD D:GLN244 4.9 47.2 1.0 CB D:GLU42 4.9 36.0 1.0

Zinc binding site 3 out of 3 in the Ligand Binding Domain of GLUA2 (Ampa/Glutamate Receptor) Bound to (-)- Kaitocephalin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ligand Binding Domain of GLUA2 (Ampa/Glutamate Receptor) Bound to (-)- Kaitocephalin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn303 b:27.4 occ:1.00 NE2 D:HIS23 2.3 29.9 1.0 OE1 D:GLU30 2.8 31.2 1.0 CD D:GLU30 3.2 40.9 1.0 CD2 D:HIS23 3.2 28.8 1.0 CE1 D:HIS23 3.3 27.5 1.0 OE2 D:GLU30 3.3 49.1 1.0 NZ D:LYS20 4.1 33.2 1.0 CG D:GLU30 4.3 32.6 1.0 CD D:LYS20 4.3 28.9 1.0 ND1 D:HIS23 4.4 27.0 1.0 CG D:HIS23 4.4 28.6 1.0 O D:GLU30 4.5 29.4 1.0 CE D:LYS20 4.8 31.7 1.0 CD1 D:LEU26 4.9 37.9 1.0

A.H.Ahmed, M.Hamada, T.Shinada, Y.Ohfune, L.Weerasinghe, P.P.Garner, R.E.Oswald. The Structure of (-)-Kaitocephalin Bound to the Ligand Binding Domain of the (S)-Alpha-Amino-3-Hydroxy-5-Methyl-4-Isoxazolepropionic Acid (Ampa)/Glutamate Receptor, GLUA2. J.Biol.Chem. V. 287 41007 2012.
ISSN: ISSN 0021-9258
PubMed: 23076153
DOI: 10.1074/JBC.M112.416362