Zinc in PDB 4f31: Kainate Bound to the D655A Mutant of the Ligand Binding Domain of GLUA3

The structure of Kainate Bound to the D655A Mutant of the Ligand Binding Domain of GLUA3, PDB code: 4f31 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)	33.73 / 2.29
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.234, 116.473, 52.406, 90.00, 95.56, 90.00
R / Rfree (%)	18.7 / 24.8

The binding sites of Zinc atom in the Kainate Bound to the D655A Mutant of the Ligand Binding Domain of GLUA3 (pdb code 4f31). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Kainate Bound to the D655A Mutant of the Ligand Binding Domain of GLUA3, PDB code: 4f31:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Kainate Bound to the D655A Mutant of the Ligand Binding Domain of GLUA3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Kainate Bound to the D655A Mutant of the Ligand Binding Domain of GLUA3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:36.1 occ:1.00 CD B:GLU166 3.0 31.8 1.0 OE1 B:GLU166 3.0 29.2 1.0 CB B:GLU166 3.2 44.2 1.0 OE2 B:GLU166 3.2 18.9 1.0 CG B:GLU166 3.6 39.3 1.0 O B:HOH524 3.8 38.2 1.0 N B:SER168 3.8 34.7 1.0 CA B:GLU166 4.1 42.2 1.0 CA B:PRO167 4.3 36.7 1.0 C B:PRO167 4.5 36.6 1.0 CB B:SER168 4.6 29.1 1.0 CA B:SER168 4.7 33.7 1.0 C B:GLU166 4.7 40.5 1.0 N B:PRO167 4.8 34.2 1.0

Zinc binding site 2 out of 4 in the Kainate Bound to the D655A Mutant of the Ligand Binding Domain of GLUA3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Kainate Bound to the D655A Mutant of the Ligand Binding Domain of GLUA3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:39.1 occ:1.00 OE1 B:GLU42 2.2 37.6 1.0 NE2 B:HIS46 2.3 37.7 1.0 O B:HOH512 2.4 32.9 1.0 CD2 B:HIS46 3.2 35.2 1.0 CD B:GLU42 3.2 37.3 1.0 CE1 B:HIS46 3.3 36.7 1.0 NZ B:LYS45 3.4 40.8 1.0 CE B:LYS45 3.5 44.9 1.0 OE2 B:GLU42 3.6 40.0 1.0 O B:HOH488 3.9 45.9 1.0 CD2 B:LEU241 4.2 31.2 1.0 ND1 B:HIS46 4.4 38.8 1.0 CG B:HIS46 4.4 36.1 1.0 CD2 B:LEU246 4.4 41.7 1.0 CG B:GLU42 4.6 34.7 1.0 O B:HOH513 4.8 34.3 1.0 CB B:GLU42 4.8 29.0 1.0 CD B:LYS45 4.9 42.0 1.0 CB B:LYS45 5.0 34.4 1.0 O B:GLU42 5.0 30.9 1.0 CA B:GLU42 5.0 29.2 1.0

Zinc binding site 3 out of 4 in the Kainate Bound to the D655A Mutant of the Ligand Binding Domain of GLUA3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Kainate Bound to the D655A Mutant of the Ligand Binding Domain of GLUA3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:38.7 occ:1.00 OE1 D:GLU166 2.6 53.9 1.0 CD D:GLU166 2.7 52.2 1.0 O D:HOH473 2.7 19.9 1.0 O D:HOH474 3.0 34.7 1.0 OE2 D:GLU166 3.2 59.8 1.0 CG D:GLU166 3.3 46.6 1.0 N D:SER168 3.8 36.4 1.0 CB D:GLU166 4.0 44.5 1.0 CA D:PRO167 4.3 40.8 1.0 C D:PRO167 4.4 41.5 1.0 CB D:SER168 4.5 37.5 1.0 CA D:SER168 4.6 38.0 1.0 CA D:GLU166 4.7 38.7 1.0

Zinc binding site 4 out of 4 in the Kainate Bound to the D655A Mutant of the Ligand Binding Domain of GLUA3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Kainate Bound to the D655A Mutant of the Ligand Binding Domain of GLUA3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn303 b:39.1 occ:1.00 NE2 D:HIS46 2.2 38.1 1.0 OE1 D:GLU42 2.3 38.1 1.0 CD D:GLU42 3.2 39.6 1.0 CD2 D:HIS46 3.2 36.3 1.0 CE1 D:HIS46 3.2 43.2 1.0 OE2 D:GLU42 3.4 44.5 1.0 NZ D:LYS45 3.9 46.2 1.0 CE D:LYS45 4.0 46.3 1.0 CD2 D:LEU241 4.1 25.1 1.0 ND1 D:HIS46 4.3 41.8 1.0 CG D:HIS46 4.3 38.1 1.0 CG D:GLU42 4.5 31.2 1.0 CD2 D:LEU246 4.7 38.5 1.0 CB D:GLU42 4.8 28.3 1.0

S.M.Holley, A.H.Ahmed, J.Srinivasan, S.E.Murthy, G.A.Weiland, R.E.Oswald, L.M.Nowak. The Loss of An Electrostatic Contact Unique to Ampa Receptor Ligand Binding Domain 2 Slows Channel Activation. Biochemistry V. 51 4015 2012.
ISSN: ISSN 0006-2960
PubMed: 22512472
DOI: 10.1021/BI3001837