Zinc in PDB 3t96: Iodowillardiine Bound to A Double Cysteine Mutant (A452C/S652C) of the Ligand Binding Domain of GLUA2

The structure of Iodowillardiine Bound to A Double Cysteine Mutant (A452C/S652C) of the Ligand Binding Domain of GLUA2, PDB code: 3t96 was solved by A.H.Ahmed, S.Wang, H.H.Chuang, R.E.Oswald, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.99 / 1.87
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.793, 114.351, 163.547, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.9

The structure of Iodowillardiine Bound to A Double Cysteine Mutant (A452C/S652C) of the Ligand Binding Domain of GLUA2 also contains other interesting chemical elements:

Iodine

(I)

3 atoms

The binding sites of Zinc atom in the Iodowillardiine Bound to A Double Cysteine Mutant (A452C/S652C) of the Ligand Binding Domain of GLUA2 (pdb code 3t96). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Iodowillardiine Bound to A Double Cysteine Mutant (A452C/S652C) of the Ligand Binding Domain of GLUA2, PDB code: 3t96:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Iodowillardiine Bound to A Double Cysteine Mutant (A452C/S652C) of the Ligand Binding Domain of GLUA2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Iodowillardiine Bound to A Double Cysteine Mutant (A452C/S652C) of the Ligand Binding Domain of GLUA2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:28.9 occ:1.00 NE2 B:HIS23 2.4 25.2 1.0 CE1 B:HIS23 3.3 27.4 1.0 CD2 B:HIS23 3.4 25.2 1.0 ND1 B:HIS23 4.4 26.1 1.0 OE2 B:GLU24 4.5 35.0 1.0 CG B:HIS23 4.5 25.1 1.0 CB B:MET19 4.7 21.9 1.0 CG B:MET19 4.7 24.7 1.0

Zinc binding site 2 out of 5 in the Iodowillardiine Bound to A Double Cysteine Mutant (A452C/S652C) of the Ligand Binding Domain of GLUA2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Iodowillardiine Bound to A Double Cysteine Mutant (A452C/S652C) of the Ligand Binding Domain of GLUA2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:22.4 occ:1.00 OE1 F:GLU166 2.2 20.0 1.0 OE1 B:GLU42 2.3 20.5 1.0 NE2 B:HIS46 2.4 21.6 1.0 OE2 F:GLU166 2.9 25.5 1.0 CD F:GLU166 2.9 22.5 1.0 CD B:GLU42 3.1 21.6 1.0 OE2 B:GLU42 3.2 20.0 1.0 CD2 B:HIS46 3.3 21.1 1.0 CE1 B:HIS46 3.3 25.7 1.0 N F:SER168 4.1 17.7 1.0 CB F:SER168 4.4 17.2 1.0 O F:ALA165 4.4 16.8 1.0 CG F:GLU166 4.4 21.7 1.0 ND1 B:HIS46 4.4 20.5 1.0 CG B:HIS46 4.4 22.4 1.0 CA F:SER168 4.5 16.2 1.0 CG B:GLU42 4.5 19.1 1.0 CD2 B:LEU241 4.7 21.5 1.0 C F:PRO167 4.8 19.7 1.0 CD B:LYS45 4.8 27.2 1.0 CB F:GLU166 5.0 24.7 1.0 CB B:GLU42 5.0 15.7 1.0

Zinc binding site 3 out of 5 in the Iodowillardiine Bound to A Double Cysteine Mutant (A452C/S652C) of the Ligand Binding Domain of GLUA2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Iodowillardiine Bound to A Double Cysteine Mutant (A452C/S652C) of the Ligand Binding Domain of GLUA2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn3 b:27.4 occ:1.00 CG D:GLU24 2.4 37.6 1.0 CD D:GLU24 2.4 37.9 1.0 OE2 D:GLU24 2.6 37.5 1.0 NE2 D:HIS23 2.7 30.6 1.0 OE1 D:GLU24 3.2 44.5 1.0 CD2 D:HIS23 3.3 31.3 1.0 CE1 D:HIS23 3.9 30.9 1.0 CB D:GLU24 3.9 38.6 1.0 CG D:HIS23 4.6 31.6 1.0 O D:HOH375 4.6 37.9 1.0 CA D:GLU24 4.7 37.8 1.0 O D:HOH401 4.8 39.8 1.0 ND1 D:HIS23 4.8 27.5 1.0

Zinc binding site 4 out of 5 in the Iodowillardiine Bound to A Double Cysteine Mutant (A452C/S652C) of the Ligand Binding Domain of GLUA2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Iodowillardiine Bound to A Double Cysteine Mutant (A452C/S652C) of the Ligand Binding Domain of GLUA2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn262 b:61.6 occ:1.00 OE1 D:GLU42 2.4 33.7 1.0 NE2 D:HIS46 2.4 46.7 1.0 O D:HOH1004 2.5 49.4 1.0 CD2 D:HIS46 3.3 39.9 1.0 CD D:GLU42 3.3 35.4 1.0 CE1 D:HIS46 3.5 46.4 1.0 OE2 D:GLU42 3.6 43.0 1.0 CE D:LYS45 3.7 41.8 1.0 NZ D:LYS45 3.9 46.6 1.0 CD2 D:LEU241 4.1 28.4 1.0 CG D:HIS46 4.5 40.6 1.0 ND1 D:HIS46 4.5 46.1 1.0 CG D:GLU42 4.6 27.8 1.0 OE1 D:GLN244 4.8 46.7 1.0 CB D:GLU42 5.0 24.6 1.0

Zinc binding site 5 out of 5 in the Iodowillardiine Bound to A Double Cysteine Mutant (A452C/S652C) of the Ligand Binding Domain of GLUA2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Iodowillardiine Bound to A Double Cysteine Mutant (A452C/S652C) of the Ligand Binding Domain of GLUA2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn262 b:20.8 occ:1.00 OE1 F:GLU42 2.4 19.2 1.0 NE2 F:HIS46 2.5 18.6 1.0 CD F:GLU42 3.1 21.6 1.0 OE2 F:GLU42 3.2 24.5 1.0 CE1 F:HIS46 3.3 21.7 1.0 CD2 F:HIS46 3.6 18.9 1.0 OE1 F:GLN244 3.6 31.9 1.0 CD2 F:LEU241 3.7 19.0 1.0 NZ F:LYS45 4.2 20.7 1.0 CE F:LYS45 4.4 21.4 1.0 ND1 F:HIS46 4.5 20.5 1.0 CG F:GLU42 4.5 16.2 1.0 CG F:HIS46 4.7 19.7 1.0 CD1 F:LEU246 4.8 25.4 1.0 CD F:GLN244 4.8 32.7 1.0

A.H.Ahmed, S.Wang, H.H.Chuang, R.E.Oswald. Mechanism of Ampa Receptor Activation By Partial Agonists: Disulfide Trapping of Closed Lobe Conformations. J.Biol.Chem. V. 286 35257 2011.
ISSN: ISSN 0021-9258
PubMed: 21846932
DOI: 10.1074/JBC.M111.269001